Group Title: Genome biology
Title: The Amborella genome: an evolutionary reference for plant biology
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Title: The Amborella genome: an evolutionary reference for plant biology
Physical Description: Book
Language: English
Creator: Soltis, Douglas
Albert, Victor
Leebens-Mack, Jim
Palmer, Jeffrey
Wing, Rod
dePamphilis, Claude
Ma, Hong
Carlson, John
Altman, Naomi
Kim, Sangtae
Wall, P. K.
Zuccolo, Andrea
Soltis, Pamela
Publisher: Genome Biology
Publication Date: 2008
 Notes
Abstract: The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
General Note: Periodical Abbreviation:Genome Biol.
General Note: Start page 402
General Note: M3: 10.1186/gb-2008-9-3-402
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Bibliographic ID: UF00099977
Volume ID: VID00001
Source Institution: University of Florida
Holding Location: University of Florida
Rights Management: Open Access: http://www.biomedcentral.com/info/about/openaccess/
Resource Identifier: issn - 1465-6906
http://genomebiology.com/2008/9/3/402

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Correspondence

The Amborella genome: an evolutionary reference for plant biology
Douglas E Soltis1, Victor A Albert2,3, Jim Leebens-Mack4,

Jeffrey D Palmer5, Rod A Wing6, Claude W dePamphilis7, Hong Ma7,

John E Carlson8, Naomi Altman9, Sangtae Kim1o, P Kerr Wall7,

Andrea Zuccolo6 and Pamela S Soltis11

Addresses: 'Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA. 2Joint Centre for
Bioinformatics in Oslo, University of Oslo and Rikshospitalet HF, Blindern, NO-0316 Oslo, Norway. 3Department of Biological Sciences,
University at Buffalo (SUNY), Buffalo, NY 14260-1300, USA. 4Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
5Department of Biology, Indiana University, Bloomington, IN 47405, USA. 6Department of Plant Sciences, University of Arizona, Tucson, AZ
85721, USA. 7Department of Biology, the Huck Institutes of the Life Sciences, and the Institute of Molecular Evolutionary Genetics,
Pennsylvania State University, University Park, PA 16802, USA. 8School of Forest Resources, Pennsylvania State University, University
Park, PA 16802, USA. 9Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA. loNational Institute of
Biological Resources, Incheon 404-170, Korea. "Florida Museum of Natural History and the Genetics Institute, University of Florida,
Gainesville, FL 32611, USA.

Correspondence: Pamela S Soltis. Email: psoltis@flmnh.ufl.edu


Published: 10 March 2008
Genome Biology 2008, 9:402 (doi: 10.1 186/gb-2008-9-3-402)
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2008/9/3/402
2008 BioMed Central Ltd



Abstract
The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant
angiosperms, will be an exceptional resource for plant genomics.


The origin and evolution of the angio-
sperms is one of the great terrestrial
radiations and has had manifold effects
on the global biota. Today, flowering
plants generate the vast majority of
human food, either directly or indirectly
as animal feed, and account for a huge
proportion of land-based photosyn-
thesis and carbon sequestration. With a
fossil record that extends back to just
over 130 million years ago, flowering
plants have diversified to include
250,000 to possibly 400,000 species
occupying nearly every habitable terres-
trial environment, and many aquatic
ones. Understanding how angiosperms
have accomplished this feat over a
relatively short span of evolutionary
time will elucidate many of the key
processes underlying the assembly of


Earth's plant/animal associations and
entire ecosystems.

Many scientists have understood the
importance of broad, comparative
genome sequencing since the beginning
of the Arabidopsis thaliana and rice
(Oryyza sativa) genome sequencing
projects [1-4]. Arabidopsis, a relative of
cabbage, had already become the
premier model for plant genetics, and
half the world's dependence on rice for
food makes that crop plant an impor-
tant model for the genetic architecture
of traits important to humanity. More
recently, poplar (Populus trichocarpa),
grapevine (Vitis vinifera) and papaya
(Carica papaya) have been sequenced
as genomic models for woody crop
plants [5-12]. These advances have been


motivated by the realization that
understanding the structure and
evolution of plant genomes would
contribute to society through enhance-
ments to agriculture and forestry [13].

However, the few angiosperm nuclear
genomes that have been sequenced so
far reside on just two limbs within the
angiosperm branch of the Tree of Life
[14,15] and, therefore, aid us little in
understanding the characteristics of the
last common ancestor of all angio-
sperms (Figure i). Many key angiosperm
innovations, such as the origin of the
flower and fruit, diverse pollination
systems and double fertilization, large
water-conducting vessel elements,
diverse biochemical pathways, and
many of the specific genes that regulate


Genome Biology 2008, 9:402







Genome Biolog& 2008, Volume 9, Issue 3, Article 402 Soltis et al. 402.2


Figure I
The position of Amborella in the angiosperm phylogenetic tree. Taxa for which whole-genome sequences have been published are indicated in
parentheses. The node highlighted by a star on the tree identifies the 'ancestral angiosperm', or most recent common ancestor of all living angiosperms.
An Amborella genome sequence will allow the ancestral genes and genomic features of living angiosperms to be identified and will provide the essential
root for angiosperm comparative genomics. Based on [14,15].


key growth and developmental proces-
ses, appeared first among the basal angio-
sperm lineages [16-20]. A