A genome triplication associated with early diversification of the core eudicots

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Title:
A genome triplication associated with early diversification of the core eudicots
Series Title:
Genome Biology
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Mixed Material
Language:
English
Creator:
Jiao, Yuannian
Leebens-Mack, Jim
Ayyampalayam, Saravanaraj
Bowers, John E.
McKain, Michael R.
McNeal, Joel
Rolf, Megan
Ruzicka, Daniel R
Wafula, Eric
Wickett, Norman J.
Wu, Xiaolei
Zhang, Yong
Wang, Jun
Zhang, Yeting
Carpenter, Eric J
Deyholos, Michael K.
Kutchan, Toni M.
Chanderbali, Andre S.
Soltis, Pamela S.
Stevenson, Dennis W.
McCombie, Richard
Pires, Chris J.
Wong, Gane Ka-Shu
Soltis, Douglas E
dePamphilis, Claude W.
Publisher:
BioMed Central
Publication Date:

Notes

Abstract:
Background: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of wellresolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. Conclusions: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

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University of Florida
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doi - 10.1186/gb-2012-13-1-r3
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AA00010537:00001


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ui gb-2012-13-1-r3ji 1465-6906fm
dochead Research
bibl
title
p A genome triplication associated with early diversification of the core eudicots
aug
au id A1 snm Jiaofnm Yuannianinsr iid I1 I2 email yxj129@psu.edu
A2 Leebens-MackJimI3 jleebensmack@plantbio.uga.edu
A3 AyyampalayamSaravanarajraj@plantbio.uga.edu
A4 Bowersmi EJohnjebowers@uga.edu
A5 McKainRMichaelmrmckain@gmail.com
A6 McNealJoelI4 jmcneal@plantbio.uga.edu
A7 RolfMeganI5 mrolf@danforthcenter.org
A8 RuzickaRDanieldruzicka@danforthcenter.org
A9 WafulaEricekw10@psu.edu
A10 WickettJNormanI6 nwickett@chicagobotanic.org
A11 WuXiaoleiI7 wuxiaolei@genomics.org.cn
A12 ZhangYongzhangy@genomics.org.cn
A13 WangJunI8 wangj@genomics.org.cn
A14 ZhangYetingI9 yzz119@psu.edu
A15 CarpenterJEricI10 ejc@ualberta.ca
A16 DeyholosKMichaeldeyholos@ualberta.ca
A17 KutchanMTonitmkutchan@danforthcenter.org
A18 ChanderbaliSAndreI11 I12 achander@ufl.edu
A19 SoltisSPamelapsoltis@flmnh.ufl.edu
A20 StevensonWDennisI13 dws@nybg.org
A21 McCombieRichardI14 mccombie@cshl.edu
A22 Piresmnm ChrisJI15 piresjc@missouri.edu
A23 WongKa-ShuGaneI16 gane@ualberta.ca
A24 SoltisEDouglasdsoltis@botany.ufl.edu
A25 ca yes dePamphilisWClaudecwd3@psu.edu
insg
ins Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
Department of Biology, Institute of Molecular Evolutionary Genetics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
Department of Biology and Physics, Kennesaw State University, Kennesaw, GA 30144, USA
Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
Division of Plant Science and Conservation, Chicago Botanic Garden, Glencoe, IL 60022, USA
Beijing Genomics Institute-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
The Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Biology, University of Copenhagen, Store Kannikestræde 11, 1169 København K, Denmark
Intercollege Graduate Degree Program in Genetics, The Pennsylvania State University, University Park, PA 16802, USA
Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Department of Biology, University of Florida, Gainesville, FL 32611, USA
New York Botanical Garden, Bronx, New York, NY 10458, USA
Genome Research Center, Cold Spring Harbor Laboratory, 500 Sunnyside Blvd, Woodbury, NY 11797, USA
Division of Biological Sciences, University of Missouri, Columbia, MI 65211, USA
Departments of Biological Sciences and Medicine, Department of Biological Sciences, University of Alberta, Edmonton AB, T6G 2E9, Canada
source Genome Biology
issn 1465-6906
pubdate 2012
volume 13
issue 1
fpage R3
url http://genomebiology.com/2012/13/1/R3
xrefbib pubidlist pubid idtype doi 10.1186/gb-2012-13-1-r3pmpid 22280555
history rec date day 3month 11year 2011acc 2612012pub 2612012
cpyrt 2012collab Jiao et al.; licensee BioMed Central Ltd.note This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
abs
sec
st
Abstract
Background
Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.
Results
To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago.
Conclusions
The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.
bdy
Background
Gene duplication provides the raw genetic material for the evolution of functional novelty and is considered to be a driving force in evolution abbrgrp
abbr bid B1 1
B2 2
. A major source of gene duplication is whole genome duplication (WGD; polyploidy), which involves the doubling of the entire genome. WGD has played a major role in the evolution of most eukaryotes, including ciliates
B3 3
, fungi
B4 4
, flowering plants
B5 5
B6 6
B7 7
B8 8
B9 9
B10 10
B11 11
B12 12
B13 13
B14 14
B15 15
B16 16
, and vertebrates
B17 17
B18 18
B19 19
. Studies in these lineages support an association between WGD and gene duplications
6
B20 20
, functional divergence in duplicate gene pairs
B21 21
B22 22
, phenotypic novelty
B23 23
, and possible increases in species diversity
B24 24
B25 25
driven by variation in gene loss and retention among diverging polyploidy sub-populations
B26 26
B27 27
B28 28
B29 29
.
There is growing consensus that one or more rounds of WGD played a major role early in the evolution of flowering plants
2
5
7
8
9
13
B30 30
B31 31
. Early synteny-based and phylogenomic analyses of the it Arabidopsis genome revealed multiple WGD events
8
9
. The oldest of these WGD events was placed before the monocot-eudicot divergence, a second WGD was hypothesized to be shared among most, if not all, eudicots, and a more recent WGD was inferred to have occurred before diversification of the Brassicales
9
. Synteny analyses of the recently sequenced nuclear genomes of Vitis vinifera (wine grape, grapevine)
B32 32
and Carica papaya (papaya tree)
7
provided more conclusive evidence for a somewhat different scenario in terms of the number and timing of WGDs early in the history of angiosperms. Each Vitis (or Carica) genome segment can be syntenic with up to four segments in the Arabidopsis genome, implicating two WGDs in the Arabidopsis lineage after separation from the Vitis (or Carica) lineage
7
12
32
. The more ancient one (β) appears to have occurred around the time of the Cretaceous-Tertiary extinction
10
. Analyses of the genome structure of Vitis revealed triplicate sets of syntenic gene blocks
11
32
. Because the blocks are all similarly diverged, and thus were probably generated at around the same time in the past, the triplicated genome structure is likely to have been generated by an ancient hexaploidy event, possibly similar to the two successive WGDs likely to have produced Triticum aestivum
B33 33
. Although the mechanism is not clear at this point, the origin of this triplicated genome structure is commonly referred to as gamma or γ (hereafter γ refers to the gamma event). Comparisons of available genome sequences for other core rosid species (including Carica, Populus, and Arabidopsis) and the recently sequenced potato genome (an asterid, Solanum tuberosum) show evidence of one or more rounds of polyploidy with the most ancient event within each genome represented by triplicated gene blocks showing interspecific synteny with triplicated blocks in the Vitis genome
7
11
B34 34
B35 35
. The most parsimonious explanation of these patterns is that γ occurred in a common ancestor of rosids and asterids, because all sequenced genomes within these lineages share a triplicate genome structure
12
35
.
Despite this growing body of evidence from genome sequences, the phylogenetic placement of γ on the angiosperm tree of life remains equivocal (for example,
13
). As described above, the γ event is readily apparent in analyses of sequenced core eudicot genomes, and recent comparisons of regions of the Amborella genome and the Vitis synteny blocks indicate that the γ event occurred after the origin and early diversification of angiosperms
B36 36
. In addition, comparisons of the Vitis synteny blocks with bacterial artificial chromosome sequences from the Musa (a monocot) genome provide weak evidence that γ postdates the divergence of monocots and eudicots
11
.
As an alternative to synteny comparisons, a phylogenomic approach has also been used successfully to determine the relative timing of WGD events. By mapping paralogs created by a given WGD onto phylogenetic trees, we can determine whether the paralogs resulted from a duplication event before or after a given branching event
9
. In a recent study, Jiao et al.
5
used a similar strategy to identify two bouts of concerted gene duplications that are hypothesized to be derived from successive genome duplications in common ancestors of living seed plants and angiosperms. When using a phylogenomic approach, extensive rate variation among species could lead to incorrect phylogenetic inferences and then possibly also result in the incorrect placement of duplication events
11
. Gene or taxon sampling can reduce variation in branch lengths and the impact of long-branch attraction in gene tree estimates (for example,
B37 37
B38 38
B39 39
). Therefore, effective use of the phylogenomic approach requires consideration of possible differences in substitution rates and careful taxon sampling to divide long branches that can lead to artifacts in phylogenetic analyses.
The availability of transcriptome data produced by both traditional (Sanger) and next-generation cDNA sequencing methods has grown rapidly in recent years
B40 40
B41 41
. In PlantGDB, very large Sanger EST datasets from multiple members of Asteraceae (for example, Helianthus annuus, sunflower) and Solanaceae (for example, S. tuberosum, potato), in particular, provide good coverage of the gene sets from the two largest asterid lineages. With advances in next-generation sequencing, comprehensive transcriptome datasets are being generated for an expanding number of species. For example, the Ancestral Angiosperm Genome Project has generated large, multi-tissue cDNA datasets of magnoliids and other basal angiosperms, including Aristolochia, Persea, Liriodendron, Nuphar and Amborella
5
. The Monocot Tree of Life project
B42 42
is generating deep transcriptome datasets for at least 50 monocot species that previously have not been the focus of genome-scale sequencing. The 1000 Green Plant Transcriptome Project
B43 43
is generating at least 3 Gb of Illumina paired-end RNAseq data from each of 1,000 plant species from green algae through angiosperms (Viridiplantae). In this study, we draw upon these resources, including an initial collection of basal eudicot species that have been very deeply sequenced by the 1000 Green Plant Transcriptome Project. Six members of Papaveraceae (Argemone mexicana, Eschscholzia californica, and four species of Papaver) have been targeted for especially deep sequencing, with over 12 Gb of cDNA sequence derived from four or five tissue-specific RNAseq libraries. Three other basal eudicots (Podophyllum peltatum (Berberidaceae), Akebia trifoliata (Lardizabalaceae), and Platanus occidentalis (Platanaceae)) sequenced by the 1000 Green Plant (1KP) Transcriptome Project, and EST sets available for additional strategically placed species (for example,
B44 44
B45 45
) were employed for phylogenomic estimation of the timing of the γ event. Assembled unigenes (sequences produced from assembly of EST data sets) were sorted into gene families and then the phylogenetic analyses of gene families were performed to test alternative hypotheses for the phylogenetic placement of the γ event.
Results and discussion
Since the γ event was first identified in a groundbreaking phylogenomic analysis of the Arabidopsis genome
9
, its timing has been hypothesized to have predated the origin of angiosperms (for example,
25
B46 46
), the divergence of monocots and eudicots (for example,
B47 47
) and the divergence of asterid and rosid eudicot clades (for example,
11
35
) (Figure figr fid F1 1). Most recent analyses suggest that γ occurred within the eudicots, but the timing of the γ event relative to the diversification of core eudicots remains unclear
13
. Resolving whether γ occurred just before the radiation of core eudicots or earlier, in a common ancestor of all eudicots, has implications for our understanding of the relationship between polyploidization, diversification rates, and morphological novelty (for example,
14
).
fig Figure 1caption Schematic phylogenetic tree of flowering plantstext
b Schematic phylogenetic tree of flowering plants. BR1 to BR4 denote potential time points when the γ event may have occurred. BR1, monocots + eudicots duplication; BR2, eudicot-wide duplication; BR3, core eudicot-wide duplication; BR4, rosid-wide duplication.
graphic file gb-2012-13-1-r3-1
Phylogenomic placement of the γ polyploidy event
To ascertain the timing of the γ event relative to the origin and early diversification of eudicots, we mainly focused on dating paralogous gene pairs that are retained on synteny blocks in Vitis
11
12
. Vitis displays the most complete retention for γ blocks among all genomes sequenced to date, and thus provides the best target for phylogenomic mining of the γ history. Vitis also represents the sister group to all other members of the rosid lineage (APG III, 2009)
B48 48
B49 49
, so homologous genes were sampled from other species of rosids, asterids, basal eudicots, monocots, and basal angiosperms in order to estimate the timing of the γ event in relation to the divergence of these lineages. Genes were clustered into 'orthogroups' (homologous genes that derive from a single gene in the common ancestor of the focal taxa) using OrthoMCL
B50 50
with eight sequenced angiosperm genomes (Table tblr tid T1 1). By excluding Vitis pairs that are not included in the same orthogroups, and requiring that orthogroups contained both monocots and non-Vitis eudicots, 900 pairs of Vitis genes were retained from 781 orthogroups. These orthogroups were used in our investigation of the γ duplication event.
tbl Table 1Summary of datasets for eight sequenced plant genomes included in this studytblbdy cols 3
r
c left
Species
Annotation version
center
Number of annotated genes
cspan
hr
Arabidopsis thaliana (thale cress)
TAIR version 9
27,379
Carica papaya (papaya)
ASGPB release
25,536
Cucumis sativus (cucumber)
BGI release
21,635
Populus trichocarpa (black cottonwood)
JGI version 2.0
41,377
Glycine max (soybean)
Phytozome version 1.0
55,787
Vitis vinifera (grape vine)
Genoscope release
30,434
Oryza sativa (rice)
RGAP release 6.1
56,979
Sorghum bicolor
JGI version 1.4
34,496
tblfn
These eight genome sequences were used to construct orthogroups, which were then populated with additional unigenes of asterids, basal eudicots, non-grass monocots, and basal angiosperms. The number of annotated genes in each genome is indicated. ASGPB, Advanced Studies of Genomics, Proteomics and Bioinformatics; JGI, Joint Genome Institute; RGAP, Rice Genome Annotation Project; TAIR, The Arabidopsis Information Resource.
To verify that the phylogenetic placement of the γ event was shared by rosids and asterids, and to test whether it was shared by all eudicots or by eudicots and monocots (near angiosperm-wide), these orthogroups were then populated with unigenes of asterids, basal eudicots, non-grass monocots, and basal angiosperms (Table T2 2). Grasses are known to be distinct from other angiosperms in their high rate of nucleotide substitutions, and codon biases within the grasses make this clade distinct from other angiosperms, including non-grass monocots (for example,
B51 51
B52 52
), so inclusion of non-grass monocots was necessary to reduce artifacts in gene tree estimation. More generally, when dealing with phylogenomic-scale datasets, we strive for adequate taxon sampling to cut long branches, but avoid adding a large proportion of unigenes with low coverage. Inadequate taxon sampling could lead to spurious inference of phylogeny, while incomplete sequences (that is, low-coverage unigenes) can greatly degrade branch support and resolution of phylogenetic trees.
hint_layout double Table 2Summary of unigene sequences of asterids, basal eudicots, non-grass monocots, and basal angiosperms included in phylogenetic study7
Species
Lineage
Source
Number of reads/ESTs
Size of data
Assembly method(s)
Number of unigenes
Panax quinquefolius
Asterid
NCBI-SRA
209,745
89.7 Mb
MIRA
22,881
Lindenbergia phillipensis
Asterid
PPGP
69,545,362
5.9 Gb
CLC
104,904
Helianthus annuus
Asterid
TIGR PTA
93,279
NA
Megablast-CAP3
44,662
Solanum tuberosum
Asterid
TIGR PTA
219,485
NA
Megablast-CAP3
81,072
Mimulus gutatus
Asterid
PlantGDB
231,012
NA
Vmatch-PaCE-CAP3
39,577
Papaver somniferum
Basal eudicot
1KP + SRA
140,604,904 + 3,709,876
10.3 Gb + 1.3 Gb
MIRA-SOAPDenovo-CAP3
252,894
Papaver setigerum
Basal eudicot
1KP
134,478,938
9.8 Gb
SOAPDenovo-CAP3
406,167
Papaver rhoeas
Basal eudicot
1KP
157,506,374
11.5 Gb
SOAPDenovo-CAP3
383,426
Papaver bracteatum
Basal eudicot
1KP
89,663,900
6.5 Gb
SOAPDenovo-CAP3
201,564
Eschscholzia californica
Basal eudicot
NCBI + SRA + 1KP
14,381 + 559,470 + 133,422,402
6.8 Mb + 55 Mb + 9.7 Gb
MIRA-SOAPDenovo-CAP3
165,260
Argemone mexicana
Basal eudicot
1KP + NCBI
144,520,360 + 1,692
10.5 Gb + 1 Mb
SOAPDenovo- CAP3
148,533
Akebia trifoliata
Basal eudicot
1KP
29,156,514
2.1 Gb
CLC-CAP3
46,024
Podophyllum pelatum
Basal eudicot
1KP
20,139,210
1.5 Gb
CLC-CAP3
31,472
Platanus occidentalis
Basal eudicot
1KP
25,508,642
1.9 Gb
CLC-CAP3
42,373
Aquilegia formosa x Aquilegia pubescens
Basal eudicot
PlantGDB
85,040
NA
Vmatch-PaCE-CAP3
19,615
Mesembryanthemum crystallinum
Caryophillid
PlantGDB
27,553
NA
Vmatch-PaCE-CAP3
11,317
Beta vulgaris
Caryophillid
PlantGDB
25,883
NA
Vmatch-PaCE-CAP3
18,009
Acorus americanus
Monocot
MonATOL + 1KP
149,320 + 15,427,316
44.9 Mb + 1.1 Gb
MIRA-SOAPDenovo-CAP3
59,453
Chamaedorea seifrizii
Monocot
MonATOL
33,100,948
2.5 Gb
CLC
68,489
Chlorophytum rhizopendulum
Monocot
MonATOL
59,505,714
4.5 Gb
CLC
58,766
Neoregelia sp.
Monocot
MonATOL
49,121,506
3.7 Gb
CLC
63,269
Typha angustifolia
Monocot
MonATOL
70,733,124
5.7 Gb
CLC
57,980
Persea americana (avocado)
Magnoliid
AAGP
2,336,819
683 Mb
MIRA
132,532
Aristolochia fimbriata (Dutchman's pipe)
Magnoliid
AAGP
3,930,505
880 Mb
MIRA
155,371
Liriodendron tulipifera (yellow-poplar)
Magnoliid
AAGP
2,327,654
543 Mb
MIRA
137,923
Nuphar advena (yellow pond lily)
Basal angiosperm
AAGP
3,889,719
1.1 Gb
MIRA
289,773
Amborella trichopoda
Basal angiosperm
AAGP
2,943,273
776 Mb
MIRA
208394
1KP, 1000 Green Plant Transcriptome Project; AAGP, Ancestral Angiosperm Genome Project 44; MonATOL, Monocot Tree of Life Project 42; NA, not available; NCBI, National Center for Biotechnology Information; PPGP, Parasitic Plant Genome Project B65 65; SRA, Sequence Read Archive; TIGR PTA, The Institute for Genomic Research Plant Transcript Assemblies B66 66.
To phylogenetically place the γ event with confidence, we adopted the following support-based approach. Three relevant bootstrap values were taken into account when evaluating support for a particular duplication. For example, given a topology of (((clade2)bootstrap2,(clade3)bootstrap3)bootstrap1), bootstrap2 and bootstrap3 are the bootstrap values supporting clade2 (clade2 here will include one of the Vitis γ duplicates) and clade3 (including the other Vitis duplicate), respectively, while bootstrap1 is the bootstrap value supporting the larger clade including clade2 and clade3. The value of bootstrap1 indicates the degree of confidence in the inferred ancestral node joining clades 2 and 3. In this study, when bootstrap1, and at least one of bootstrap2 and bootstrap3 were ≥50% (or 80%), we determined whether an asterid, basal eudicot, monocot, or basal angiosperm was contained in clades 2 or 3 (for example, asterids in Figures F2 2 and F3 3) or sister to their common ancestor (node defining clade 1) with a bootstrap value (BS) ≥50% (or 80%; for example, basal eudicots, monocots and basal angiosperms in Figures 2 and 3).
Figure 2Exemplar maximum likelihood phylogeny of Ortho 1202
Exemplar maximum likelihood phylogeny of Ortho 1202. RAxML topology of an orthogroup (Ortho 1202) indicating that the γ paralogs of Vitis were duplicated before the split of rosids and asterids and after the early radiation of eudicots. The scored bootstrap (BS) value for this duplication is over 80%, because nodes #1 and #2 (and/or #3) have BS 80%. Legend: green star = core eudicot duplication; colored circles = recent independent duplications; numbers = bootstrap support values./p
/textgraphic file="gb-2012-13-1-r3-2"//fig
fig id="F3"titlepFigure 3/p/titlecaptionpExemplar maximum likelihood phylogeny of Ortho 1083/p/captiontext
pbExemplar maximum likelihood phylogeny of Ortho 1083/b. RAxML topology of an orthogroup (Ortho 1083) indicates that the γ paralogs of itVitis /itwere duplicated before the split of rosids and asterids, and after the early radiation of eudicots. The scored bootstrap (BS) value for this duplication is over 50%, because nodes #1 has BS < 80%. Legend: green star = core eudicot duplication; colored circles = recent independent duplications; numbers = bootstrap support values./p
/textgraphic file="gb-2012-13-1-r3-3"//fig
pHomologous sequences were identified for 769 of the 781 orthogroups and were subsequently used for phylogenetic analysis. For example, orthogroup 1202 was well populated with unigenes of asterids, basal eudicots, non-grass monocots, and basal angiosperms (Figure figr fid="F2"2/figr). Two itVitis /itgenes, which were located on a syntenic block, were clustered into two clades, both of which include genes from asterids and other rosids. This phylogenetic tree supports (BS ≥80%) the duplication of two itVitis /itgenes before the split of rosids and asterids and after the divergence of basal eudicots, indicating that γ is restricted to core eudicots (BR3 of Figure figr fid="F1"1/figr; Figure figr fid="F2"2/figr). In another example, only one asterid unigene passed the quality control steps and was clustered into orthogroup 1083. This asterid unigene was grouped into one of the duplicated clades, also supporting (BS ≥50%) a duplication in the common ancestor of extant core eudicots (BR3 of Figure figr fid="F1"1/figr; Figure figr fid="F3"3/figr). Only a few duplications of itVitis /itgene pairs were identified as occurring before the divergence of monocots and eudicots (BR1 of Figure figr fid="F1"1/figr; seven duplications with BS ≥50%), or restricted to rosids (BR4 of Figure figr fid="F1"1/figr; six duplications with BS ≥50%, four duplications with BS ≥80%). We identified 168 itVitis /itgene pairs that were duplicated after the split of basal eudicots (BR3 of Figure figr fid="F1"1/figr) with BS ≥50%, and 80 of these had BS ≥80%. We also found that 70 itVitis /itgenes were duplicated before the separation of basal eudicots (BR2 of Figure figr fid="F1"1/figr) with BS ≥50% and 19 with BS ≥80% (Table tblr tid="T3"3/tblr). Therefore, our phylogenomic analysis provided very strong support that γ occurred before the divergence of rosids and asterids, after the split of monocots and eudicots, and most likely after the earliest diversification of eudicots./p
tbl id="T3"titlepTable 3/p/titlecaptionpPhylogenetic timing of itVitis /itγ duplications inferred from orthogroup phylogenetic histories/p/captiontblbdy cols="9"
r
c
p/
/c
c cspan="2" ca="center"
p
bBR1/b
/p
/c
c cspan="2" ca="center"
p
bBR2/b
/p
/c
c cspan="2" ca="center"
p
bBR3/b
/p
/c
c cspan="2" ca="center"
p
bBR4/b
/p
/c
/r
r
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bBS ≥ 80/b
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bBS ≥ 50/b
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bBS ≥ 80/b
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bBS ≥ 50/b
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bBS ≥ 80/b
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/tblbdytblfn
pBRx designations are illustrated in Figure 1. Bootstrap (BS) ≥80 and BS ≥50 are counts of nodes resolved with BS ≥80 or ≥50, respectively./p
/tblfn/tbl
/sec
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pMolecular dating of the γ duplications/p
/st
pTo estimate the absolute date of the γ event, we calibrated 161 of the 168 orthogroups supporting (BS ≥50%) a core eudicot-wide duplication and 66 of the 70 orthogroups supporting a eudicot-wide duplication, and then estimated the duplication times using the program r8s abbrgrp
abbr bid="B53"53/abbr
/abbrgrp (Materials and methods). We then analyzed the distribution of the inferred duplication times using a Bayesian method that assigned divergence time estimates to classes specified by a mixture model abbrgrp
abbr bid="B54"54/abbr
/abbrgrp. The distribution of duplication times of core eudicot-wide itVitis /itpairs shows a peak at 117 ± 1 (95% confidence interval) (Figure figr fid="F4"4a/figr), and the distribution of all eudicot-wide duplication times has a peak at 133 ± 1 million years ago (mya) (Figure figr fid="F4"4b/figr). Dating estimates have additional sources of error beyond the sampling effects accounted for in standard error estimates (for example, abbrgrp
abbr bid="B55"55/abbr
/abbrgrp). However, the clear pattern is that the duplication branch points occurred over a narrow window of time very close to the eudicot calibration point that represents the first documented appearance of tricolpate pollen in the fossil record. We also analyzed the 80 nodes and 19 nodes showing duplication shared by core eudicots and all eudicots, respectively, with bootstrap support ≥80% (Figure figr fid="F4"4d, e/figr) and found similar distributions (116 ± 1 mya for core eudicot duplications and 135 ± 2 mya for all eudicot duplications). The inferred dates for itVitis /itduplications shared either by core eudicots or all eudicots are very close to each other, and are concentrated around 125 mya. We also investigated the distribution of all inferred duplication times together (core eudicot-wide and eudicot-wide). Even given a time constraint (125 mya) that would split the date estimates for core eudicot and eudicot-wide duplications, the distributions of combined inferred duplication times show only one significant peak, with a mean at 121 mya for orthogroups with bootstrap support ≥50% (Figure figr fid="F4"4c/figr) and 120 mya for orthogroups with bootstrap support ≥80% (Figure figr fid="F4"4f/figr). A single peak observed for the combined data (Figure figr fid="F4"4c/figr) suggests that the genome-scale event(s) leading to the triplicated genome structure of core eudicots occurred in a narrow window of time nearly coincident with the sudden appearance of eudicot pollen-types in the fossil record abbrgrp
abbr bid="B56"56/abbr
/abbrgrp./p
fig id="F4"titlepFigure 4/p/titlecaptionpAge distribution of γ duplications/p/captiontext
pbAge distribution of γ duplications/b. b(a) /bThe inferred duplication times for 161 γ duplication nodes that support core eudicot-wide duplication (BS ≥50%) were analyzed by EMMIX to determine whether these duplications occurred randomly over time or within some small timeframe. Each component is written as 'colormean molecular timingproportion' where 'color' is the component (curve) color and 'proportion' is the percentage of duplication nodes assigned to the identified component. There is one statistically significant component: green117 (mya)1. b(b) /bDistribution of inferred γ duplication times from 66 orthogroups that support a eudicot-wide duplication with BS ≥50%. There is one statistically significant component: blue133 (mya)1. b(c) /bDistribution of inferred γ duplication times from combination of (a) and (b) shows one significant component: purple121 (mya)1. b(d-f) /bCorresponding distributions of inferred duplication times from orthogroups with BS ≥80%. One significant component in (d), green116 (mya)1; one in (e), blue135 (mya)1; and one in (f), purple120 (mya)1./p
/textgraphic file="gb-2012-13-1-r3-4"//fig
/sec
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pHexaploidization and early eudicot radiation are close in time/p
/st
pMany of the gene trees showed no resolution or low bootstrap support for nodes distinguishing hypotheses BR2 and BR3. If the γ event had occurred almost anywhere along the long branch leading to eudicots, this event would have been relatively easy to resolve. The lack of resolution of the timing of duplication events around the basal eudicot speciation nodes suggests that the γ event may have occurred during a rapid species radiation. Another possibility could be due to the nature of hexaploidization. If, as our analyses suggest, the polyploidy event (see below for possible scenarios) occurred soon after the divergence of basal eudicots, the substitution rates for γ paralogs could vary. For example, one duplicate could evolve very slowly while the other evolves at an accelerated rate abbrgrp
abbr bid="B4"4/abbr
/abbrgrp. These possibilities could add significant challenges to the precise resolution of events occurring at or near the branch points for basal versus core eudicot lineages. Despite these challenges, most well-resolved gene trees support the hypothesis that the γ event occurred in association with the origin and diversification of the core eudicots, after the core eudicot lineage diverged from the Ranunculales (BR3 of Figure figr fid="F1"1/figr)./p
/sec
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pNature of the γ event/p
/st
pAn additional question is whether the ancient hexaploid common ancestor was formed by one or two WGDs that occurred over a very short period (for example, as with hexaploid wheat). It was demonstrated that two of the three homologous regions were more fractionated than the third, suggesting a possible mechanism for the γ event abbrgrp
abbr bid="B34"34/abbr
/abbrgrp. In one proposed scenario, a genome duplication event generated a tetraploid, which then hybridized with a diploid to generate a (probably sterile) triploid. Finally, a second WGD event doubled the triploid genome to generate a fertile hexaploid. Alternatively, unreduced gametes of a tetraploid and a diploid could have fused to generate a hexaploid directly. Another characterization of syntenic blocks indicates that the three corresponding regions are generally equidistant from one another abbrgrp
abbr bid="B11"11/abbr
/abbrgrp. Our analyses of duplication points in the phylogenomic analyses resolve only a single peak in estimated dates for the 'γ event', which would be consistent with either scenario, given that any complex scenario would involve ancient events that occurred within a brief period of time. More evidence is needed to establish a more definitive mechanism for the apparent hexaploidization (that is, as one versus two events, allopolyploid versus autopolyploid)./p
/sec
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pRate variations between paralogs of itVitis/it
/p
/st
pIn another attempt to increase resolving power, itKsubs /sub
/itdistributions for duplicate itVitis /itgenes were investigated. The itKsubs /sub
/itdistributions of itVitis /itpairs supporting a core eudicot-wide duplication inferred from phylogenetic analyses show one significant peak at itKsubs /sub
/it~1.03 (Figure figr fid="F5"5a/figr). The itKsubs /sub
/itvalues for eudicot-wide duplicate itVitis /itpairs were not well clustered, and their distribution shows one peak at 1.31, which indicates slightly more divergence for these itVitis /itpairs (Figure figr fid="F5"5b/figr). This result is consistent with phylogenetic analyses that show this set of duplications occurred somewhat earlier (all eudicot-wide versus core eudicot-wide). We also investigated the distribution of all itKsubs /sub
/itvalues together (core eudicot-wide and eudicot-wide). Three statistically significant peaks were identified: 0.3, 1.02 and 1.40 (Figure figr fid="F5"5c/figr). Finally, we estimated itKsubs /sub
/itvalues for all (2,191) pairs of itVitis /itγ paralogs identified by Tang itet al. /it
abbrgrp
abbr bid="B11"11/abbr
/abbrgrp in analyses of syntenic blocks. We were able to detect four significant components using the mixture model implemented with EMMIX (McLachlan itet al. /it
abbrgrp
abbr bid="B54"54/abbr
/abbrgrp): 0.12, 1.09, 1.85, and 2.7 (Figure figr fid="F5"5d/figr). This itKsubs /sub
/itdistribution clearly shows that the major peak (approximately 1.09; green curve in Figure figr fid="F5"5d/figr) was close to the peak of itKsubs /sub
/itdistribution of core eudicot-wide duplicates (at approximately 1.03; Figure figr fid="F5"5a/figr). This intriguing pattern (Figure figr fid="F5"5c, d/figr) could be a consequence of stable hexaploidy arising from two WGDs, one in the common ancestor of all eudicots and one in the common ancestor of core eudicots. However, there are no consistent patterns of duplications for entire syntenic blocks; for example, some syntenic blocks have genes consistently duplicated in core eudicots, while other syntenic blocks were duplicated eudicot-wide (results not shown). Alternatively, this pattern also could be consistent with the hypothesis of an allopolyploidy event for γ. If two ancestral genomes were involved in the hexaploidization and the itVitis /itgenome had evolved slowly, two significant peaks might be detected abbrgrp
abbr bid="B57"57/abbr
/abbrgrp. A third possibility is that itVitis /itpairs supporting a eudicot-wide duplication may be the products of pre-WGD tandem or segmental duplications that were misidentified as syntenic γ paralogs due to loss of alternative copies through the fractionation process. These hypotheses will have to be tested through comparative analyses as additional plant genomes, especially of outgroups (for example, itAquilegia, Amborella/it) and other basal eudicots (eg., itBuxus, Trochodendron/it), are sequenced./p
fig id="F5"titlepFigure 5/p/titlecaptionpitKsubs /sub/itdistributions of paralogs in itVitis /itfrom syntenic block analysis/p/captiontext
pbitKsubs /sub/itdistributions of paralogs in itVitis /itfrom syntenic block analysis/b. Methods for sequence alignment and estimation of itKsubs /sub/itwere as reported (Cui itet al. /it2006), but were here limited to paralogous gene pairs retained on syntenic blocks in the itVitis /itgenome. Colored lines superimposed on itKsubs /sub/itdistribution represent significant duplication components identified by likelihood mixture model as in Figure 4 (Materials and methods). a, itKsubs /sub/itdistribution of 168 itVitis /itpairs supporting core eudicot-wide duplication in phylogenetic analysis. One statistically significant component: green1.031. b, itKsubs /sub/itdistribution of 70 itVitis /itpairs showing all eudicot-wide duplications on phylogenies. One significant component: blue1.311. c, itKsubs /sub/itdistribution of combination of itVitis /itpairs supporting core eudicot- (a) and eudicot-wide duplications (b) on phylogenies. Three significant components: black0.30.01, green1.020.70, blue1.400.29. d, itKsubs /sub/itdistribution of 2191 paralogous pairs were identified from syntenic block analysis. Four significant components: black0.120.02, green1.090.74, blue1.850.22, yellow2.70.02./p
/textgraphic file="gb-2012-13-1-r3-5"//fig
/sec
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pImplications of the γ event characterizing most eudicots/p
/st
pOur results suggest that the γ polyploidy event was closely coincident with a rapid radiation of major lineages of core eudicot lineages that together contain about 75% of living angiosperm species. This rapid lineage expansion following the γ event could be an important exception to the general pattern described by Mayrose itet al. /it
abbrgrp
abbr bid="B31"31/abbr
/abbrgrp, who concluded that there may generally be reduced survival of polyploid plant lineages. The eudicots consist of a graded series of generally small clades (often called early-diverging or basal eudicots) that are successive sisters to the core eudicots (abbrgrp
abbr bid="B49"49/abbr
/abbrgrp and references therein). It is within the core eudicot clade where most major lineages as well as the large majority of angiosperm species reside (for example, rosids, asterids, caryophyllids). Several key evolutionary events seem to correspond closely to the origin of the core eudicots, including the genome-wide event described here, the evolution of a pentamerous, highly synorganized flower with a well-differentiated perianth, and the production of ellagic and gallic acids abbrgrp
abbr bid="B58"58/abbr
/abbrgrp. Significantly, the duplication of several genes crucial to the establishment of floral organ identity also occurred near the origin of the core eudicots (itAP3, AP1, AG/it, and itSEP /itgene lineages) abbrgrp
abbr bid="B46"46/abbr
abbr bid="B59"59/abbr
abbr bid="B60"60/abbr
/abbrgrp, suggesting that these duplications possibly originating from the γ event may also be involved in the 'new' floral morphology that emerged in this clade abbrgrp
abbr bid="B61"61/abbr
abbr bid="B62"62/abbr
/abbrgrp./p
pThis study also helps to shed light on prior studies, where the potential timing of the γ event varied widely from possibly in an ancestor of all angiosperms abbrgrp
abbr bid="B9"9/abbr
/abbrgrp to perhaps as recent as only rosids abbrgrp
abbr bid="B63"63/abbr
/abbrgrp. A polyploid event has been detected that is angiosperm-wide, but this was an earlier event (ε, epsilon) abbrgrp
abbr bid="B5"5/abbr
/abbrgrp. Our results are consistent with a recent study that identified a signature of the γ event in the genome of the potato, an asterid abbrgrp
abbr bid="B35"35/abbr
/abbrgrp. The γ event was suggested to be absent from grass genomes in comparisons of itVitis /itand itOryza /it
abbrgrp
abbr bid="B32"32/abbr
/abbrgrp, but this finding was questioned by Tang itet al. /it
abbrgrp
abbr bid="B11"11/abbr
/abbrgrp. However, the draft genome of strawberry (itFragaria vesca/it), a rosid that shares the γ event, did not show evidence for γ in syntenic block analysis abbrgrp
abbr bid="B64"64/abbr
/abbrgrp, suggesting that either the γ event has been obscured by further rearrangements and fractionation, or expansion of the itFragaria /itgenome sequence data may be necessary. Although sequenced plant genomes are being produced at an increasing rate, a much larger source of genome-scale evidence is coming from very large-scale transcriptome studies such as the 1000 Green Plant Transcriptome Project and the Monocot Tree of Life Project. In this paper, we have used gigabases of transcriptome data from species at key branch points to phylogenetically time hundreds of ancient gene duplications. Combined with evidence from itKsubs /sub
/itanalysis and syntenic blocks, global gene family phylogenies could incorporate extensive evidence without a sequenced genome, and ultimately facilitate a much better understanding of plant evolution./p
/sec
/sec
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pConclusions/p
/st
pPhylogenetic analyses and molecular dating provide consistent and strong evidence supporting the occurrence of the γ polyploidy event after the divergence of monocots and eudicots, and before the asterid-rosid split. It is difficult to determine whether the γ event was shared by monocots or not based only on synteny patterns shared between itVitis /itand other monocot genomes abbrgrp
abbr bid="B11"11/abbr
/abbrgrp. By including massive transcriptome datasets from many additional taxa, such as basal angiosperms, non-grass monocots, basal eudicots and asterids, we employed a comprehensive phylogenomic approach, and dated gene pairs on syntenic blocks in a relatively slowly evolving species (itVitis/it) abbrgrp
abbr bid="B11"11/abbr
/abbrgrp. We were able to place the γ event(s) in a narrow window of time, most likely shortly before the origin and rapid radiation of core eudicots./p
/sec
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pMaterial and methods/p
/st
sec
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pData and assemblies/p
/st
pGenomes were obtained from various sources as given in Table tblr tid="T1"1/tblr. EST data or assemblies were obtained from sources indicated in Table tblr tid="T2"2/tblr. The largest quantities of new sequence data are represented by transcriptome datasets for nine basal eudicot species produced by Beijing Genomics Institute for the 1000 Green Plant Transcriptome Project abbrgrp
abbr bid="B43"43/abbr
/abbrgrp. The Monocot Tree of Life Project (MonATOL) generated five non-grass monocot transcriptomes. One transcriptome dataset for itLindenbergia philippensis /it(asterid) was obtained from the Parasitic Plant Genome Project abbrgrp
abbr bid="B65"65/abbr
/abbrgrp. Several methods were used for EST data assembly, according to the type and quantity of data that were available. Assemblies involving large numbers of Sanger reads were obtained either from the Plant Genome Database abbrgrp
abbr bid="B45"45/abbr
/abbrgrp or The Institute for Genomic Research (TIGR) Plant Transcript Assemblies abbrgrp
abbr bid="B66"66/abbr
/abbrgrp. Hybrid assemblies with Sanger and 454 data were performed with MIRA.Est. Short-read Illumina datasets were assembled either with itSOAP denovo /it(K-mer size = 29 and asm_flag = 2) abbrgrp
abbr bid="B67"67/abbr
/abbrgrp or with CLC Genomics Workbench (reads trimmed first, and using default parameters except minimum contig length set to 200 bases). Assemblies for species with data from more than one sequencing technology were further post-assembled with CAP3 (overlap length cutoff = 40 and overlap percent identity = 98) to merge contigs that have significant overlap but could not be assembled into contiguous sequences by primary assemblers due to either the presence of SNPs in the consensus or path ambiguity in the graph./p
/sec
sec
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pGene classification and phylogenetic analysis/p
/st
pThe OrthoMCL method abbrgrp
abbr bid="B50"50/abbr
/abbrgrp was used to construct sets of orthogroups. Amino acid alignments for each orthogroup were generated with MUSCLE, and then trimmed by removing poorly aligned regions with trimAl 1.2, using the heuristic automate1 option abbrgrp
abbr bid="B68"68/abbr
/abbrgrp. In order to sort and align transcriptome data into our eight-genome scaffold for downstream phylogenetic analyses, we first used ESTScan abbrgrp
abbr bid="B69"69/abbr
/abbrgrp to find the best reading frame for all unigenes. The best hit from a blast search against the inferred proteins of our eight-genome scaffold was then used to assign each unigene to an orthogroup. Additional sorted unigene sequences for the orthogroups of sequenced genomes were aligned at the amino acid level into the existing full alignments (before trimming) of eight sequenced species using ClustalX 1.8 abbrgrp
abbr bid="B70"70/abbr
/abbrgrp. Then these large alignments were trimmed again using trimAl 1.2 with the same settings. Each unigene sequence was checked and removed from the alignment if the sequence contained less than 70% of the total alignment length. Corresponding DNA sequences were then forced onto the amino acid alignments using custom Perl scripts, and DNA alignments were used in subsequent phylogenetic analysis. Maximum likelihood analyses were conducted using RAxML version 7.2.1 abbrgrp
abbr bid="B71"71/abbr
/abbrgrp, searching for the best maximum likelihood tree with the GTRGAMMA model by conducting 100 bootstrap replicates, which represents an acceptable trade-off between speed and accuracy (RAxML 7.0.4 manual)./p
/sec
sec
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pMolecular dating analyses and 95% confidence intervals/p
/st
pThe best maximum-likelihood topology for each orthogroup was used to estimate divergence times. The divergence time of the two paralogous clades in each orthogroup was estimated under the assumption of a relaxed molecular clock by applying a semi-parametric penalized likelihood approach using a truncated Newton optimization algorithm as implemented in the program R8S abbrgrp
abbr bid="B53"53/abbr
/abbrgrp. The smoothing parameter was determined by cross-validation. We used the following dates in our estimation procedure: minimum age of 131 mya abbrgrp
abbr bid="B72"72/abbr
/abbrgrp and maximum age of 309 mya for crown-group angiosperms abbrgrp
abbr bid="B73"73/abbr
/abbrgrp, and a fixed constraint age of 125 mya for crown-group eudicots abbrgrp
abbr bid="B56"56/abbr
/abbrgrp. We required that trees pass both the cross-validation procedure and provide estimates of the age of the duplication node. The collection of inferred divergence times was then analyzed by EMMIX abbrgrp
abbr bid="B54"54/abbr
/abbrgrp. For each significant component identified by EMMIX, the 95% confidence interval of the mean was then calculated./p
/sec
sec
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pFinite mixture models of genome duplications/p
/st
pTo explore the divergence patterns for duplicated genes, the inferred distribution of itKsubs /sub
/itdivergences were fitted to a mixture model comprising several component distributions in various proportions. The itKsubs /sub
/itvalue for each duplicated sequence pair was calculated using the Goldman and Yang maximum likelihood method implemented in codeml with the F3X4 model abbrgrp
abbr bid="B74"74/abbr
/abbrgrp. The EMMIX software was used to fit a mixture model of multivariate normal components to a given data set. The mixed populations were modelled with one to four components. The EM algorithm was repeated 100 times with random starting values, as well as 10 times with itk/it-mean starting values. The best mixture model was identified using the Bayesian information criterion./p
/sec
/sec
sec
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pAbbreviations/p
/st
pBS: bootstrap value; EST: expressed sequence tag; itKsubs/sub
/it: rate of synonymous substitutions per synonymous site; mya: million years ago; WGD: whole genome duplication./p
/sec
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pAuthors' contributions/p
/st
pYJ, JL-M and CWD conceived of the study and its design, and YJ performed all of the final analyses. YJ, JL-M, CWD drafted the primary manuscript and additional text and discussion of the research was provided by DES, PSS, JEB, NJW, TMK, GW, DWS. Tissue samples, RNA isolations, library preparation sequencing and sample and sequence management were done by MR, MRM, JM, MR, XW, YongZ, JW, ASC, MKD, RM and JCP. Data assemblies and other analyses were done by YJ, SA, DRR, EW, and YetingZ. All authors contributed to and approved the final manuscript for publication./p
/sec
/bdybm
ack
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pAcknowledgements/p
/st
pWe thank Joshua P Der for helpful comments. This work was supported in part by funds from the NSF Plant Genome Research Program (DEB 0638595, The Ancestral Angiosperm Genome Project to CWD, JL-M, PSS, DES; DEB 0701748, The Parasitic Plant Genome Project to CWD; DEB 0922742, The itAmborella /itGenome: A Reference for Plant Biology to CWD, JL-M, PSS, DES; IOS 0421604, Genomics of Comparative Seed Evolution to DWS, RM), NSF Tree of Life program ('MonATOL,' DEB 0829868, From itAcorus /itto itZingiber /it- Assembling the Phylogeny of the Monocots to DWS, JCP, JL-M, RM, CWD), National Institute on Drug Abuse (NIDA) at the National Institutes of Health (project 5R01DA025197-02 to TMK, CWD, JL-M), the Alberta 1000 Plants Initiative (1000 Green Plant Transcriptome Project, to GW) by Alberta Advanced Education and Technology, by Musea Ventures, and by BGI-Shenzhen), iPLant (to JL-M) and by the Biology Department and Plant Biology Graduate Program of Penn State University./p
/sec
/ack
refgrpbibl id="B1"augausnmOhno/snmfnmS/fnm/au/augsourceEvolution by Gene Duplication/sourcepublisherSpringer-Verlag/publisherpubdate1970/pubdate/biblbibl id="B2"titlepPolyploidy and genome evolution in plants./p/titleaugausnmAdams/snmfnmKL/fnm/auausnmWendel/snmfnmJF/fnm/au/augsourceCurr Opin Plant Biol/sourcepubdate2005/pubdatevolume8/volumefpage135/fpagelpage141/lpagexrefbibpubidlistpubid idtype="doi"10.1016j.pbi.2005.01.001/pubidpubid idtype="pmpid" link="fulltext"15752992/pubid/pubidlist/xrefbib/biblbibl id="B3"titlepGlobal trends of whole-genome duplications revealed by the ciliate itParamecium tetraurelia/it./p/titleaugausnmAury/snmfnmJM/fnm/auausnmJaillon/snmfnmO/fnm/auausnmDuret/snmfnmL/fnm/auausnmNoel/snmfnmB/fnm/auausnmJubin/snmfnmC/fnm/auausnmPorcel/snmfnmBM/fnm/auausnmSegurens/snmfnmB/fnm/auausnmDaubin/snmfnmV/fnm/auausnmAnthouard/snmfnmV/fnm/auausnmAiach/snmfnmN/fnm/auausnmArnaiz/snmfnmO/fnm/auausnmBillaut/snmfnmA/fnm/auausnmBeisson/snmfnmJ/fnm/auausnmBlanc/snmfnmI/fnm/auausnmBouhouche/snmfnmK/fnm/auausnmCamara/snmfnmF/fnm/auausnmDuharcourt/snmfnmS/fnm/auausnmGuigo/snmfnmR/fnm/auausnmGogendeau/snmfnmD/fnm/auausnmKatinka/snmfnmM/fnm/auausnmKeller/snmfnmAM/fnm/auausnmKissmehl/snmfnmR/fnm/auausnmKlotz/snmfnmC/fnm/auausnmKoll/snmfnmF/fnm/auausnmLe Mouel/snmfnmA/fnm/auausnmLepere/snmfnmG/fnm/auausnmMalinsky/snmfnmS/fnm/auausnmNowacki/snmfnmM/fnm/auausnmNowak/snmfnmJK/fnm/auausnmPlattner/snmfnmH/fnm/auetal//augsourceNature/sourcepubdate2006/pubdatevolume444/volumefpage171/fpagelpage178/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature05230/pubidpubid idtype="pmpid" link="fulltext"17086204/pubid/pubidlist/xrefbib/biblbibl id="B4"titlepProof and evolutionary analysis of ancient genome duplication in the yeast itSaccharomyces cerevisiae/it./p/titleaugausnmKellis/snmfnmM/fnm/auausnmBirren/snmfnmBW/fnm/auausnmLander/snmfnmES/fnm/au/augsourceNature/sourcepubdate2004/pubdatevolume428/volumefpage617/fpagelpage624/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature02424/pubidpubid idtype="pmpid" link="fulltext"15004568/pubid/pubidlist/xrefbib/biblbibl id="B5"titlepAncestral polyploidy in seed plants and angiosperms./p/titleaugausnmJiao/snmfnmY/fnm/auausnmWickett/snmfnmNJ/fnm/auausnmAyyampalayam/snmfnmS/fnm/auausnmChanderbali/snmfnmAS/fnm/auausnmLandherr/snmfnmL/fnm/auausnmRalph/snmfnmPE/fnm/auausnmTomsho/snmfnmLP/fnm/auausnmHu/snmfnmY/fnm/auausnmLiang/snmfnmH/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmSoltis/snmfnmDE/fnm/auausnmClifton/snmfnmSW/fnm/auausnmSchlarbaum/snmfnmSE/fnm/auausnmSchuster/snmfnmSC/fnm/auausnmMa/snmfnmH/fnm/auausnmLeebens-Mack/snmfnmJ/fnm/auausnmdePamphilis/snmfnmCW/fnm/au/augsourceNature/sourcepubdate2011/pubdatevolume473/volumefpage97/fpagelpage100/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature09916/pubidpubid idtype="pmpid" link="fulltext"21478875/pubid/pubidlist/xrefbib/biblbibl id="B6"titlepA recent polyploidy superimposed on older large-scale duplications in the itArabidopsis /itgenome./p/titleaugausnmBlanc/snmfnmG/fnm/auausnmHokamp/snmfnmK/fnm/auausnmWolfe/snmfnmKH/fnm/au/augsourceGenome Res/sourcepubdate2003/pubdatevolume13/volumefpage137/fpagelpage144/lpagexrefbibpubidlistpubid idtype="doi"10.1101gr.751803/pubidpubid idtype="pmcid"420368/pubidpubid idtype="pmpid" link="fulltext"12566392/pubid/pubidlist/xrefbib/biblbibl id="B7"titlepThe draft genome of the transgenic tropical fruit tree papaya (itCarica papaya /itLinnaeus)./p/titleaugausnmMing/snmfnmR/fnm/auausnmHou/snmfnmS/fnm/auausnmFeng/snmfnmY/fnm/auausnmYu/snmfnmQ/fnm/auausnmDionne-Laporte/snmfnmA/fnm/auausnmSaw/snmfnmJH/fnm/auausnmSenin/snmfnmP/fnm/auausnmWang/snmfnmW/fnm/auausnmLy/snmfnmBV/fnm/auausnmLewis/snmfnmKL/fnm/auausnmSalzberg/snmfnmSL/fnm/auausnmFeng/snmfnmL/fnm/auausnmJones/snmfnmMR/fnm/auausnmSkelton/snmfnmRL/fnm/auausnmMurray/snmfnmJE/fnm/auausnmChen/snmfnmC/fnm/auausnmQian/snmfnmW/fnm/auausnmShen/snmfnmJ/fnm/auausnmDu/snmfnmP/fnm/auausnmEustice/snmfnmM/fnm/auausnmTong/snmfnmE/fnm/auausnmTang/snmfnmH/fnm/auausnmLyons/snmfnmE/fnm/auausnmPaull/snmfnmRE/fnm/auausnmMichael/snmfnmTP/fnm/auausnmWall/snmfnmK/fnm/auausnmRice/snmfnmDW/fnm/auausnmAlbert/snmfnmH/fnm/auausnmWang/snmfnmML/fnm/auausnmZhu/snmfnmYJ/fnm/auetal//augsourceNature/sourcepubdate2008/pubdatevolume452/volumefpage991/fpagelpage996/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature06856/pubidpubid idtype="pmcid"2836516/pubidpubid idtype="pmpid" link="fulltext"18432245/pubid/pubidlist/xrefbib/biblbibl id="B8"titlepThe origins of genomic duplications in itArabidopsis/it./p/titleaugausnmVision/snmfnmTJ/fnm/auausnmBrown/snmfnmDG/fnm/auausnmTanksley/snmfnmSD/fnm/au/augsourceScience/sourcepubdate2000/pubdatevolume290/volumefpage2114/fpagelpage2117/lpagexrefbibpubidlistpubid idtype="doi"10.1126science.290.5499.2114/pubidpubid idtype="pmpid"11118139/pubid/pubidlist/xrefbib/biblbibl id="B9"titlepUnravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events./p/titleaugausnmBowers/snmfnmJE/fnm/auausnmChapman/snmfnmBA/fnm/auausnmRong/snmfnmJ/fnm/auausnmPaterson/snmfnmAH/fnm/au/augsourceNature/sourcepubdate2003/pubdatevolume422/volumefpage433/fpagelpage438/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature01521/pubidpubid idtype="pmpid" link="fulltext"12660784/pubid/pubidlist/xrefbib/biblbibl id="B10"titlepPlants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event./p/titleaugausnmFawcett/snmfnmJA/fnm/auausnmMaere/snmfnmS/fnm/auausnmVan de Peer/snmfnmY/fnm/au/augsourceProc Natl Acad Sci USA/sourcepubdate2009/pubdatevolume106/volumefpage5737/fpagelpage5742/lpagexrefbibpubidlistpubid idtype="doi"10.1073pnas.0900906106/pubidpubid idtype="pmcid"2667025/pubidpubid idtype="pmpid" link="fulltext"19325131/pubid/pubidlist/xrefbib/biblbibl id="B11"titlepUnraveling ancient hexaploidy through multiply-aligned angiosperm gene maps./p/titleaugausnmTang/snmfnmH/fnm/auausnmWang/snmfnmX/fnm/auausnmBowers/snmfnmJE/fnm/auausnmMing/snmfnmR/fnm/auausnmAlam/snmfnmM/fnm/auausnmPaterson/snmfnmAH/fnm/au/augsourceGenome Res/sourcepubdate2008/pubdatevolume18/volumefpage1944/fpagelpage1954/lpagexrefbibpubidlistpubid idtype="doi"10.1101gr.080978.108/pubidpubid idtype="pmcid"2593578/pubidpubid idtype="pmpid" link="fulltext"18832442/pubid/pubidlist/xrefbib/biblbibl id="B12"titlepSynteny and collinearity in plant genomes./p/titleaugausnmTang/snmfnmH/fnm/auausnmBowers/snmfnmJE/fnm/auausnmWang/snmfnmX/fnm/auausnmMing/snmfnmR/fnm/auausnmAlam/snmfnmM/fnm/auausnmPaterson/snmfnmAH/fnm/au/augsourceScience/sourcepubdate2008/pubdatevolume320/volumefpage486/fpagelpage488/lpagexrefbibpubidlistpubid idtype="doi"10.1126science.1153917/pubidpubid idtype="pmpid" link="fulltext"18436778/pubid/pubidlist/xrefbib/biblbibl id="B13"titlepA mystery unveiled./p/titleaugausnmVan de Peer/snmfnmY/fnm/au/augsourceGenome Biol/sourcepubdate2011/pubdatevolume12/volumefpage113/fpagexrefbibpubidlistpubid idtype="doi"10.1186gb-2011-12-5-113/pubidpubid idtype="pmpid" link="fulltext"21635712/pubid/pubidlist/xrefbib/biblbibl id="B14"titlepPolyploidy and angiosperm diversification./p/titleaugausnmSoltis/snmfnmDE/fnm/auausnmAlbert/snmfnmVA/fnm/auausnmLeebens-Mack/snmfnmJ/fnm/auausnmBell/snmfnmCD/fnm/auausnmPaterson/snmfnmAH/fnm/auausnmZheng/snmfnmC/fnm/auausnmSankoff/snmfnmD/fnm/auausnmDepamphilis/snmfnmCW/fnm/auausnmWall/snmfnmPK/fnm/auausnmSoltis/snmfnmPS/fnm/au/augsourceAm J Bot/sourcepubdate2009/pubdatevolume96/volumefpage336/fpagelpage348/lpagexrefbibpubidlistpubid idtype="doi"10.3732ajb.0800079/pubidpubid idtype="pmpid" link="fulltext"21628192/pubid/pubidlist/xrefbib/biblbibl id="B15"titlepThe genome of the mesopolyploid crop species itBrassica rapa/it./p/titleaugausnmWang/snmfnmX/fnm/auausnmWang/snmfnmH/fnm/auausnmWang/snmfnmJ/fnm/auausnmSun/snmfnmR/fnm/auausnmWu/snmfnmJ/fnm/auausnmLiu/snmfnmS/fnm/auausnmBai/snmfnmY/fnm/auausnmMun/snmfnmJH/fnm/auausnmBancroft/snmfnmI/fnm/auausnmCheng/snmfnmF/fnm/auausnmHuang/snmfnmS/fnm/auausnmLi/snmfnmX/fnm/auausnmHua/snmfnmW/fnm/auausnmFreeling/snmfnmM/fnm/auausnmPires/snmfnmJC/fnm/auausnmPaterson/snmfnmAH/fnm/auausnmChalhoub/snmfnmB/fnm/auausnmWang/snmfnmB/fnm/auausnmHayward/snmfnmA/fnm/auausnmSharpe/snmfnmAG/fnm/auausnmPark/snmfnmBS/fnm/auausnmWeisshaar/snmfnmB/fnm/auausnmLiu/snmfnmB/fnm/auausnmLi/snmfnmB/fnm/auausnmTong/snmfnmC/fnm/auausnmSong/snmfnmC/fnm/auausnmDuran/snmfnmC/fnm/auausnmPeng/snmfnmC/fnm/auausnmGeng/snmfnmC/fnm/auausnmKoh/snmfnmC/fnm/auetal//augsourceNat Genet/sourcepubdate2011/pubdatevolume43/volumefpage1035/fpagelpage1039/lpagexrefbibpubidlistpubid idtype="doi"10.1038ng.919/pubidpubid idtype="pmpid" link="fulltext"21873998/pubid/pubidlist/xrefbib/biblbibl id="B16"titlepIndependent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae./p/titleaugausnmSchranz/snmfnmME/fnm/auausnmMitchell-Olds/snmfnmT/fnm/au/augsourcePlant Cell/sourcepubdate2006/pubdatevolume18/volumefpage1152/fpagelpage1165/lpagexrefbibpubidlistpubid idtype="doi"10.1105tpc.106.041111/pubidpubid idtype="pmcid"1456871/pubidpubid idtype="pmpid" link="fulltext"16617098/pubid/pubidlist/xrefbib/biblbibl id="B17"titlepTwo rounds of whole genome duplication in the ancestral vertebrate./p/titleaugausnmDehal/snmfnmP/fnm/auausnmBoore/snmfnmJL/fnm/au/augsourcePLoS Biol/sourcepubdate2005/pubdatevolume3/volumefpagee314/fpagexrefbibpubidlistpubid idtype="doi"10.1371journal.pbio.0030314/pubidpubid idtype="pmcid"1197285/pubidpubid idtype="pmpid" link="fulltext"16128622/pubid/pubidlist/xrefbib/biblbibl id="B18"titlepFugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes./p/titleaugausnmChristoffels/snmfnmA/fnm/auausnmKoh/snmfnmEG/fnm/auausnmChia/snmfnmJM/fnm/auausnmBrenner/snmfnmS/fnm/auausnmAparicio/snmfnmS/fnm/auausnmVenkatesh/snmfnmB/fnm/au/augsourceMol Biol Evol/sourcepubdate2004/pubdatevolume21/volumefpage1146/fpagelpage1151/lpagexrefbibpubidlistpubid idtype="doi"10.1093molbevmsh114/pubidpubid idtype="pmpid" link="fulltext"15014147/pubid/pubidlist/xrefbib/biblbibl id="B19"titlepGenome duplication in the teleost fish itTetraodon nigroviridis /itreveals the early vertebrate proto-karyotype./p/titleaugausnmJaillon/snmfnmO/fnm/auausnmAury/snmfnmJM/fnm/auausnmBrunet/snmfnmF/fnm/auausnmPetit/snmfnmJL/fnm/auausnmStange-Thomann/snmfnmN/fnm/auausnmMauceli/snmfnmE/fnm/auausnmBouneau/snmfnmL/fnm/auausnmFischer/snmfnmC/fnm/auausnmOzouf-Costaz/snmfnmC/fnm/auausnmBernot/snmfnmA/fnm/auausnmNicaud/snmfnmS/fnm/auausnmJaffe/snmfnmD/fnm/auausnmFisher/snmfnmS/fnm/auausnmLutfalla/snmfnmG/fnm/auausnmDossat/snmfnmC/fnm/auausnmSegurens/snmfnmB/fnm/auausnmDasilva/snmfnmC/fnm/auausnmSalanoubat/snmfnmM/fnm/auausnmLevy/snmfnmM/fnm/auausnmBoudet/snmfnmN/fnm/auausnmCastellano/snmfnmS/fnm/auausnmAnthouard/snmfnmV/fnm/auausnmJubin/snmfnmC/fnm/auausnmCastelli/snmfnmV/fnm/auausnmKatinka/snmfnmM/fnm/auausnmVacherie/snmfnmB/fnm/auausnmBiemont/snmfnmC/fnm/auausnmSkalli/snmfnmZ/fnm/auausnmCattolico/snmfnmL/fnm/auausnmPoulain/snmfnmJ/fnm/auetal//augsourceNature/sourcepubdate2004/pubdatevolume431/volumefpage946/fpagelpage957/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature03025/pubidpubid idtype="pmpid" link="fulltext"15496914/pubid/pubidlist/xrefbib/biblbibl id="B20"titlepWidespread genome duplications throughout the history of flowering plants./p/titleaugausnmCui/snmfnmL/fnm/auausnmWall/snmfnmPK/fnm/auausnmLeebens-Mack/snmfnmJH/fnm/auausnmLindsay/snmfnmBG/fnm/auausnmSoltis/snmfnmDE/fnm/auausnmDoyle/snmfnmJJ/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmCarlson/snmfnmJE/fnm/auausnmArumuganathan/snmfnmK/fnm/auausnmBarakat/snmfnmA/fnm/auausnmAlbert/snmfnmVA/fnm/auausnmMa/snmfnmH/fnm/auausnmdePamphilis/snmfnmCW/fnm/au/augsourceGenome Res/sourcepubdate2006/pubdatevolume16/volumefpage738/fpagelpage749/lpagexrefbibpubidlistpubid idtype="doi"10.1101gr.4825606/pubidpubid idtype="pmcid"1479859/pubidpubid idtype="pmpid" link="fulltext"16702410/pubid/pubidlist/xrefbib/biblbibl id="B21"titlepExpression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of itArabidopsis/it./p/titleaugausnmDuarte/snmfnmJM/fnm/auausnmCui/snmfnmL/fnm/auausnmWall/snmfnmPK/fnm/auausnmZhang/snmfnmQ/fnm/auausnmZhang/snmfnmX/fnm/auausnmLeebens-Mack/snmfnmJ/fnm/auausnmMa/snmfnmH/fnm/auausnmAltman/snmfnmN/fnm/auausnmdePamphilis/snmfnmCW/fnm/au/augsourceMol Biol Evol/sourcepubdate2006/pubdatevolume23/volumefpage469/fpagelpage478/lpagexrefbibpubid idtype="pmpid" link="fulltext"16280546/pubid/xrefbib/biblbibl id="B22"titlepThe monosaccharide transporter gene family in itArabidopsis /itand rice: a history of duplications, adaptive evolution, and functional divergence./p/titleaugausnmJohnson/snmfnmDA/fnm/auausnmThomas/snmfnmMA/fnm/au/augsourceMol Biol Evol/sourcepubdate2007/pubdatevolume24/volumefpage2412/fpagelpage2423/lpagexrefbibpubidlistpubid idtype="doi"10.1093molbevmsm184/pubidpubid idtype="pmpid" link="fulltext"17827171/pubid/pubidlist/xrefbib/biblbibl id="B23"titlepGene duplication: a drive for phenotypic diversity and cause of human disease./p/titleaugausnmConrad/snmfnmB/fnm/auausnmAntonarakis/snmfnmSE/fnm/au/augsourceAnnu Rev Genomics Hum Genet/sourcepubdate2007/pubdatevolume8/volumefpage17/fpagelpage35/lpagexrefbibpubidlistpubid idtype="doi"10.1146annurev.genom.8.021307.110233/pubidpubid idtype="pmpid" link="fulltext"17386002/pubid/pubidlist/xrefbib/biblbibl id="B24"titlepFrom 2R to 3R: evidence for a fish-specific genome duplication (FSGD)./p/titleaugausnmMeyer/snmfnmA/fnm/auausnmVan de Peer/snmfnmY/fnm/au/augsourceBioessays/sourcepubdate2005/pubdatevolume27/volumefpage937/fpagelpage945/lpagexrefbibpubidlistpubid idtype="doi"10.1002bies.20293/pubidpubid idtype="pmpid" link="fulltext"16108068/pubid/pubidlist/xrefbib/biblbibl id="B25"titlepGenome duplication and the origin of angiosperms./p/titleaugausnmDe Bodt/snmfnmS/fnm/auausnmMaere/snmfnmS/fnm/auausnmVan de Peer/snmfnmY/fnm/au/augsourceTrends Ecol Evol/sourcepubdate2005/pubdatevolume20/volumefpage591/fpagelpage597/lpagexrefbibpubidlistpubid idtype="doi"10.1016j.tree.2005.07.008/pubidpubid idtype="pmpid" link="fulltext"16701441/pubid/pubidlist/xrefbib/biblbibl id="B26"titlepThe origin of interspecific genomic incompatibility via gene duplication./p/titleaugausnmLynch/snmfnmM/fnm/auausnmForce/snmfnmAG/fnm/au/augsourceAm Nat/sourcepubdate2000/pubdatevolume156/volumefpage590/fpagelpage605/lpagexrefbibpubid idtype="doi"10.1086316992/pubid/xrefbib/biblbibl id="B27"titlepMultiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts./p/titleaugausnmWolfe/snmfnmKH/fnm/auausnmScannell/snmfnmDR/fnm/auausnmByrne/snmfnmKP/fnm/auausnmGordon/snmfnmJL/fnm/auausnmWong/snmfnmS/fnm/au/augsourceNature/sourcepubdate2006/pubdatevolume440/volumefpage341/fpagelpage345/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature04562/pubidpubid idtype="pmpid" link="fulltext"16541074/pubid/pubidlist/xrefbib/biblbibl id="B28"titlepGenome duplication, divergent resolution and speciation./p/titleaugausnmTaylor/snmfnmJS/fnm/auausnmVan de Peer/snmfnmY/fnm/auausnmMeyer/snmfnmA/fnm/au/augsourceTrends Genet/sourcepubdate2001/pubdatevolume17/volumefpage299/fpagelpage301/lpagexrefbibpubidlistpubid idtype="doi"10.1016S0168-9525(01)02318-6/pubidpubid idtype="pmpid" link="fulltext"11377777/pubid/pubidlist/xrefbib/biblbibl id="B29"titlepA model for divergent, allopatric speciation of polyploid pteridophytes resulting from silencing of duplicate-gene expression./p/titleaugausnmWerth/snmfnmCR/fnm/auausnmWindham/snmfnmMD/fnm/au/augsourceAm Nat/sourcepubdate1991/pubdatevolume137/volumefpage515/fpagelpage526/lpagexrefbibpubid idtype="doi"10.1086285180/pubid/xrefbib/biblbibl id="B30"titlepPaleopolyploidy in the Brassicales: analyses of the itCleome /ittranscriptome elucidate the history of genome duplications in itArabidopsis /itand other Brassicales./p/titleaugausnmBarker/snmfnmMS/fnm/auausnmVogel/snmfnmH/fnm/auausnmSchranz/snmfnmME/fnm/au/augsourceGenome Biol Evol/sourcepubdate2009/pubdatevolume5/volumefpage391/fpagelpage399/lpage/biblbibl id="B31"titlepRecently formed polyploid plants diversify at lower rates./p/titleaugausnmMayrose/snmfnmI/fnm/auausnmZhan/snmfnmSH/fnm/auausnmRothfels/snmfnmCJ/fnm/auausnmMagnuson-Ford/snmfnmK/fnm/auausnmBarker/snmfnmMS/fnm/auausnmRieseberg/snmfnmLH/fnm/auausnmOtto/snmfnmSP/fnm/au/augsourceScience/sourcepubdate2011/pubdatevolume333/volumefpage1257/fpagexrefbibpubidlistpubid idtype="doi"10.1126science.1207205/pubidpubid idtype="pmpid" link="fulltext"21852456/pubid/pubidlist/xrefbib/biblbibl id="B32"titlepThe grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla./p/titleaugausnmJaillon/snmfnmO/fnm/auausnmAury/snmfnmJM/fnm/auausnmNoel/snmfnmB/fnm/auausnmPolicriti/snmfnmA/fnm/auausnmClepet/snmfnmC/fnm/auausnmCasagrande/snmfnmA/fnm/auausnmChoisne/snmfnmN/fnm/auausnmAubourg/snmfnmS/fnm/auausnmVitulo/snmfnmN/fnm/auausnmJubin/snmfnmC/fnm/auausnmVezzi/snmfnmA/fnm/auausnmLegeai/snmfnmF/fnm/auausnmHugueney/snmfnmP/fnm/auausnmDasilva/snmfnmC/fnm/auausnmHorner/snmfnmD/fnm/auausnmMica/snmfnmE/fnm/auausnmJublot/snmfnmD/fnm/auausnmPoulain/snmfnmJ/fnm/auausnmBruyere/snmfnmC/fnm/auausnmBillault/snmfnmA/fnm/auausnmSegurens/snmfnmB/fnm/auausnmGouyvenoux/snmfnmM/fnm/auausnmUgarte/snmfnmE/fnm/auausnmCattonaro/snmfnmF/fnm/auausnmAnthouard/snmfnmV/fnm/auausnmVico/snmfnmV/fnm/auausnmDel Fabbro/snmfnmC/fnm/auausnmAlaux/snmfnmM/fnm/auausnmDi Gaspero/snmfnmG/fnm/auausnmDumas/snmfnmV/fnm/auetal//augsourceNature/sourcepubdate2007/pubdatevolume449/volumefpage463/fpagelpage467/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature06148/pubidpubid idtype="pmpid" link="fulltext"17721507/pubid/pubidlist/xrefbib/biblbibl id="B33"titlepThe structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat./p/titleaugausnmDvorak/snmfnmJ/fnm/auausnmLuo/snmfnmMC/fnm/auausnmYang/snmfnmZL/fnm/auausnmZhang/snmfnmHB/fnm/au/augsourceTheor Appl Genet/sourcepubdate1998/pubdatevolume97/volumefpage657/fpagelpage670/lpagexrefbibpubid idtype="doi"10.1007s001220050942/pubid/xrefbib/biblbibl id="B34"titlepThe value of nonmodel genomes and an expample using synmap within CoGe to dissect the hexaploidy that predates the rosids./p/titleaugausnmLyons/snmfnmE/fnm/auausnmPedersen/snmfnmB/fnm/auausnmKane/snmfnmJ/fnm/auausnmFreeling/snmfnmM/fnm/au/augsourceTropical Plant Biol/sourcepubdate2008/pubdatevolume1/volumefpage181/fpagelpage190/lpagexrefbibpubid idtype="doi"10.1007s12042-008-9017-y/pubid/xrefbib/biblbibl id="B35"titlepGenome sequence and analysis of the tuber crop potato./p/titleaugausnmXu/snmfnmX/fnm/auausnmPan/snmfnmS/fnm/auausnmCheng/snmfnmS/fnm/auausnmZhang/snmfnmB/fnm/auausnmMu/snmfnmD/fnm/auausnmNi/snmfnmP/fnm/auausnmZhang/snmfnmG/fnm/auausnmYang/snmfnmS/fnm/auausnmLi/snmfnmR/fnm/auausnmWang/snmfnmJ/fnm/auausnmOrjeda/snmfnmG/fnm/auausnmGuzman/snmfnmF/fnm/auausnmTorres/snmfnmM/fnm/auausnmLozano/snmfnmR/fnm/auausnmPonce/snmfnmO/fnm/auausnmMartinez/snmfnmD/fnm/auausnmDe la Cruz/snmfnmG/fnm/auausnmChakrabarti/snmfnmSK/fnm/auausnmPatil/snmfnmVU/fnm/auausnmSkryabin/snmfnmKG/fnm/auausnmKuznetsov/snmfnmBB/fnm/auausnmRavin/snmfnmNV/fnm/auausnmKolganova/snmfnmTV/fnm/auausnmBeletsky/snmfnmAV/fnm/auausnmMardanov/snmfnmAV/fnm/auausnmDi Genova/snmfnmA/fnm/auausnmBolser/snmfnmDM/fnm/auausnmMartin/snmfnmDM/fnm/auausnmLi/snmfnmG/fnm/auausnmYang/snmfnmY/fnm/auetal//augsourceNature/sourcepubdate2011/pubdatevolume475/volumefpage189/fpagelpage195/lpagexrefbibpubidlistpubid idtype="doi"10.1038nature10158/pubidpubid idtype="pmpid" link="fulltext"21743474/pubid/pubidlist/xrefbib/biblbibl id="B36"titlepA physical map for the itAmborella trichopoda /itgenome sheds light on the evolution of angiosperm genome structure./p/titleaugausnmZuccolo/snmfnmA/fnm/auausnmBowers/snmfnmJE/fnm/auausnmEstill/snmfnmJC/fnm/auausnmXiong/snmfnmZ/fnm/auausnmLuo/snmfnmM/fnm/auausnmSebastian/snmfnmA/fnm/auausnmGoicoechea/snmfnmJL/fnm/auausnmCollura/snmfnmK/fnm/auausnmYu/snmfnmY/fnm/auausnmJiao/snmfnmY/fnm/auausnmDuarte/snmfnmJ/fnm/auausnmTang/snmfnmH/fnm/auausnmAyyampalayam/snmfnmS/fnm/auausnmRounsley/snmfnmS/fnm/auausnmKudma/snmfnmD/fnm/auausnmPaterson/snmfnmAH/fnm/auausnmPires/snmfnmJC/fnm/auausnmChanderbali/snmfnmA/fnm/auausnmSoltis/snmfnmDE/fnm/auausnmChamala/snmfnmS/fnm/auausnmBarbazuk/snmfnmB/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmAlbert/snmfnmVA/fnm/auausnmMa/snmfnmH/fnm/auausnmMandoli/snmfnmD/fnm/auausnmBanks/snmfnmJ/fnm/auausnmCarlson/snmfnmJE/fnm/auausnmTomkins/snmfnmJ/fnm/auausnmDepamphilis/snmfnmCW/fnm/auausnmWing/snmfnmRA/fnm/auetal//augsourceGenome Biol/sourcepubdate2011/pubdatevolume12/volumefpageR48/fpagexrefbibpubidlistpubid idtype="doi"10.1186gb-2011-12-5-r48/pubidpubid idtype="pmcid"3219971/pubidpubid idtype="pmpid" link="fulltext"21619600/pubid/pubidlist/xrefbib/biblbibl id="B37"titlepIdentifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone./p/titleaugausnmLeebens-Mack/snmfnmJ/fnm/auausnmRaubeson/snmfnmLA/fnm/auausnmCui/snmfnmL/fnm/auausnmKuehl/snmfnmJV/fnm/auausnmFourcade/snmfnmMH/fnm/auausnmChumley/snmfnmTW/fnm/auausnmBoore/snmfnmJL/fnm/auausnmJansen/snmfnmRK/fnm/auausnmdepamphilis/snmfnmCW/fnm/au/augsourceMol Biol Evol/sourcepubdate2005/pubdatevolume22/volumefpage1948/fpagelpage1963/lpagexrefbibpubidlistpubid idtype="doi"10.1093molbevmsi191/pubidpubid idtype="pmpid" link="fulltext"15944438/pubid/pubidlist/xrefbib/biblbibl id="B38"titlepCases in which parsimony or compatibility methods will be positively misleading./p/titleaugausnmFelsenstein/snmfnmJ/fnm/au/augsourceSyst Zool/sourcepubdate1978/pubdatevolume27/volumefpage401/fpagelpage410/lpagexrefbibpubid idtype="doi"10.23072412923/pubid/xrefbib/biblbibl id="B39"titlepA framework for the quantitative study of evolutionary trees./p/titleaugausnmHendy/snmfnmMD/fnm/auausnmPenny/snmfnmD/fnm/au/augsourceSyst Zool/sourcepubdate1989/pubdatevolume38/volumefpage297/fpagelpage309/lpagexrefbibpubid idtype="doi"10.23072992396/pubid/xrefbib/biblbibl id="B40"titlepThe TIGR plant transcript assemblies database./p/titleaugausnmChilds/snmfnmKL/fnm/auausnmHamilton/snmfnmJP/fnm/auausnmZhu/snmfnmW/fnm/auausnmLy/snmfnmE/fnm/auausnmCheung/snmfnmF/fnm/auausnmWu/snmfnmH/fnm/auausnmRabinowicz/snmfnmPD/fnm/auausnmTown/snmfnmCD/fnm/auausnmBuell/snmfnmCR/fnm/auausnmChan/snmfnmAP/fnm/au/augsourceNucleic Acids Res/sourcepubdate2007/pubdatevolume35/volumefpageD846/fpagelpage851/lpagexrefbibpubidlistpubid idtype="doi"10.1093nargkl785/pubidpubid idtype="pmcid"1669722/pubidpubid idtype="pmpid" link="fulltext"17088284/pubid/pubidlist/xrefbib/biblbibl id="B41"titlepArchiving next generation sequencing data./p/titleaugausnmShumway/snmfnmM/fnm/auausnmCochrane/snmfnmG/fnm/auausnmSugawara/snmfnmH/fnm/au/augsourceNucleic Acids Res/sourcepubdate2010/pubdatevolume38/volumefpageD870/fpagelpage871/lpagexrefbibpubidlistpubid idtype="doi"10.1093nargkp1078/pubidpubid idtype="pmcid"2808927/pubidpubid idtype="pmpid" link="fulltext"19965774/pubid/pubidlist/xrefbib/biblbibl id="B42"titlepMonocot Tree of Life Project./p/titleurlhttp:www.botany.wisc.edugivnishmonocotatol.htm/url/biblbibl id="B43"titlep1000 Green Plant Transcriptome Project./p/titleurlhttp:www.onekp.com/url/biblbibl id="B44"titlepAncestral Angiosperm Genome Project./p/titleurlhttp:ancangio.uga.edu/url/biblbibl id="B45"titlepPlantGDB./p/titleurlhttp:www.plantgdb.org/url/biblbibl id="B46"titlepThe evolution of the itSEPALLATA /itsubfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history./p/titleaugausnmZahn/snmfnmLM/fnm/auausnmKong/snmfnmH/fnm/auausnmLeebens-Mack/snmfnmJH/fnm/auausnmKim/snmfnmS/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmLandherr/snmfnmLL/fnm/auausnmSoltis/snmfnmDE/fnm/auausnmDepamphilis/snmfnmCW/fnm/auausnmMa/snmfnmH/fnm/au/augsourceGenetics/sourcepubdate2005/pubdatevolume169/volumefpage2209/fpagelpage2223/lpagexrefbibpubidlistpubid idtype="doi"10.1534genetics.104.037770/pubidpubid idtype="pmcid"1449606/pubidpubid idtype="pmpid" link="fulltext"15687268/pubid/pubidlist/xrefbib/biblbibl id="B47"titlepBuffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication./p/titleaugausnmChapman/snmfnmBA/fnm/auausnmBowers/snmfnmJE/fnm/auausnmFeltus/snmfnmFA/fnm/auausnmPaterson/snmfnmAH/fnm/au/augsourceProc Natl Acad Sci USA/sourcepubdate2006/pubdatevolume103/volumefpage2730/fpagelpage2735/lpagexrefbibpubidlistpubid idtype="doi"10.1073pnas.0507782103/pubidpubid idtype="pmcid"1413778/pubidpubid idtype="pmpid" link="fulltext"16467140/pubid/pubidlist/xrefbib/biblbibl id="B48"titlepRosid radiation and the rapid rise of angiosperm-dominated forests./p/titleaugausnmWang/snmfnmH/fnm/auausnmMoore/snmfnmMJ/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmBell/snmfnmCD/fnm/auausnmBrockington/snmfnmSF/fnm/auausnmAlexandre/snmfnmR/fnm/auausnmDavis/snmfnmCC/fnm/auausnmLatvis/snmfnmM/fnm/auausnmManchester/snmfnmSR/fnm/auausnmSoltis/snmfnmDE/fnm/au/augsourceProc Natl Acad Sci USA/sourcepubdate2009/pubdatevolume106/volumefpage3853/fpagelpage3858/lpagexrefbibpubidlistpubid idtype="doi"10.1073pnas.0813376106/pubidpubid idtype="pmcid"2644257/pubidpubid idtype="pmpid" link="fulltext"19223592/pubid/pubidlist/xrefbib/biblbibl id="B49"titlepAngiosperm phylogeny: 17 genes, 640 taxa./p/titleaugausnmSoltis/snmfnmDE/fnm/auausnmSmith/snmfnmSA/fnm/auausnmCellinese/snmfnmN/fnm/auausnmWurdack/snmfnmKJ/fnm/auausnmTank/snmfnmDC/fnm/auausnmBrockington/snmfnmSF/fnm/auausnmRefulio-Rodriguez/snmfnmNF/fnm/auausnmWalker/snmfnmJB/fnm/auausnmMoore/snmfnmMJ/fnm/auausnmCarlsward/snmfnmBS/fnm/auausnmBell/snmfnmCD/fnm/auausnmLatvis/snmfnmM/fnm/auausnmCrawley/snmfnmS/fnm/auausnmBlack/snmfnmC/fnm/auausnmDiouf/snmfnmD/fnm/auausnmXi/snmfnmZ/fnm/auausnmRushworth/snmfnmCA/fnm/auausnmGitzendanner/snmfnmMA/fnm/auausnmSytsma/snmfnmKJ/fnm/auausnmQiu/snmfnmYL/fnm/auausnmHilu/snmfnmKW/fnm/auausnmDavis/snmfnmCC/fnm/auausnmSanderson/snmfnmMJ/fnm/auausnmBeaman/snmfnmRS/fnm/auausnmOlmstead/snmfnmRG/fnm/auausnmJudd/snmfnmWS/fnm/auausnmDonoghue/snmfnmMJ/fnm/auausnmSoltis/snmfnmPS/fnm/au/augsourceAm J Bot/sourcepubdate2011/pubdatevolume98/volumefpage704/fpagelpage730/lpagexrefbibpubidlistpubid idtype="doi"10.3732ajb.1000404/pubidpubid idtype="pmpid" link="fulltext"21613169/pubid/pubidlist/xrefbib/biblbibl id="B50"titlepOrthoMCL: identification of ortholog groups for eukaryotic genomes./p/titleaugausnmLi/snmfnmL/fnm/auausnmStoeckert/snmfnmCJ/fnmsufJr/suf/auausnmRoos/snmfnmDS/fnm/au/augsourceGenome Res/sourcepubdate2003/pubdatevolume13/volumefpage2178/fpagelpage2189/lpagexrefbibpubidlistpubid idtype="doi"10.1101gr.1224503/pubidpubid idtype="pmcid"403725/pubidpubid idtype="pmpid" link="fulltext"12952885/pubid/pubidlist/xrefbib/biblbibl id="B51"titlepA unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders itAsparagales /itand itPoales/it./p/titleaugausnmKuhl/snmfnmJC/fnm/auausnmCheung/snmfnmF/fnm/auausnmYuan/snmfnmQP/fnm/auausnmMartin/snmfnmW/fnm/auausnmZewdie/snmfnmY/fnm/auausnmMcCallum/snmfnmJ/fnm/auausnmCatanach/snmfnmA/fnm/auausnmRutherford/snmfnmP/fnm/auausnmSink/snmfnmKC/fnm/auausnmJenderek/snmfnmM/fnm/auausnmPrince/snmfnmJP/fnm/auausnmTown/snmfnmCD/fnm/auausnmHavey/snmfnmMJ/fnm/au/augsourcePlant Cell/sourcepubdate2004/pubdatevolume16/volumefpage114/fpagelpage125/lpagexrefbibpubidlistpubid idtype="doi"10.1105tpc.017202/pubidpubid idtype="pmcid"301399/pubidpubid idtype="pmpid" link="fulltext"14671025/pubid/pubidlist/xrefbib/biblbibl id="B52"titlepComparative genomic analyses in itAsparagus/it./p/titleaugausnmKuhl/snmfnmJC/fnm/auausnmHavey/snmfnmMJ/fnm/auausnmMartin/snmfnmWJ/fnm/auausnmCheung/snmfnmF/fnm/auausnmYuan/snmfnmQP/fnm/auausnmLandherr/snmfnmL/fnm/auausnmHu/snmfnmY/fnm/auausnmLeebens-Mack/snmfnmJ/fnm/auausnmTown/snmfnmCD/fnm/auausnmSink/snmfnmKC/fnm/au/augsourceGenome/sourcepubdate2005/pubdatevolume48/volumefpage1052/fpagelpage1060/lpagexrefbibpubidlistpubid idtype="doi"10.1139g05-073/pubidpubid idtype="pmpid" link="fulltext"16391674/pubid/pubidlist/xrefbib/biblbibl id="B53"titlepr8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock./p/titleaugausnmSanderson/snmfnmMJ/fnm/au/augsourceBioinformatics/sourcepubdate2003/pubdatevolume19/volumefpage301/fpagelpage302/lpagexrefbibpubidlistpubid idtype="doi"10.1093bioinformatics19.2.301/pubidpubid idtype="pmpid" link="fulltext"12538260/pubid/pubidlist/xrefbib/biblbibl id="B54"titlepThe Emmix software for the fitting of mixtures of normal and t-components./p/titleaugausnmMcLachlan/snmfnmGJ/fnm/auausnmPeel/snmfnmD/fnm/auausnmBasford/snmfnmKE/fnm/auausnmAdams/snmfnmP/fnm/au/augsourceJ Stat Softw/sourcepubdate1999/pubdatevolume4/volumefpagei02/fpage/biblbibl id="B55"titlepHow to summarize estimates of ancestral divergence times./p/titleaugausnmMorrison/snmfnmDA/fnm/au/augsourceEvol Bioinform Online/sourcepubdate2008/pubdatevolume4/volumefpage75/fpagelpage95/lpagexrefbibpubidlistpubid idtype="pmcid"2614201/pubidpubid idtype="pmpid" link="fulltext"19204810/pubid/pubidlist/xrefbib/biblbibl id="B56"augausnmDoyle/snmfnmJA/fnm/auausnmHotton/snmfnmCL/fnm/au/augsourcePollen and Spores. Patterns of Diversification/sourcepublisherOxford: Clarendon/publisherpubdate1991/pubdate/biblbibl id="B57"titlepSymposium II: Polyploidy, Heterosis, and Genomic Plasticity./p/titleaugaucnmAmerican Society of Plant Biologists/cnm/au/augurlhttp:abstracts.aspb.orgpb2010publicS02S022.html/url/biblbibl id="B58"augausnmSoltis/snmfnmDE/fnm/auausnmSoltis/snmfnmPS/fnm/auausnmEndress/snmfnmPK/fnm/auausnmChase/snmfnmMW/fnm/au/augsourcePhylogeny and Evolution of Angiosperms/sourcepublisherSunderland, MA: Sinauer Associates/publisherpubdate2005/pubdate/biblbibl id="B59"titlepDuplication and diversification in the itAPETALA1FRUITFULL /itfloral homeotic gene lineage: Implications for the evolution of floral development./p/titleaugausnmLitt/snmfnmA/fnm/auausnmIrish/snmfnmVF/fnm/au/augsourceGenetics/sourcepubdate2003/pubdatevolume165/volumefpage821/fpagelpage833/lpagexrefbibpubidlistpubid idtype="pmcid"1462802/pubidpubid idtype="pmpid" link="fulltext"14573491/pubid/pubidlist/xrefbib/biblbibl id="B60"titlepGene duplication and floral developmental genetics of basal eudicots./p/titleaugausnmKramer/snmfnmEM/fnm/auausnmZimmer/snmfnmEA/fnm/au/augsourceAdv Bot Res/sourcepubdate2006/pubdatevolume44/volumefpage353/fpagelpage384/lpage/biblbibl id="B61"titlepFloral variation and floral genetics in basal angiosperms./p/titleaugausnmSoltis/snmfnmPS/fnm/auausnmBrockington/snmfnmSF/fnm/auausnmYoo/snmfnmMJ/fnm/auausnmPiedrahita/snmfnmA/fnm/auausnmLatvis/snmfnmM/fnm/auausnmMoore/snmfnmMJ/fnm/auausnmChanderbali/snmfnmAS/fnm/auausnmSoltis/snmfnmDE/fnm/au/augsourceAm J Bot/sourcepubdate2009/pubdatevolume96/volumefpage110/fpagelpage128/lpagexrefbibpubidlistpubid idtype="doi"10.3732ajb.0800182/pubidpubid idtype="pmpid" link="fulltext"21628179/pubid/pubidlist/xrefbib/biblbibl id="B62"titlepConservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower./p/titleaugausnmChanderbali/snmfnmAS/fnm/auausnmYoo/snmfnmMJ/fnm/auausnmZahn/snmfnmLM/fnm/auausnmBrockington/snmfnmSF/fnm/auausnmWall/snmfnmPK/fnm/auausnmGitzendanner/snmfnmMA/fnm/auausnmAlbert/snmfnmVA/fnm/auausnmLeebens-Mack/snmfnmJ/fnm/auausnmAltman/snmfnmNS/fnm/auausnmMa/snmfnmH/fnm/auausnmDepamphilis/snmfnmCW/fnm/auausnmSoltis/snmfnmDE/fnm/auausnmSoltis/snmfnmPS/fnm/au/augsourceProc Natl Acad Sci USA/sourcepubdate2010/pubdatevolume107/volumefpage22570/fpagelpage22575/lpagexrefbibpubidlistpubid idtype="doi"10.1073pnas.1013395108/pubidpubid idtype="pmcid"3012471/pubidpubid idtype="pmpid" link="fulltext"21149731/pubid/pubidlist/xrefbib/biblbibl id="B63"titlepThe genome of black cottonwood, itPopulus trichocarpa /it(Torr. & Gray)./p/titleaugausnmTuskan/snmfnmGA/fnm/auausnmDiFazio/snmfnmS/fnm/auausnmJansson/snmfnmS/fnm/auausnmBohlmann/snmfnmJ/fnm/auausnmGrigoriev/snmfnmI/fnm/auausnmHellsten/snmfnmU/fnm/auausnmPutnam/snmfnmN/fnm/auausnmRalph/snmfnmS/fnm/auausnmRombauts/snmfnmS/fnm/auausnmSalamov/snmfnmA/fnm/auausnmSchein/snmfnmJ/fnm/auausnmSterck/snmfnmL/fnm/auausnmAerts/snmfnmA/fnm/auausnmBhalerao/snmfnmRR/fnm/auausnmBhalerao/snmfnmRP/fnm/auausnmBlaudez/snmfnmD/fnm/auausnmBoerjan/snmfnmW/fnm/auausnmBrun/snmfnmA/fnm/auausnmBrunner/snmfnmA/fnm/auausnmBusov/snmfnmV/fnm/auausnmCampbell/snmfnmM/fnm/auausnmCarlson/snmfnmJ/fnm/auausnmChalot/snmfnmM/fnm/auausnmChapman/snmfnmJ/fnm/auausnmChen/snmfnmGL/fnm/auausnmCooper/snmfnmD/fnm/auausnmCoutinho/snmfnmPM/fnm/auausnmCouturier/snmfnmJ/fnm/auausnmCovert/snmfnmS/fnm/auausnmCronk/snmfnmQ/fnm/auetal//augsourceScience/sourcepubdate2006/pubdatevolume313/volumefpage1596/fpagelpage1604/lpagexrefbibpubidlistpubid idtype="doi"10.1126science.1128691/pubidpubid idtype="pmpid" link="fulltext"16973872/pubid/pubidlist/xrefbib/biblbibl id="B64"titlepThe genome of woodland strawberry (itFragaria vesca/it)./p/titleaugausnmFolta/snmfnmKM/fnm/auausnmShulaev/snmfnmV/fnm/auausnmSargent/snmfnmDJ/fnm/auausnmCrowhurst/snmfnmRN/fnm/auausnmMockler/snmfnmTC/fnm/auausnmFolkerts/snmfnmO/fnm/auausnmDelcher/snmfnmAL/fnm/auausnmJaiswal/snmfnmP/fnm/auausnmMockaitis/snmfnmK/fnm/auausnmListon/snmfnmA/fnm/auausnmMane/snmfnmSP/fnm/auausnmBurns/snmfnmP/fnm/auausnmDavis/snmfnmTM/fnm/auausnmSlovin/snmfnmJP/fnm/auausnmBassil/snmfnmN/fnm/auausnmHellens/snmfnmRP/fnm/auausnmEvans/snmfnmC/fnm/auausnmHarkins/snmfnmT/fnm/auausnmKodira/snmfnmC/fnm/auausnmDesany/snmfnmB/fnm/auausnmCrasta/snmfnmOR/fnm/auausnmJensen/snmfnmRV/fnm/auausnmAllan/snmfnmAC/fnm/auausnmMichael/snmfnmTP/fnm/auausnmSetubal/snmfnmJC/fnm/auausnmCelton/snmfnmJM/fnm/auausnmRees/snmfnmDJG/fnm/auausnmWilliams/snmfnmKP/fnm/auausnmHolt/snmfnmSH/fnm/auausnmRojas/snmfnmJJR/fnm/auetal//augsourceNat Genet/sourcepubdate2011/pubdatevolume43/volumefpage109/fpagelpageU151/lpagexrefbibpubidlistpubid idtype="doi"10.1038ng.740/pubidpubid idtype="pmpid" link="fulltext"21186353/pubid/pubidlist/xrefbib/biblbibl id="B65"titlepParasitic Plant Genome Project./p/titleurlhttp:ppgp.huck.psu.edu/url/biblbibl id="B66"titlepTIGR Plant Transcript Assemblies database./p/titleurlhttp:plantta.jcvi.org/url/biblbibl id="B67"titlepDe novo assembly of human genomes with massively parallel short read sequencing./p/titleaugausnmLi/snmfnmR/fnm/auausnmZhu/snmfnmH/fnm/auausnmRuan/snmfnmJ/fnm/auausnmQian/snmfnmW/fnm/auausnmFang/snmfnmX/fnm/auausnmShi/snmfnmZ/fnm/auausnmLi/snmfnmY/fnm/auausnmLi/snmfnmS/fnm/auausnmShan/snmfnmG/fnm/auausnmKristiansen/snmfnmK/fnm/auausnmYang/snmfnmH/fnm/auausnmWang/snmfnmJ/fnm/au/augsourceGenome Res/sourcepubdate2010/pubdatevolume20/volumefpage265/fpagelpage272/lpagexrefbibpubidlistpubid idtype="doi"10.1101gr.097261.109/pubidpubid idtype="pmcid"2813482/pubidpubid idtype="pmpid" link="fulltext"20019144/pubid/pubidlist/xrefbib/biblbibl id="B68"titleptrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses./p/titleaugausnmCapella-Gutierrez/snmfnmS/fnm/auausnmSilla-Martinez/snmfnmJM/fnm/auausnmGabaldon/snmfnmT/fnm/au/augsourceBioinformatics/sourcepubdate2009/pubdatevolume25/volumefpage1972/fpagelpage1973/lpagexrefbibpubidlistpubid idtype="doi"10.1093bioinformaticsbtp348/pubidpubid idtype="pmcid"2712344/pubidpubid idtype="pmpid" link="fulltext"19505945/pubid/pubidlist/xrefbib/biblbibl id="B69"titlepESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences./p/titleaugausnmIseli/snmfnmC/fnm/auausnmJongeneel/snmfnmCV/fnm/auausnmBucher/snmfnmP/fnm/au/augsourceProc Int Conf Intell Syst Mol Biol/sourcepubdate1999/pubdatefpage138/fpagelpage148/lpage/biblbibl id="B70"titlepMultiple sequence alignment using ClustalW and ClustalX./p/titleaugausnmThompson/snmfnmJD/fnm/auausnmGibson/snmfnmTJ/fnm/auausnmHiggins/snmfnmDG/fnm/au/augsourceCurr Protoc Bioinformatics/sourcepubdate2002/pubdatevolumeChapter 2/volumefpageUnit 2.3/fpagexrefbibpubid idtype="pmpid" link="fulltext"18792934/pubid/xrefbib/biblbibl id="B71"titlepRAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models./p/titleaugausnmStamatakis/snmfnmA/fnm/au/augsourceBioinformatics/sourcepubdate2006/pubdatevolume22/volumefpage2688/fpagelpage2690/lpagexrefbibpubidlistpubid idtype="doi"10.1093bioinformaticsbtl446/pubidpubid idtype="pmpid" link="fulltext"16928733/pubid/pubidlist/xrefbib/biblbibl id="B72"titlepRecords of angiospermid pollen entry into the English Early Cretaceous succession./p/titleaugausnmHughes/snmfnmNF/fnm/auausnmMcdougall/snmfnmAB/fnm/au/augsourceRev Palaeobot Palynol/sourcepubdate1987/pubdatevolume50/volumefpage255/fpagelpage272/lpagexrefbibpubid idtype="doi"10.10160034-6667(87)90003-0/pubid/xrefbib/biblbibl id="B73"titlepImplications of fossil conifers for the phylogenetic relationships of living families./p/titleaugausnmMiller/snmfnmCN/fnm/au/augsourceBot Rev/sourcepubdate1999/pubdatevolume65/volumefpage239/fpagelpage277/lpagexrefbibpubid idtype="doi"10.1007BF02857631/pubid/xrefbib/biblbibl id="B74"titlepPAML: a program package for phylogenetic analysis by maximum likelihood./p/titleaugausnmYang/snmfnmZH/fnm/au/augsourceComput Appl Biosci/sourcepubdate1997/pubdatevolume13/volumefpage555/fpagelpage556/lpagexrefbibpubid idtype="pmpid"9367129/pubid/xrefbib/bibl/refgrp
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epdcx:valueString A genome triplication associated with early diversification of the core eudicots
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Abstract
Background
Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.
Results
To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago.
Conclusions
The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.
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Jiao, Yuannian
Leebens-Mack, Jim
Ayyampalayam, Saravanaraj
Bowers, John E.
McKain, Michael R
McNeal, Joel
Rolf, Megan
Ruzicka, Daniel R
Wafula, Eric
Wickett, Norman J
Wu, Xiaolei
Zhang, Yong
Wang, Jun
Zhang, Yeting
Carpenter, Eric J
Deyholos, Michael K
Kutchan, Toni M
Chanderbali, Andre S
Soltis, Pamela S
Stevenson, Dennis W
McCombie, Richard
Pires, Chris J
Wong, Gane KA-SHU
Soltis, Douglas E
dePamphilis, Claude W
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BioMed Central Ltd
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Jiao et al.; licensee BioMed Central Ltd.
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Genome Biology. 2012 Jan 26;13(1):R3
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RESEARCH OpenAccessAgenometriplicationassociatedwithearly diversificationofthecoreeudicotsYuannianJiao1,2,JimLeebens-Mack3,SaravanarajAyyampalayam3,JohnEBowers3,MichaelRMcKain3, JoelMcNeal3,4,MeganRolf5,DanielRRuzicka5,EricWafula2,NormanJWickett2,6,XiaoleiWu7,YongZhang7, JunWang7,8,YetingZhang2,9,EricJCarpenter10,MichaelKDeyholos10,ToniMKutchan5,AndreSChanderbali11,12, PamelaSSoltis11,DennisWStevenson13,RichardMcCombie14,JChrisPires15,GaneKa-ShuWong7,16, DouglasESoltis12andClaudeWdePamphilis1,2*AbstractBackground: Althoughitisagreedthatamajorpolyploidyevent,gamma,occurredwithintheeudicots,the phylogeneticplacementoftheeventremainsunclear. Results: Todeterminewhenthispolyploidizationoccurredrelativetospeciationeventsinangiospermhistory,we employedaphylogenomicapproachtoinvestigatethetimingofgenesetduplicationslocatedonsyntenic gammablocks.Wepopulated769putativegenefamilieswithlargesetsofhomologsobtainedfrompublic transcriptomesofbasalangiosperms,magnoliids,asterids,andmorethan91.8gigabasesofnewnext-generation transcriptomesequencesofnon-grassmonocotsandbasaleudicots.Theoverwhelmingmajority(95%)ofwellresolvedgammaduplicationswasplacedbeforetheseparationofrosidsandasteridsandafterthesplitof monocotsandeudicots,providingstrongevidencethatthegammapolyploidyeventoccurredearlyineudicot evolution.Further,themajorityofgeneduplicationswasplacedafterthedivergenceoftheRanunculalesandcore eudicots,indicatingthatthegammaappearstoberestrictedtocoreeudicots.Moleculardatingestimatesindicate thattheduplicationeventswereintenselyconcentratedaround117millionyearsago. Conclusions: Therapidradiationofcoreeudicotlineagesthatgaverisetonearly75%ofangiospermspecies appearstohaveoccurredcoincidentallyorshortlyfollowingthegammatriplicationevent.Reconciliationofgene treeswithaspeciesphylogenycanelucidatethetimingofmajoreventsingenomeevolution,evenwhen genomesequencesareonlyavailableforasubsetofspeciesrepresentedinthegenetrees.Comprehensive transcriptomedatasetsarevaluablecomplementstogenomesequencesforhigh-resolutionphylogenomicanalysis.BackgroundGeneduplicationprovidestherawgeneticmaterialfor theevolutionoffunctionalnoveltyandisconsideredto beadrivingforceinevolution[1,2].Amajorsourceof geneduplicationiswholegenomeduplication(WGD; polyploidy),whichinvolvesthedoublingoftheentire genome.WGDhasplayedamajorroleintheevolution ofmosteukaryotes,includingciliates[3],fungi[4],floweringplants[5-16],andvertebrates[17-19].Studiesin theselineagessupportanassociationbetweenWGD andgeneduplications[6,20 ],functionaldivergencein duplicategenepairs[21,22],phenotypicnovelty[23], andpossibleincreasesinspeciesdiversity[24,25]driven byvariationingenelossandretentionamongdiverging polyploidysub-populations[26-29]. Thereisgrowingconsensusthatoneormoreroundsof WGDplayedamajorroleearlyintheevolutionoffloweringplants[2,5,7-9,13,30,31].Earlysynteny-basedandphylogenomicanalysesofthe Arabidopsis genomerevealed multipleWGDevents[8,9].TheoldestoftheseWGD eventswasplacedbeforethemonocot-eudicotdivergence, asecondWGDwashypothesizedtobesharedamong most,ifnotall,eudicots,andamorerecentWGDwas inferredtohaveoccurredbeforediversificationofthe *Correspondence:cwd3@psu.edu1IntercollegeGraduateDegreePrograminPlantBiology,ThePennsylvania StateUniversity,UniversityPark,PA16802,USA FulllistofauthorinformationisavailableattheendofthearticleJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 2012Jiaoetal.;licenseeBioMedCentralLtd.ThisisanopenaccessarticledistributedunderthetermsoftheCreativeCommons AttributionLicense(http://creativecommons.org/licenses/by/2.0),whichpermitsunrestricteduse,distribution,andreproductionin anymedium,providedtheoriginalworkisproperlycited.

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Brassicales[9].Syntenyanalysesoftherecentlysequenced nucleargenomesof Vitisvinifera (winegrape,grapevine) [32]and Caricapapaya (papayatree)[7]providedmore conclusiveevidenceforasomewhatdifferentscenarioin termsofthenumberandtimingofWGDsearlyinthehistoryofangiosperms.Each Vitis (or Carica )genomesegmentcanbesyntenicwithuptofoursegmentsinthe Arabidopsis genome,implicatingtwoWGDsinthe Arabidopsis lineageafterseparationfromthe Vitis (or Carica ) lineage[7,12,32].Themoreancientone( b )appearsto haveoccurredaroundthetimeoftheCretaceous-Tertiary extinction[10].Analysesofthegenomestructureof Vitis revealedtriplicatesetsofsyntenicgeneblocks[11,32]. Becausetheblocksareallsimilarlydiverged,andthus wereprobablygeneratedataroundthesametimeinthe past,thetriplicatedgenomestructureislikelytohave beengeneratedbyanancienthexaploidyevent,possibly similartothetwosuccessiveWGDslikelytohaveproduced Triticumaestivum [33].Althoughthemechanismis notclearatthispoint,theoriginofthistriplicatedgenome structureiscommonlyreferredtoasgammaor g (hereafter g referstothegammaevent).Comparisonsofavailablegenomesequencesforothercorerosidspecies (including Carica,Populus ,andArabidopsis )andthe recentlysequencedpotatogenome(anasterid, Solanum tuberosum )showevidenceofoneormoreroundsofpolyploidywiththemostancienteventwithineachgenome representedbytriplicatedgeneblocksshowinginterspecificsyntenywithtriplicatedblocksinthe Vitis genome [7,11,34,35].Themostparsimoniousexplanationofthese patternsisthat g occurredinacommonancestorofrosids andasterids,becauseallsequencedgenomeswithinthese lineagesshareatriplicategenomestructure[12,35]. Despitethisgrowingbodyofevidencefromgenome sequences,thephylogeneticplacementof g onthe angiospermtreeofliferemainsequivocal(forexample, [13]).Asdescribedabove,the g eventisreadilyapparent inanalysesofsequencedcoreeudicotgenomes,and recentcomparisonsofregionsofthe Amborella genome andthe Vitis syntenyblocksindicatethatthe g event occurredaftertheoriginandearlydiversificationof angiosperms[36].Inaddition,comparisonsofthe Vitis syntenyblockswithbacterialartificialchromosome sequencesfromthe Musa (amonocot)genomeprovide weakevidencethat g postdatesthedivergenceofmonocotsandeudicots[11]. Asanalternativetosyntenycomparisons,aphylogenomicapproachhasalsobeenusedsuccessfullytodeterminetherelativetimingofWGDevents.Bymapping paralogscreatedbyagivenWGDontophylogenetic trees,wecandeterminewhethertheparalogsresulted fromaduplicationeventbeforeorafteragivenbranchingevent[9].Inarecentstudy,Jiao etal. [5]usedasimilarstrategytoidentifytwoboutsofconcertedgene duplicationsthatarehypothesizedtobederivedfrom successivegenomeduplicationsincommonancestorsof livingseedplantsandangiosperms.Whenusingaphylogenomicapproach,extensiv eratevariationamongspeciescouldleadtoincorrectphylogeneticinferencesand thenpossiblyalsoresultintheincorrectplacementof duplicationevents[11].Geneortaxonsamplingcan reducevariationinbranchlengthsandtheimpactof long-branchattractioningenetreeestimates(forexample,[37-39]).Therefore,effectiveuseofthephylogenomicapproachrequiresconsiderationofpossible differencesinsubstitutionratesandcarefultaxonsamplingtodividelongbranchesthatcanleadtoartifactsin phylogeneticanalyses. Theavailabilityoftranscriptomedataproducedbyboth traditional(Sanger)andnext-generationcDNAsequencingmethodshasgrownrapidlyinrecentyears[40,41]. InPlantGDB,verylargeSangerESTdatasetsfrommultiplemembersofAsteraceae(forexample, Helianthus annuus ,sunflower)andSolanaceae(forexample, S.tuberosum ,potato),inparticular,providegoodcoverageofthegenesetsfromthetwolargestasteridlineages. Withadvancesinnext-generation s equencing,comprehensivetranscriptomedatasetsarebeinggeneratedforan expandingnumberofspecies.Forexample,theAncestral AngiospermGenomeProjecthasgeneratedlarge,multitissuecDNAdatasetsofmagnoliidsandotherbasal angiosperms,including Aristolochia,Persea,Liriodendron,Nuphar and Amborella [5].TheMonocotTreeof Lifeproject[42]isgeneratingdeeptranscriptomedatasetsforatleast50monocotspeciesthatpreviouslyhave notbeenthefocusofgenome-scalesequencing.The 1000GreenPlantTranscriptomeProject[43]isgeneratingatleast3GbofIlluminapaired-endRNAseqdata fromeachof1,000plantspeciesfromgreenalgae throughangiosperms(Viridiplantae).Inthisstudy,we drawupontheseresources,includinganinitialcollection ofbasaleudicotspeciesthathavebeenverydeeply sequencedbythe1000GreenPlantTranscriptomeProject.SixmembersofPapaveraceae( Argemonemexicana, Eschscholziacalifornica ,andfourspeciesof Papaver ) havebeentargetedforespeciallydeepsequencing,with over12GbofcDNAsequencederivedfromfourorfive tissue-specificRNAseqlibraries.Threeotherbasaleudicots(Podophyllumpeltatum (Berberidaceae), Akebiatrifoliata (Lardizabalaceae),and Platanusoccidentalis (Platanaceae))sequencedbythe1000GreenPlant(1KP) TranscriptomeProject,andESTsetsavailableforadditionalstrategicallyplacedspecies(forexample,[44,45]) wereemployedforphylogenomicestimationofthetimingofthe g event.Assembledunigenes(sequencesproducedfromassemblyofESTdatasets)weresortedinto genefamiliesandthenthephylogeneticanalysesofgeneJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page2of14

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familieswereperformedtotestalternativehypothesesfor thephylogeneticplacementofthe g event.ResultsanddiscussionSincethe g eventwasfirstidentifiedinagroundbreakingphylogenomicanalysisofthe Arabidopsis genome [9],itstiminghasbeenhypothesizedtohavepredated theoriginofangiosperms(forexample,[25,46]),the divergenceofmonocotsandeudicots(forexample,[47]) andthedivergenceofasteridandrosideudicotclades (forexample,[11,35])(Figure1).Mostrecentanalyses suggestthat g occurredwithintheeudicots,butthetimingofthe g eventrelativetothediversificationofcore eudicotsremainsunclear[13].Resolvingwhether g occurredjustbeforetheradiationofcoreeudicotsor earlier,inacommonancestorofalleudicots,hasimplicationsforourunderstandingoftherelationship betweenpolyploidization,diversificationrates,andmorphologicalnovelty(forexample,[14]).Phylogenomicplacementofthe g polyploidyeventToascertainthetimingofthe g eventrelativetotheoriginandearlydiversificationofeudicots,wemainly focusedondatingparalogousgenepairsthatareretained onsyntenyblocksin Vitis [11,12]. Vitis displaysthemost completeretentionfor g blocksamongallgenomes sequencedtodate,andthusprovidesthebesttargetfor phylogenomicminingofthe g history. Vitis alsorepresentsthesistergrouptoallothermembersoftherosid lineage(APGIII,2009)[48,49],sohomologousgenes weresampledfromotherspeciesofrosids,asterids,basal eudicots,monocots,andbas alangiospermsinorderto estimatethetimingofthe g eventinrelationtothedivergenceoftheselineages.Geneswereclusteredinto Figure1 Schematicphylogenetictreeoffloweringplants .BR1toBR4denotepotentialtimepointswhenthe g eventmayhaveoccurred. BR1,monocots+eudicotsduplication;BR2,eudicot-wideduplication;BR3,coreeudicot-wideduplication;BR4,rosid-wideduplication. Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page3of14

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orthogroups (homologousgenesthatderivefromasinglegeneinthecommonancestorofthefocaltaxa)using OrthoMCL[50]witheightsequencedangiospermgenomes(Table1).Byexcluding Vitis pairsthatarenot includedinthesameorthogroups,andrequiringthat orthogroupscontainedbothmonocotsandnonVitis eudicots,900pairsof Vitis geneswereretainedfrom781 orthogroups.Theseorthogroupswereusedinourinvestigationofthe g duplicationevent. Toverifythatthephylogeneticplacementofthe g eventwassharedbyrosidsandasterids,andtotest whetheritwassharedbyalleudicotsorbyeudicotsand monocots(nearangiosperm-wide),theseorthogroups werethenpopulatedwithunigenesofasterids,basal eudicots,non-grassmonocots,andbasalangiosperms (Table2).Grassesareknowntobedistinctfromother angiospermsintheirhighrateofnucleotidesubstitutions,andcodonbiaseswithinthegrassesmakethis cladedistinctfromotherangiosperms,includingnongrassmonocots(forexample,[51,52]),soinclusionof non-grassmonocotswasnecessarytoreduceartifactsin genetreeestimation.Moregenerally,whendealingwith phylogenomic-scaledatasets,westriveforadequate taxonsamplingtocutlongbranches,butavoidaddinga largeproportionofunigeneswithlowcoverage.Inadequatetaxonsamplingcouldleadtospuriousinferenceof phylogeny,whileincompletesequences(thatis,low-coverageunigenes)cangreatlydegradebranchsupportand resolutionofphylogenetictrees. Tophylogeneticallyplacethe g eventwithconfidence, weadoptedthefollowingsupport-basedapproach.Three relevantbootstrapvaluesweretakenintoaccountwhen evaluatingsupportforaparticularduplication.Forexample,givenatopologyof(((clade2)bootstrap2,(clade3) bootstrap3)bootstrap1),bootstrap2andbootstrap3are thebootstrapvaluessupportingclade2(clade2herewill includeoneofthe Vitis g duplicates)andclade3(includingtheother Vitis duplicate),respectively,whilebootstrap1isthebootstrapvaluesupportingthelargerclade includingclade2andclade3.Thevalueofbootstrap1 indicatesthedegreeofconfidenceintheinferredancestralnodejoiningclades2and3.Inthisstudy,whenbootstrap1,andatleastoneofbootstrap2andbootstrap3 were 50%(or80%),wedeterminedwhetheranasterid, basaleudicot,monocot,orbasalangiospermwascontainedinclades2or3(forexample,asteridsinFigures2 and3)orsistertotheircommonancestor(nodedefining clade1)withabootstrapvalue(BS) 50%(or80%;for example,basaleudicots,monocotsandbasalangiosperms inFigures2and3). Homologoussequenceswereidentifiedfor769ofthe 781orthogroupsandweresubsequentlyusedforphylogeneticanalysis.Forexample,orthogroup1202waswell populatedwithunigenesofasterids,basaleudicots,nongrassmonocots,andbasalangiosperms(Figure2).Two Vitis genes,whichwerelocatedonasyntenicblock,were clusteredintotwoclades,bothofwhichincludegenes fromasteridsandotherrosids.Thisphylogenetictree supports(BS 80%)theduplicationoftwo Vitis genes beforethesplitofrosidsandasteridsandafterthedivergenceofbasaleudicots,indicatingthat g isrestrictedto coreeudicots(BR3ofFigure1;Figure2).Inanother example,onlyoneasteridunigenepassedthequalitycontrolstepsandwasclusteredintoorthogroup1083.This asteridunigenewasgroupedintooneoftheduplicated clades,alsosupporting(BS 50%)aduplicationinthe commonancestorofextantcoreeudicots(BR3ofFigure 1;Figure3).Onlyafewduplicationsof Vitis genepairs wereidentifiedasoccurrin gbeforethedivergenceof monocotsandeudicots(BR1ofFigure1;sevenduplicationswithBS 50%),orrestrictedtorosids(BR4of Figure1;sixduplicationswithBS 50%,fourduplications withBS 80%).Weidentified168 Vitis genepairsthat wereduplicatedafterthesplitofbasaleudicots(BR3of Figure1)withBS 50%,and80ofthesehadBS 80%. Wealsofoundthat70 Vitis geneswereduplicatedbefore theseparationofbasaleudicots(BR2ofFigure1)with BS 50%and19withBS 80%(Table3).Therefore,our phylogenomicanalysisprovidedverystrongsupportthat g occurredbeforethedivergenceofrosidsandasterids, Table1SummaryofdatasetsforeightsequencedplantgenomesincludedinthisstudySpecies Annotationversion Numberofannotatedgenes Arabidopsisthaliana (thalecress) TAIRversion9 27,379 Caricapapaya (papaya) ASGPBrelease 25,536 Cucumissativus (cucumber) BGIrelease 21,635 Populustrichocarpa (blackcottonwood) JGIversion2.0 41,377 Glycinemax (soybean) Phytozomeversion1.0 55,787 Vitisvinifera (grapevine) Genoscoperelease 30,434 Oryzasativa (rice) RGAPrelease6.1 56,979 Sorghumbicolor JGIversion1.4 34,496Theseeightgenomesequenceswereusedtoconstructorthogroups,whichwerethenpopulatedwithadditionalunigenesofasterids,basaleudicots,non-grass monocots,andbasalangiosperms.Thenumberofannotatedgenesineachgenomeisindicated.ASGPB,AdvancedStudiesofGenomics,Proteomicsand Bioinformatics;JGI,JointGenomeInstitute;RGAP,RiceGenomeAnnotationProject;TAIR,TheArabidopsisInformationResource.Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page4of14

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afterthesplitofmonocotsandeudicots,andmostlikely aftertheearliestdiversificationofeudicots.Moleculardatingofthe g duplicationsToestimatetheabsolutedateofthe g event,wecalibrated161ofthe168orthogroupssupporting(BS 50%) acoreeudicot-wideduplicationand66ofthe70 orthogroupssupportingaeudicot-wideduplication,and thenestimatedtheduplicationtimesusingtheprogram r8s[53](Materialsandmeth ods).Wethenanalyzedthe distributionoftheinferredduplicationtimesusinga Bayesianmethodthatassigneddivergencetimeestimates toclassesspecifiedbyamixturemodel[54].Thedistributionofduplicationtimesofcoreeudicot-wide Vitis pairsshowsapeakat1171(95%confidenceinterval) (Figure4a),andthedistributionofalleudicot-wideduplicationtimeshasapeakat1331millionyearsago (mya)(Figure4b).Datinge stimateshaveadditional sourcesoferrorbeyondthesamplingeffectsaccounted forinstandarderrorestimates(forexample,[55]).However,theclearpatternisthattheduplicationbranch pointsoccurredoveranarrowwindowoftimeveryclose totheeudicotcalibrationpointthatrepresentsthefirst documentedappearanceoftricolpatepolleninthefossil Table2Summaryofunigenesequencesofasterids,basaleudicots,non-grassmonocots,andbasalangiosperms includedinphylogeneticstudySpecies LineageSourceNumberofreads/ESTsSizeofdataAssembly method(s) Numberof unigenes Panaxquinquefolius AsteridNCBI-SRA 209,745 89.7MbMIRA 22,881 Lindenbergiaphillipensis AsteridPPGP 69,545,362 5.9GbCLC 104,904 Helianthusannuus AsteridTIGRPTA 93,279 NAMegablast-CAP344,662 Solanumtuberosum AsteridTIGRPTA 219,485 NAMegablast-CAP381,072 Mimulusgutatus AsteridPlantGDB 231,012 NAVmatch-PaCE-CAP339,577 Papaversomniferum Basaleudicot1KP+SRA140,604,904+3,709,87610.3Gb+1.3GbMIRASOAPDenovo-CAP3 252,894 Papaversetigerum Basaleudicot1KP 134,478,938 9.8GbSOAPDenovo-CAP3406,167 Papaverrhoeas Basaleudicot1KP 157,506,374 11.5GbSOAPDenovo-CAP3383,426 Papaverbracteatum Basaleudicot1KP 89,663,900 6.5GbSOAPDenovo-CAP3201,564 Eschscholziacalifornica BasaleudicotNCBI+SRA+ 1KP 14,381+559,470+ 133,422,402 6.8Mb+55Mb+ 9.7Gb MIRASOAPDenovo-CAP3 165,260 Argemonemexicana Basaleudicot1KP+NCBI144,520,360+1,69210.5Gb+1MbSOAPDenovoCAP3 148,533 Akebiatrifoliata Basaleudicot1KP 29,156,514 2.1GbCLC-CAP3 46,024 Podophyllumpelatum Basaleudicot1KP 20,139,210 1.5GbCLC-CAP3 31,472 Platanusoccidentalis Basaleudicot1KP 25,508,642 1.9GbCLC-CAP3 42,373 Aquilegiaformosa x Aquilegia pubescens BasaleudicotPlantGDB 85,040 NAVmatch-PaCE-CAP319,615 Mesembryanthemum crystallinum CaryophillidPlantGDB 27,553 NAVmatch-PaCE-CAP311,317 Betavulgaris CaryophillidPlantGDB 25,883 NAVmatch-PaCE-CAP318,009 Acorusamericanus MonocotMonATOL+ 1KP 149,320+15,427,31644.9Mb+1.1GbMIRASOAPDenovo-CAP3 59,453 Chamaedoreaseifrizii MonocotMonATOL 33,100,948 2.5GbCLC 68,489 Chlorophytumrhizopendulum MonocotMonATOL 59,505,714 4.5GbCLC 58,766 Neoregelia sp. MonocotMonATOL 49,121,506 3.7GbCLC 63,269 Typhaangustifolia MonocotMonATOL 70,733,124 5.7GbCLC 57,980 Perseaamericana (avocado)MagnoliidAAGP 2,336,819 683MbMIRA 132,532 Aristolochiafimbriata (Dutchman spipe) MagnoliidAAGP 3,930,505 880MbMIRA 155,371 Liriodendrontulipifera (yellowpoplar) MagnoliidAAGP 2,327,654 543MbMIRA 137,923 Nupharadvena (yellowpond lily) Basal angiosperm AAGP 3,889,719 1.1GbMIRA 289,773 Amborellatrichopoda Basal angiosperm AAGP 2,943,273 776MbMIRA 2083941KP,1000GreenPlantTranscriptomeProject;AAGP,AncestralAngiospermGenomeProject[44];MonATOL,MonocotTreeofLifeProject[42];NA,notavailable; NCBI,NationalCenterforBiotechnologyInformation;PPGP,ParasiticPlantGenomeProject[65];SRA,SequenceReadArchive;TIGRPTA,TheInstituteforGenomic ResearchPlantTranscriptAssemblies[66].Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page5of14

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record.Wealsoanalyzedthe80nodesand19nodes showingduplicationsharedbycoreeudicotsandalleudicots,respectively,withbootstrapsupport 80%(Figure 4d,e)andfoundsimilardistributions(1161myafor coreeudicotduplicationsand1352myaforalleudicot duplications).Theinferreddatesfor Vitis duplications sharedeitherbycoreeudicotsoralleudicotsarevery closetoeachother,andareconcentratedaround125 mya.Wealsoinvestigatedthedistributionofallinferred duplicationtimestogether(c oreeudicot-wideandeudicot-wide).Evengivenatimeconstraint(125mya)that wouldsplitthedateestimatesforcoreeudicotandeudicot-wideduplications,thedistributionsofcombined inferredduplicationtimesshowonlyonesignificant Amborella trichopoda b4 c2129 Papaver somniferum 7351 Eschscholzia californica 35239 92 Papaver rhoeas 249067 Papaver rhoeas 48932 Papaver rhoeas 162860 68 100 89 Populus trichocarpa 0003s21540 Populus trichocarpa 0001s04750 100 Populus trichocarpa 1020s00200 Populus trichocarpa 1020s00210 Populus trichocarpa 0001s04740 100 100 98 Vitis vinifera GSVIVT00024731001 Glycine max 14g38710 Glycine max 18g05690 100 Carica papaya supercontig 119.95 Cucumis sativus 142900 57 Solanum tuberosum TA25116 4113 Mimulus guttatus7117 Lindenbergia phillipensis 96262 100 84 96 Glycine max 19g33210 Glycine max 03g30290 100 Vitis vinifera GSVIVT00025407001 Arabidopsis thaliana AT3G5806 0 Lindenbergia phillipensis 95847 Panax quinquefolius 3903 95 77 88 89 82 97 Chlorophytum rhizopendulum 52723 Chamaedorea seifrizii 13550 Neoregelia sp. 8364 Typha angustifolia 36449 Typha angustifolia 53757 75 78 Sorghum bicolor Sb01g041820 Oryza sativa Os03g12530 100 100 84 Persea americana b4 c5230 Persea americana b4 c4145 100 97 Liriodendron tulipifera b3 c4952 77 Nuphar advena b3 c4633 0 .1 rosids asterids basal eudicots monocotsbasal angiosperms 1 2 3 Figure2 ExemplarmaximumlikelihoodphylogenyofOrtho1202 .RAxMLtopologyofanorthogroup(Ortho1202)indicatingthatthe g paralogsof Vitis wereduplicatedbeforethesplitofrosidsandasteridsandaftertheearlyradiationofeudicots.Thescoredbootstrap(BS)value forthisduplicationisover80%,becausenodes#1and#2(and/or#3)haveBS>80%.Legend:greenstar=coreeudicotduplication;colored circles=recentindependentduplications;numbers=bootstrapsupportvalues. Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page6of14

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Oryza sativa Os01g46700 Sorghum bicolor Sb03g029850 100 Sorghum bicolor Sb03g001640 Oryza sativa Os01g11952 100 Neoregelia sp. 40704 100 100 Vitis vinifera GSVIVT00037113001 Populus trichocarpa 0012s02120 Populus trichocarpa 0015s01670 100 Arabidopsis thaliana AT5G53430 Arabidopsis thaliana AT4G27910 100 Carica papaya supercontig 3.73 79 88 Cucumis sativus 32070 Glycine max 04g41500 Glycine max 06g13330 100 85 100 100 Vitis vinifera GSVIVT00027049001 Cucumis sativus 348660 Glycine max 16g02800 Glycine max 07g06190 100 Glycine max 03g37370 100 97 Arabidopsis thaliana AT3G61740 Carica papaya supercontig 96.10 99 Populus trichocarpa 0002s17180 Populus trichocarpa 0014s09400 100 98 100 Lindenbergia phillipensis 19460 100 56 Eschscholzia californica 95037 Eschscholzia californica 56188 76 Eschscholzia californica 10658 100 Papaver bracteatum 42604 Papaver bracteatum 130345 100 63 68 Nuphar advena b3 c21977 0 .1 rosids asterids basal eudicots monocotsbasal angiosperms 1 3 2 Figure3 ExemplarmaximumlikelihoodphylogenyofOrtho1083 .RAxMLtopologyofanorthogroup(Ortho1083)indicatesthatthe g paralogsof Vitis wereduplicatedbeforethesplitofrosidsandasterids,andaftertheearlyradiationofeudicots.Thescoredbootstrap(BS)value forthisduplicationisover50%,becausenodes#1hasBS<80%.Legend:greenstar=coreeudicotduplication;coloredcircles=recent independentduplications;numbers=bootstrapsupportvalues. Table3Phylogenetictimingof Vitis g duplicationsinferredfromorthogroupphylogenetichistoriesBR1 BR2 BR3 BR4 Ortho BS 80BS 50BS 80BS 50BS 80BS 50BS 80BS 50 Duplications 0 7 19 70 80 168 4 6 Percent 0% 2.8%18.3%27.9%77.7%67% 4% 2.3%BRxdesignationsareillustratedinFigure1.Bootstrap(BS) 80andBS 50arecountsofnodesresolvedwithBS 80or 50,respectively.Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page7of14

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peak,withameanat121myafororthogroupswithbootstrapsupport 50%(Figure4c)and120myafor orthogroupswithbootstrapsupport 80%(Figure4f).A singlepeakobservedforthecombineddata(Figure4c) suggeststhatthegenome-scaleevent(s)leadingtothetriplicatedgenomestructureofcoreeudicotsoccurredina narrowwindowoftimenearlycoincidentwiththesuddenappearanceofeudicotpollen-typesinthefossil record[56].Hexaploidizationandearlyeudicotradiationareclosein timeManyofthegenetreesshowednoresolutionorlow bootstrapsupportfornodesdistinguishinghypotheses BR2andBR3.Ifthe g eventhadoccurredalmostanywherealongthelongbranchleadingtoeudicots,this eventwouldhavebeenrelativelyeasytoresolve.Thelack ofresolutionofthetimingofduplicationeventsaround thebasaleudicotspeciationnodessuggeststhatthe g eventmayhaveoccurredduringarapidspeciesradiation. Anotherpossibilitycouldbeduetothenatureofhexaploidization.If,asouranaly sessuggest,thepolyploidy event(seebelowforpossiblescenarios)occurredsoon afterthedivergenceofbasaleudicots,thesubstitution ratesfor g paralogscouldvary.Forexample,oneduplicatecouldevolveveryslowlywhiletheotherevolvesat anacceleratedrate[4].Thesepossibilitiescouldaddsignificantchallengestothepreciseresolutionofevents occurringatornearthebranchpointsforbasalversus coreeudicotlineages.Despitethesechallenges,most well-resolvedgenetreessupportthehypothesisthatthe g eventoccurredinassociationwiththeoriginanddiversificationofthecoreeudicots,afterthecoreeudicotlineagedivergedfromtheRanunculales(BR3ofFigure1).Natureofthe g eventAnadditionalquestioniswhethertheancienthexaploid commonancestorwasformedbyoneortwoWGDs Frequency6080100120140 6080100120140FrequencyDivergence time (mya) ( a )( b )( c ) (d) (e) (f) 102030405060700 0 6080100120140 10203040 0 6080100120140 0 6080120160200 0102030405060 6080120160200 608010014018 0 051015202530 608010014018 0 120140160180200 0510152025 120140160180200 0 120140160180 01234567 120140160180 0 Figure4 Agedistributionof g duplications (a) Theinferredduplicationtimesfor161 g duplicationnodesthatsupportcoreeudicot-wide duplication(BS 50%)wereanalyzedbyEMMIXtodeterminewhethertheseduplicationsoccurredrandomlyovertimeorwithinsomesmall timeframe.Eachcomponentiswrittenas color/meanmoleculartiming/proportion where color isthecomponent(curve)colorand proportion isthepercentageofduplicationnodesassignedtotheidentifiedcomponent.Thereisonestatisticallysignificantcomponent:green/117(mya)/1. (b) Distributionofinferred g duplicationtimesfrom66orthogroupsthatsupportaeudicot-wideduplicationwithBS 50%.Thereisone statisticallysignificantcomponent:blue/133(mya)/1. (c) Distributionofinferred g duplicationtimesfromcombinationof(a)and(b)showsone significantcomponent:purple/121(mya)/1. (d-f) CorrespondingdistributionsofinferredduplicationtimesfromorthogroupswithBS 80%.One significantcomponentin(d),green/116(mya)/1;onein(e),blue/135(mya)/1;andonein(f),purple/120(mya)/1. Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page8of14

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thatoccurredoveraveryshortperiod(forexample,as withhexaploidwheat).Itwasdemonstratedthattwoof thethreehomologousregionsweremorefractionated thanthethird,suggestingapossiblemechanismforthe g event[34].Inoneproposedscenario,agenomeduplicationeventgeneratedatetraploid,whichthenhybridizedwithadiploidtogeneratea(probablysterile) triploid.Finally,asecondWGDeventdoubledthetriploidgenometogenerateafertilehexaploid.Alternatively,unreducedgametesofatetraploidandadiploid couldhavefusedtogenerateahexaploiddirectly. Anothercharacterizationofsyntenicblocksindicates thatthethreecorrespondingregionsaregenerallyequidistantfromoneanother[11].Ouranalysesofduplicationpointsinthephylogenomicanalysesresolveonlya singlepeakinestimateddatesforthe g event ,which wouldbeconsistentwitheitherscenario,giventhatany complexscenariowouldinvolveancienteventsthat occurredwithinabriefperiodoftime.Moreevidenceis neededtoestablishamoredefinitivemechanismforthe apparenthexaploidization(thatis,asoneversustwo events,allopolyploidversusautopolyploid).Ratevariationsbetweenparalogsof VitisInanotherattempttoincreaseresolvingpower, Ksdistributionsforduplicate Vitis geneswereinvestigated.The Ksdistributionsof Vitis pairssupportingacoreeudicot-wide duplicationinferredfromphylogeneticanalysesshowone significantpeakat Ks~1.03(Figure5a).The Ksvaluesfor eudicot-wideduplicate Vitis pairswerenotwellclustered, andtheirdistributionshowsonepeakat1.31,whichindicatesslightlymoredivergenceforthese Vitis pairs(Figure 5b).Thisresultisconsistentwithphylogeneticanalyses thatshowthissetofduplicationsoccurredsomewhatearlier(alleudicot-wideversuscoreeudicot-wide).Wealso investigatedthedistributionofall Ksvaluestogether(core eudicot-wideandeudicot-wide).Threestatisticallysignificantpeakswereidentified:0.3,1.02and1.40(Figure5c). Finally,weestimated Ksvaluesforall(2,191)pairsof Vitis g paralogsidentifiedbyTang etal. [11]inanalysesofsyntenicblocks.Wewereabletodetectfoursignificantcomponentsusingthemixturemodelimplementedwith EMMIX(McLachlan etal. [54]):0.12,1.09,1.85,and2.7 (Figure5d).This Ksdistributionclearlyshowsthatthe majorpeak(approximately1.09;greencurveinFigure5d) wasclosetothepeakof Ksdistributionofcoreeudicotwideduplicates(atapproximately1.03;Figure5a).This intriguingpattern(Figure5c,d)couldbeaconsequenceof stablehexaploidyarisin gfromtwoWGDs,oneinthe commonancestorofalleudicotsandoneinthecommon ancestorofcoreeudicots.However,therearenoconsistentpatternsofduplicationsforentiresyntenicblocks;for example,somesyntenicblockshavegenesconsistently duplicatedincoreeudicots,whileothersyntenicblocks wereduplicatedeudicot-wide(resultsnotshown).Alternatively,thispatternalsocouldbeconsistentwiththe hypothesisofanallopolyploidyeventfor g .Iftwoancestral genomeswereinvolvedinthehexaploidizationandthe Vitis genomehadevolvedslowly,twosignificantpeaks mightbedetected[57].Athirdpossibilityisthat Vitis pairssupportingaeudicot-wideduplicationmaybethe productsofpre-WGDtandemorsegmentalduplications thatweremisidentifiedassyntenic g paralogsduetoloss ofalternativecopiesthroughthefractionationprocess. Thesehypotheseswillhavetobetestedthroughcomparativeanalysesasadditionalplantgenomes,especiallyof outgroups(forexample, Aquilegia,Amborella )andother basaleudicots(eg., Buxus,Trochodendron ),aresequenced.Implicationsofthe g eventcharacterizingmosteudicotsOurresultssuggestthatthe g polyploidyeventwasclosely coincidentwitharapidradiationofmajorlineagesofcore eudicotlineagesthattogethercontainabout75%ofliving angiospermspecies.Thisrapidlineageexpansionfollowingthe g eventcouldbeanimportantexceptiontothe generalpatterndescribedbyMayrose etal. [31],whoconcludedthattheremaygenerallybereducedsurvivalof polyploidplantlineages.Theeudicotsconsistofagraded seriesofgenerallysmallclades(oftencalledearly-diverging orbasaleudicots)thataresuccessivesisterstothecore eudicots([49]andreferencestherein).Itiswithinthecore eudicotcladewheremostmajorlineagesaswellasthe largemajorityofangiospermspeciesreside(forexample, rosids,asterids,caryophylli ds).Severalkeyevolutionary eventsseemtocorrespondcloselytotheoriginofthecore eudicots,includingthegenome-wideeventdescribedhere, theevolutionofapentamerous,highlysynorganized flowerwithawell-differentiatedperianth,andtheproductionofellagicandgallicacids[58].Significantly,theduplicationofseveralgenescrucialtotheestablishmentof floralorganidentityalsooccurredneartheoriginofthe coreeudicots( AP3,AP1,AG ,andSEP genelineages) [46,59,60],suggestingthattheseduplications-possibly originatingfromthe g event-mayalsobeinvolvedinthe new floralmorphologythatemergedinthisclade[61,62]. Thisstudyalsohelpstoshedlightonpriorstudies, wherethepotentialtimingofthe g eventvariedwidely frompossiblyinanancestorofallangiosperms[9]to perhapsasrecentasonlyrosids[63].Apolyploidevent hasbeendetectedthatisangiosperm-wide,butthiswas anearlierevent( ,epsilon)[5].Ourresultsareconsistentwitharecentstudythatidentifiedasignatureof the g eventinthegenomeofthepotato,anasterid[35]. The g eventwassuggestedtobeabsentfromgrassgenomesincomparisonsof Vitis and Oryza [32],butthis findingwasquestionedbyTang etal. [11].However, thedraftgenomeofstrawberry( Fragariavesca ),arosid thatsharesthe g event,didnotshowevidencefor g inJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page9of14

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syntenicblockanalysis[64],suggestingthateitherthe g eventhasbeenobscuredbyfurtherrearrangementsand fractionation,orexpansionofthe Fragaria genome sequencedatamaybenecessary.Althoughsequenced plantgenomesarebeingproducedatanincreasingrate, amuchlargersourceofgenome-scaleevidenceis comingfromverylarge-scaletranscriptomestudiessuch asthe1000GreenPlantTranscriptomeProjectandthe MonocotTreeofLifeProject.Inthispaper,wehave usedgigabasesoftranscriptomedatafromspeciesatkey branchpointstophylogeneticallytimehundredsof ancientgeneduplications.Combinedwithevidence K s Frequency ( a )( b ) (c) 0.01.02.03.0 050100150200 0.01.02.03.0 0.00.51.01.52.02.53.0 051015202530 0.00.51.01.52.02.53.0 0.00.51.01.52.02.53. 0 02468 0.00.51.01.52.02.53. 0 0.00.51.01.52.02.53.0 010203040 0.00.51.01.52.02.53.0 (d)Frequency Figure5 Ksdistributionsofparalogsin Vitis fromsyntenicblockanalysis .Methodsforsequencealignmentandestimationof Kswereas reported(Cui etal. 2006),butwereherelimitedtoparalogousgenepairsretainedonsyntenicblocksinthe Vitis genome.Coloredlines superimposedon KsdistributionrepresentsignificantduplicationcomponentsidentifiedbylikelihoodmixturemodelasinFigure4(Materials andmethods).a, Ksdistributionof168 Vitis pairssupportingcoreeudicot-wideduplicationinphylogeneticanalysis.Onestatisticallysignificant component:green/1.03/1.b, Ksdistributionof70 Vitis pairsshowingalleudicot-wideduplicationsonphylogenies.Onesignificantcomponent: blue/1.31/1.c, Ksdistributionofcombinationof Vitis pairssupportingcoreeudicot-(a)andeudicot-wideduplications(b)onphylogenies.Three significantcomponents:black/0.3/0.01,green/1.02/0.70,blue/1.40/0.29.d, Ksdistributionof2191paralogouspairswereidentifiedfromsyntenic blockanalysis.Foursignificantcomponents:black/0.12/0.02,green/1.09/0.74,blue/1.85/0.22,yellow/2.7/0.02. Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page10of14

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from Ksanalysisandsyntenicblocks,globalgenefamily phylogeniescouldincorporateextensiveevidencewithoutasequencedgenome,andultimatelyfacilitatea muchbetterunderstandingofplantevolution.ConclusionsPhylogeneticanalysesandmoleculardatingprovideconsistentandstrongevidencesupportingtheoccurrence ofthe g polyploidyeventafterthedivergenceofmonocotsandeudicots,andbeforetheasterid-rosidsplit.Itis difficulttodeterminewhetherthe g eventwassharedby monocotsornotbasedonlyonsyntenypatternsshared between Vitis andothermonocotgenomes[11].By includingmassivetranscriptomedatasetsfrommany additionaltaxa,suchasbasalangiosperms,non-grass monocots,basaleudicotsan dasterids,weemployeda comprehensivephylogenomicapproach,anddatedgene pairsonsyntenicblocksinarelativelyslowlyevolving species( Vitis )[11].Wewereabletoplacethe g event(s) inanarrowwindowoftime,mostlikelyshortlybefore theoriginandrapidradiationofcoreeudicots.MaterialandmethodsDataandassembliesGenomeswereobtainedfromvarioussourcesasgiven inTable1.ESTdataorassemblieswereobtainedfrom sourcesindicatedinTable2.Thelargestquantitiesof newsequencedataarerepresentedbytranscriptome datasetsforninebasaleudicotspeciesproducedbyBeijingGenomicsInstituteforthe1000GreenPlantTranscriptomeProject[43].TheMonocotTreeofLife Project(MonATOL)generate dfivenon-grassmonocot transcriptomes.Onetranscriptomedatasetfor Lindenbergiaphilippensis (asterid)wasobtainedfromtheParasiticPlantGenomeProject[65].Severalmethodswere usedforESTdataassembly,accordingtothetypeand quantityofdatathatwereavailable.AssembliesinvolvinglargenumbersofSangerreadswereobtainedeither fromthePlantGenomeDatabase[45]orTheInstitute forGenomicResearch(TIGR)PlantTranscriptAssemblies[66].HybridassemblieswithSangerand454data wereperformedwithMIRA.Est.Short-readIllumina datasetswereassembledeitherwith SOAPdenovo (Kmersize=29andasm_flag=2)[67]orwithCLC GenomicsWorkbench(readstrimmedfirst,andusing defaultparametersexceptminimumcontiglengthsetto 200bases).Assembliesforspecieswithdatafrommore thanonesequencingtechnologywerefurtherpostassembledwithCAP3(overlaplengthcutoff=40and overlappercentidentity=98)tomergecontigsthat havesignificantoverlapbutcouldnotbeassembledinto contiguoussequencesbyp rimaryassemblersdueto eitherthepresenceofSNPsintheconsensusorpath ambiguityinthegraph.GeneclassificationandphylogeneticanalysisTheOrthoMCLmethod[50]wasusedtoconstructsets oforthogroups.Aminoacidalignmentsforeach orthogroupweregeneratedwithMUSCLE,andthen trimmedbyremovingpoorlyalignedregionswithtrimAl1.2,usingtheheuristicautomate1option[68].In ordertosortandaligntranscriptomedataintoour eight-genomescaffoldfordownstreamphylogeneticanalyses,wefirstusedESTScan [69]tofindthebestreadingframeforallunigenes.Thebesthitfromablast searchagainsttheinferredproteinsofoureight-genome scaffoldwasthenusedtoassigneachunigenetoan orthogroup.Additionalsortedunigenesequencesforthe orthogroupsofsequencedgenomeswerealignedatthe aminoacidlevelintotheexistingfullalignments(before trimming)ofeightsequencedspeciesusingClustalX1.8 [70].Thentheselargealignmentsweretrimmedagain usingtrimAl1.2withthesamesettings.Eachunigene sequencewascheckedandremovedfromthealignment ifthesequencecontainedlessthan70%ofthetotal alignmentlength.CorrespondingDNAsequenceswere thenforcedontotheaminoacidalignmentsusingcustomPerlscripts,andDNAalignmentswereusedinsubsequentphylogeneticanalysis.Maximumlikelihood analyseswereconductedusingRAxMLversion7.2.1 [71],searchingforthebestmaximumlikelihoodtree withtheGTRGAMMAmodelbyconducting100bootstrapreplicates,whichrepresentsanacceptabletrade-off betweenspeedandaccuracy(RAxML7.0.4manual).Moleculardatinganalysesand95%confidenceintervalsThebestmaximum-likelihoodtopologyforeach orthogroupwasusedtoestimatedivergencetimes.The divergencetimeofthetwoparalogouscladesineach orthogroupwasestimatedundertheassumptionofa relaxedmolecularclockbyapplyingasemi-parametric penalizedlikelihoodapproachusingatruncatedNewton optimizationalgorithmasimplementedintheprogram R8S[53].Thesmoothingparameterwasdeterminedby cross-validation.Weusedthefollowingdatesinour estimationprocedure:minimumageof131mya[72] andmaximumageof309myaforcrown-groupangiosperms[73],andafixedconstraintageof125myafor crown-groupeudicots[56].Werequiredthattreespass boththecross-validationprocedureandprovideestimatesoftheageoftheduplicationnode.Thecollection ofinferreddivergencetimeswasthenanalyzedby EMMIX[54].Foreachsignificantcomponentidentified byEMMIX,the95%confidenceintervalofthemean wasthencalculated.FinitemixturemodelsofgenomeduplicationsToexplorethedivergencepatternsforduplicatedgenes, theinferreddistributionof KsdivergenceswerefittedtoJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page11of14

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amixturemodelcomprisingseveralcomponentdistributionsinvariousproportions.The Ksvalueforeach duplicatedsequencepairwascalculatedusingtheGoldmanandYangmaximumlikelihoodmethodimplementedincodemlwiththeF3X4model[74].TheEMMIX softwarewasusedtofitamixturemodelofmultivariate normalcomponentstoagivendataset.Themixed populationsweremodelledwithonetofourcomponents.TheEMalgorithmwasrepeated100timeswith randomstartingvalues,aswellas10timeswith k -mean startingvalues.Thebestmixturemodelwasidentified usingtheBayesianinformationcriterion.Abbreviations BS:bootstrapvalue;EST:expressedsequencetag; Ks:rateofsynonymous substitutionspersynonymoussite;mya:millionyearsago;WGD:whole genomeduplication. Acknowledgements WethankJoshuaPDerforhelpfulcomments.Thisworkwassupportedin partbyfundsfromtheNSFPlantGenomeResearchProgram(DEB0638595, TheAncestralAngiospermGenomeProjecttoCWD,JL-M,PSS,DES;DEB 0701748,TheParasiticPlantGenomeProjecttoCWD;DEB0922742,The Amborella Genome:AReferenceforPlantBiologytoCWD,JL-M,PSS,DES; IOS0421604,GenomicsofComparativeSeedEvolutiontoDWS,RM),NSF TreeofLifeprogram( MonATOL, DEB0829868,From Acorus to Zingiber AssemblingthePhylogenyoftheMonocotstoDWS,JCP,JL-M,RM,CWD), NationalInstituteonDrugAbuse(NIDA)attheNationalInstitutesofHealth (project5R01DA025197-02toTMK,CWD,JL-M),theAlberta1000Plants Initiative(1000GreenPlantTranscriptomeProject,toGW)byAlberta AdvancedEducationandTechnology,byMuseaVentures,andbyBGIShenzhen),iPLant(toJL-M)andbytheBiologyDepartmentandPlant BiologyGraduateProgramofPennStateUniversity. Authordetails1IntercollegeGraduateDegreePrograminPlantBiology,ThePennsylvania StateUniversity,UniversityPark,PA16802,USA.2DepartmentofBiology, InstituteofMolecularEvolutionaryGenetics,HuckInstitutesoftheLife Sciences,ThePennsylvaniaStateUniversity,UniversityPark,PA16802,USA.3DepartmentofPlantBiology,UniversityofGeorgia,Athens,GA30602,USA.4DepartmentofBiologyandPhysics,KennesawStateUniversity,Kennesaw, GA30144,USA.5DonaldDanforthPlantScienceCenter,975NorthWarson Road,StLouis,MO63132,USA.6DivisionofPlantScienceandConservation, ChicagoBotanicGarden,Glencoe,IL60022,USA.7BeijingGenomicsInstituteShenzhen,BeiShanIndustrialZone,YantianDistrict,Shenzhen518083, China.8TheNovoNordiskFoundationCenterforBasicMetabolicResearch, DepartmentofBiology,UniversityofCopenhagen,StoreKannikestrde11, 1169KbenhavnK,Denmark.9IntercollegeGraduateDegreeProgramin Genetics,ThePennsylvaniaStateUniversity,UniversityPark,PA16802,USA.10DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton, AlbertaT6G2E9,Canada.11FloridaMuseumofNaturalHistory,Universityof Florida,Gainesville,FL32611,USA.12DepartmentofBiology,Universityof Florida,Gainesville,FL32611,USA.13NewYorkBotanicalGarden,Bronx,New York,NY10458,USA.14GenomeResearchCenter,ColdSpringHarbor Laboratory,500SunnysideBlvd,Woodbury,NY11797,USA.15Divisionof BiologicalSciences,UniversityofMissouri,Columbia,MI65211,USA.16DepartmentsofBiologicalSciencesandMedicine,Departmentof BiologicalSciences,UniversityofAlberta,EdmontonAB,T6G2E9,Canada. Authors contributions YJ,JL-MandCWDconceivedofthestudyanditsdesign,andYJperformed allofthefinalanalyses.YJ,JL-M,CWDdraftedtheprimarymanuscriptand additionaltextanddiscussionoftheresearchwasprovidedbyDES,PSS,JEB, NJW,TMK,GW,DWS.Tissuesamples,RNAisolations,librarypreparation sequencingandsampleandsequencemanagementweredonebyMR, MRM,JM,MR,XW,YongZ,JW,ASC,MKD,RMandJCP.Dataassembliesand otheranalysesweredonebyYJ,SA,DRR,EW,andYetingZ.Allauthors contributedtoandapprovedthefinalmanuscriptforpublication. Received:3November2011Accepted:26January2012 Published:26January2012 References1.OhnoS: EvolutionbyGeneDuplication Springer-Verlag;1970. 2.AdamsKL,WendelJF: Polyploidyandgenomeevolutioninplants. Curr OpinPlantBiol 2005, 8 :135-141. 3.AuryJM,JaillonO,DuretL,NoelB,JubinC,PorcelBM,SegurensB, DaubinV,AnthouardV,AiachN,ArnaizO,BillautA,BeissonJ,BlancI, BouhoucheK,CamaraF,DuharcourtS,GuigoR,GogendeauD,KatinkaM, KellerAM,KissmehlR,KlotzC,KollF,LeMouelA,LepereG,MalinskyS, NowackiM,NowakJK,PlattnerH, etal : Globaltrendsofwhole-genome duplicationsrevealedbytheciliate Parameciumtetraurelia Nature 2006, 444 :171-178. 4.KellisM,BirrenBW,LanderES: Proofandevolutionaryanalysisofancient genomeduplicationintheyeast Saccharomycescerevisiae Nature 2004, 428 :617-624. 5.JiaoY,WickettNJ,AyyampalayamS,ChanderbaliAS,LandherrL,RalphPE, TomshoLP,HuY,LiangH,SoltisPS,SoltisDE,CliftonSW,SchlarbaumSE, SchusterSC,MaH,Leebens-MackJ,dePamphilisCW: Ancestralpolyploidy inseedplantsandangiosperms. Nature 2011, 473 :97-100. 6.BlancG,HokampK,WolfeKH: Arecentpolyploidysuperimposedon olderlarge-scaleduplicationsinthe Arabidopsis genome. GenomeRes 2003, 13 :137-144. 7.MingR,HouS,FengY,YuQ,Dionne-LaporteA,SawJH,SeninP,WangW, LyBV,LewisKL,SalzbergSL,FengL,JonesMR,SkeltonRL,MurrayJE, ChenC,QianW,ShenJ,DuP,EusticeM,TongE,TangH,LyonsE,PaullRE, MichaelTP,WallK,RiceDW,AlbertH,WangML,ZhuYJ, etal : Thedraft genomeofthetransgenictropicalfruittreepapaya( Caricapapaya Linnaeus). Nature 2008, 452 :991-996. 8.VisionTJ,BrownDG,TanksleySD: Theoriginsofgenomicduplicationsin Arabidopsis Science 2000, 290 :2114-2117. 9.BowersJE,ChapmanBA,RongJ,PatersonAH: Unravellingangiosperm genomeevolutionbyphylogeneticanalysisofchromosomalduplication events. Nature 2003, 422 :433-438. 10.FawcettJA,MaereS,VandePeerY: Plantswithdoublegenomesmight havehadabetterchancetosurvivetheCretaceous-Tertiaryextinction event. ProcNatlAcadSciUSA 2009, 106 :5737-5742. 11.TangH,WangX,BowersJE,MingR,AlamM,PatersonAH: Unraveling ancienthexaploidythroughmultiply-alignedangiospermgenemaps. GenomeRes 2008, 18 :1944-1954. 12.TangH,BowersJE,WangX,MingR,AlamM,PatersonAH: Syntenyand collinearityinplantgenomes. Science 2008, 320 :486-488. 13.VandePeerY: Amysteryunveiled. GenomeBiol 2011, 12 :113. 14. Soltis DE,AlbertVA,Leebens-MackJ,BellCD,PatersonAH,ZhengC, SankoffD,DepamphilisCW,WallPK,SoltisPS: Polyploidyandangiosperm diversification. AmJBot 2009, 96 :336-348. 15.WangX,WangH,WangJ,SunR,WuJ,LiuS,BaiY,MunJH,BancroftI, ChengF,HuangS,LiX,HuaW,FreelingM,PiresJC,PatersonAH, ChalhoubB,WangB,HaywardA,SharpeAG,ParkBS,WeisshaarB,LiuB, LiB,TongC,SongC,DuranC,PengC,GengC,KohC, etal : Thegenome ofthemesopolyploidcropspecies Brassicarapa NatGenet 2011, 43 :1035-1039. 16.SchranzME,Mitchell-OldsT: Independentancientpolyploidyeventsin thesisterfamiliesBrassicaceaeandCleomaceae. PlantCell 2006, 18 :1152-1165. 17.DehalP,BooreJL: Tworoundsofwholegenomeduplicationinthe ancestralvertebrate. PLoSBiol 2005, 3 :e314. 18.ChristoffelsA,KohEG,ChiaJM,BrennerS,AparicioS,VenkateshB: Fugu genomeanalysisprovidesevidenceforawhole-genomeduplication earlyduringtheevolutionofray-finnedfishes. MolBiolEvol 2004, 21 :1146-1151. 19.JaillonO,AuryJM,BrunetF,PetitJL,Stange-ThomannN,MauceliE, BouneauL,FischerC,Ozouf-CostazC,BernotA,NicaudS,JaffeD,FisherS, LutfallaG,DossatC,SegurensB,DasilvaC,SalanoubatM,LevyM,BoudetN, CastellanoS,AnthouardV,JubinC,CastelliV,KatinkaM,VacherieB, BiemontC,SkalliZ,CattolicoL,PoulainJ, etal : GenomeduplicationintheJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page12of14

PAGE 13

teleostfish Tetraodonnigroviridis revealstheearlyvertebrateprotokaryotype. Nature 2004, 431 :946-957. 20.CuiL,WallPK,Leebens-MackJH,LindsayBG,SoltisDE,DoyleJJ,SoltisPS, CarlsonJE,ArumuganathanK,BarakatA,AlbertVA,MaH,dePamphilisCW: Widespreadgenomeduplicationsthroughoutthehistoryofflowering plants. GenomeRes 2006, 16 :738-749. 21.DuarteJM,CuiL,WallPK,ZhangQ,ZhangX,Leebens-MackJ,MaH, AltmanN,dePamphilisCW: Expressionpatternshiftsfollowing duplicationindicativeofsubfunctionalizationandneofunctionalization inregulatorygenesof Arabidopsis MolBiolEvol 2006, 23 :469-478. 22.JohnsonDA,ThomasMA: Themonosaccharidetransportergenefamilyin Arabidopsis andrice:ahistoryofduplications,adaptiveevolution,and functionaldivergence. MolBiolEvol 2007, 24 :2412-2423. 23.ConradB,AntonarakisSE: Geneduplication:adriveforphenotypic diversityandcauseofhumandisease. AnnuRevGenomicsHumGenet 2007, 8 :17-35. 24.MeyerA,VandePeerY: From2Rto3R:evidenceforafish-specific genomeduplication(FSGD). Bioessays 2005, 27 :937-945. 25.DeBodtS,MaereS,VandePeerY: Genomeduplicationandtheoriginof angiosperms. TrendsEcolEvol 2005, 20 :591-597. 26.LynchM,ForceAG: Theoriginofinterspecificgenomicincompatibility viageneduplication. AmNat 2000, 156 :590-605. 27.WolfeKH,ScannellDR,ByrneKP,GordonJL,WongS: Multipleroundsof speciationassociatedwithreciprocalgenelossinpolyploidyeasts. Nature 2006, 440 :341-345. 28.TaylorJS,VandePeerY,MeyerA: Genomeduplication,divergent resolutionandspeciation. TrendsGenet 2001, 17 :299-301. 29.WerthCR,WindhamMD: Amodelfordivergent,allopatricspeciationof polyploidpteridophytesresultingfromsilencingofduplicate-gene expression. AmNat 1991, 137 :515-526. 30.BarkerMS,VogelH,SchranzME: PaleopolyploidyintheBrassicales: analysesofthe Cleome transcriptomeelucidatethehistoryofgenome duplicationsin Arabidopsis andotherBrassicales. GenomeBiolEvol 2009, 5 :391-399. 31.MayroseI,ZhanSH,RothfelsCJ,Magnuson-FordK,BarkerMS,RiesebergLH, OttoSP: Recentlyformedpolyploidplantsdiversifyatlowerrates. Science 2011, 333 :1257. 32. Jaillon O,AuryJM,NoelB,PolicritiA,ClepetC,CasagrandeA,ChoisneN, AubourgS,VituloN,JubinC,VezziA,LegeaiF,HugueneyP,DasilvaC, HornerD,MicaE,JublotD,PoulainJ,BruyereC,BillaultA,SegurensB, GouyvenouxM,UgarteE,CattonaroF,AnthouardV,VicoV,DelFabbroC, AlauxM,DiGasperoG,DumasV, etal : Thegrapevinegenomesequence suggestsancestralhexaploidizationinmajorangiospermphyla. Nature 2007, 449 :463-467. 33.DvorakJ,LuoMC,YangZL,ZhangHB: ThestructureoftheAegilops tauschiigenepoolandtheevolutionofhexaploidwheat. TheorAppl Genet 1998, 97 :657-670. 34.LyonsE,PedersenB,KaneJ,FreelingM: Thevalueofnonmodelgenomes andanexpampleusingsynmapwithinCoGetodissectthehexaploidy thatpredatestherosids. TropicalPlantBiol 2008, 1 :181-190. 35.XuX,PanS,ChengS,ZhangB,MuD,NiP,ZhangG,YangS,LiR,WangJ, OrjedaG,GuzmanF,TorresM,LozanoR,PonceO,MartinezD,Dela CruzG,ChakrabartiSK,PatilVU,SkryabinKG,KuznetsovBB,RavinNV, KolganovaTV,BeletskyAV,MardanovAV,DiGenovaA,BolserDM, MartinDM,LiG,YangY, etal : Genomesequenceandanalysisofthe tubercroppotato. Nature 2011, 475 :189-195. 36.ZuccoloA,BowersJE,EstillJC,XiongZ,LuoM,SebastianA,GoicoecheaJL, ColluraK,YuY,JiaoY,DuarteJ,TangH,AyyampalayamS,RounsleyS, KudmaD,PatersonAH,PiresJC,ChanderbaliA,SoltisDE,ChamalaS, BarbazukB,SoltisPS,AlbertVA,MaH,MandoliD,BanksJ,CarlsonJE, TomkinsJ,DepamphilisCW,WingRA, etal : Aphysicalmapforthe Amborellatrichopoda genomeshedslightontheevolutionof angiospermgenomestructure. GenomeBiol 2011, 12 :R48. 37.Leebens-MackJ,RaubesonLA,CuiL,KuehlJV,FourcadeMH,ChumleyTW, BooreJL,JansenRK,depamphilisCW: Identifyingthebasalangiosperm nodeinchloroplastgenomephylogenies:samplingone swayoutof theFelsensteinzone. MolBiolEvol 2005, 22 :1948-1963. 38.FelsensteinJ: Casesinwhichparsimonyorcompatibilitymethodswillbe positivelymisleading. SystZool 1978, 27 :401-410. 39.HendyMD,PennyD: Aframeworkforthequantitativestudyof evolutionarytrees. SystZool 1989, 38 :297-309. 40.ChildsKL,HamiltonJP,ZhuW,LyE,CheungF,WuH,RabinowiczPD, TownCD,BuellCR,ChanAP: TheTIGRplanttranscriptassemblies database. NucleicAcidsRes 2007, 35 :D846-851. 41.ShumwayM,CochraneG,SugawaraH: Archivingnextgeneration sequencingdata. NucleicAcidsRes 2010, 38 :D870-871. 42. MonocotTreeofLifeProject.. [http://www.botany.wisc.edu/givnish/ monocotatol.htm]. 43. 1000GreenPlantTranscriptomeProject.. [http://www.onekp.com]. 44. AncestralAngiospermGenomeProject.. [http://ancangio.uga.edu]. 45. PlantGDB.. [http://www.plantgdb.org/]. 46.ZahnLM,KongH,Leebens-MackJH,KimS,SoltisPS,LandherrLL,SoltisDE, Depamphilis CW, MaH: Theevolutionofthe SEPALLATA subfamilyof MADS-boxgenes:apreangiospermoriginwithmultipleduplications throughoutangiospermhistory. Genetics 2005, 169 :2209-2223. 47.ChapmanBA,BowersJE,FeltusFA,PatersonAH: Bufferingofcrucial functionsbypaleologousduplicatedgenesmaycontributecyclicalityto angiospermgenomeduplication. ProcNatlAcadSciUSA 2006, 103 :2730-2735. 48.WangH,MooreMJ,SoltisPS,BellCD,BrockingtonSF,AlexandreR, DavisCC,LatvisM,ManchesterSR,SoltisDE: Rosidradiationandtherapid riseofangiosperm-dominatedforests. ProcNatlAcadSciUSA 2009, 106 :3853-3858. 49.SoltisDE,SmithSA,CellineseN,WurdackKJ,TankDC,BrockingtonSF, Refulio-RodriguezNF,WalkerJB,MooreMJ,CarlswardBS,BellCD,LatvisM, CrawleyS,BlackC,DioufD,XiZ,RushworthCA,GitzendannerMA, SytsmaKJ,QiuYL,HiluKW,DavisCC,SandersonMJ,BeamanRS, OlmsteadRG,JuddWS,DonoghueMJ,SoltisPS: Angiospermphylogeny: 17genes,640taxa. AmJBot 2011, 98 :704-730. 50.LiL,StoeckertCJJr,RoosDS: OrthoMCL:identificationoforthologgroups foreukaryoticgenomes. GenomeRes 2003, 13 :2178-2189. 51.KuhlJC,CheungF,YuanQP,MartinW,ZewdieY,McCallumJ,CatanachA, RutherfordP,SinkKC,JenderekM,PrinceJP,TownCD,HaveyMJ: Aunique setof11,008onionexpressedsequencetagsrevealsexpressed sequenceandgenomicdifferencesbetweenthemonocotorders Asparagales and Poales PlantCell 2004, 16 :114-125. 52.KuhlJC,HaveyMJ,MartinWJ,CheungF,YuanQP,LandherrL,HuY, Leebens-MackJ,TownCD,SinkKC: Comparativegenomicanalysesin Asparagus Genome 2005, 48 :1052-1060. 53.SandersonMJ: r8s:inferringabsoluteratesofmolecularevolutionand divergencetimesintheabsenceofamolecularclock. Bioinformatics 2003, 19 :301-302. 54.McLachlanGJ,PeelD,BasfordKE,AdamsP: TheEmmixsoftwareforthe fittingofmixturesofnormalandt-components. JStatSoftw 1999, 4 :i02. 55.MorrisonDA: Howtosummarizeestimatesofancestraldivergencetimes. EvolBioinformOnline 2008, 4 :75-95. 56.DoyleJA,HottonCL: PollenandSpores.PatternsofDiversification Oxford: Clarendon;1991. 57.AmericanSocietyofPlantBiologists: SymposiumII:Polyploidy,Heterosis, andGenomicPlasticity. [http://abstracts.aspb.org/pb2010/public/S02/S022. html]. 58.SoltisDE,SoltisPS,EndressPK,ChaseMW: PhylogenyandEvolutionof Angiosperms Sunderland,MA:SinauerAssociates;2005. 59.LittA,IrishVF: Duplicationanddiversificationinthe APETALA1/FRUITFULL floralhomeoticgenelineage:Implicationsfortheevolutionoffloral development. Genetics 2003, 165 :821-833. 60. Kramer EM,ZimmerEA: Geneduplicationandfloraldevelopmental geneticsofbasaleudicots. AdvBotRes 2006, 44 :353-384. 61.SoltisPS,BrockingtonSF,YooMJ,PiedrahitaA,LatvisM,MooreMJ, ChanderbaliAS,SoltisDE: Floralvariationandfloralgeneticsinbasal angiosperms. AmJBot 2009, 96 :110-128. 62.ChanderbaliAS,YooMJ,ZahnLM,BrockingtonSF,WallPK, GitzendannerMA,AlbertVA,Leebens-MackJ,AltmanNS,MaH, DepamphilisCW,SoltisDE,SoltisPS: Conservationandcanalizationof geneexpressionduringangiospermdiversificationaccompanythe originandevolutionoftheflower. ProcNatlAcadSciUSA 2010, 107 :22570-22575. 63.TuskanGA,DiFazioS,JanssonS,BohlmannJ,GrigorievI,HellstenU, PutnamN,RalphS,RombautsS,SalamovA,ScheinJ,SterckL,AertsA, BhaleraoRR,BhaleraoRP,BlaudezD,BoerjanW,BrunA,BrunnerA,BusovV, CampbellM,CarlsonJ,ChalotM,ChapmanJ,ChenGL,CooperD, CoutinhoPM,CouturierJ,CovertS,CronkQ, etal : ThegenomeofblackJiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page13of14

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cottonwood, Populustrichocarpa (Torr.&Gray). Science 2006, 313 :1596-1604. 64.FoltaKM,ShulaevV,SargentDJ,CrowhurstRN,MocklerTC,FolkertsO, DelcherAL,JaiswalP,MockaitisK,ListonA,ManeSP,BurnsP,DavisTM, SlovinJP,BassilN,HellensRP,EvansC,HarkinsT,KodiraC,DesanyB, CrastaOR,JensenRV,AllanAC,MichaelTP,SetubalJC,CeltonJM, ReesDJG,WilliamsKP,HoltSH,RojasJJR, etal : Thegenomeofwoodland strawberry( Fragariavesca ). NatGenet 2011, 43 :109-U151. 65. ParasiticPlantGenomeProject.. [http://ppgp.huck.psu.edu]. 66. TIGRPlantTranscriptAssembliesdatabase.. [http://plantta.jcvi.org]. 67.LiR,ZhuH,RuanJ,QianW,FangX,ShiZ,LiY,LiS,ShanG,KristiansenK, YangH,WangJ: Denovoassemblyofhumangenomeswithmassively parallelshortreadsequencing. GenomeRes 2010, 20 :265-272. 68.Capella-GutierrezS,Silla-MartinezJM,GabaldonT: trimAl:atoolfor automatedalignmenttrimminginlarge-scalephylogeneticanalyses. Bioinformatics 2009, 25 :1972-1973. 69.IseliC,JongeneelCV,BucherP: ESTScan:aprogramfordetecting, evaluating,andreconstructingpotentialcodingregionsinEST sequences. ProcIntConfIntellSystMolBiol 1999,138-148. 70.ThompsonJD,GibsonTJ,HigginsDG: Multiplesequencealignmentusing ClustalWandClustalX. CurrProtocBioinformatics 2002, Chapter2 :Unit2.3. 71.StamatakisA: RAxML-VI-HPC:maximumlikelihood-basedphylogenetic analyseswiththousandsoftaxaandmixedmodels. Bioinformatics 2006, 22 :2688-2690. 72.HughesNF,McdougallAB: Recordsofangiospermidpollenentryintothe EnglishEarlyCretaceoussuccession. RevPalaeobotPalynol 1987, 50 :255-272. 73.MillerCN: Implicationsoffossilconifersforthephylogenetic relationshipsoflivingfamilies. BotRev 1999, 65 :239-277. 74.YangZH: PAML:aprogrampackageforphylogeneticanalysisby maximumlikelihood. ComputApplBiosci 1997, 13 :555-556.doi:10.1186/gb-2012-13-1-r3 Citethisarticleas: Jiao etal .: Agenometriplicationassociatedwith earlydiversificationofthecoreeudicots. GenomeBiology 2012 13 :R3. Submit your next manuscript to BioMed Central and take full advantage of: Convenient online submission Thorough peer review No space constraints or color gure charges Immediate publication on acceptance Inclusion in PubMed, CAS, Scopus and Google Scholar Research which is freely available for redistribution Submit your manuscript at www.biomedcentral.com/submit Jiao etal GenomeBiology 2012, 13 :R3 http://genomebiology.com/2012/13/1/R3 Page14of14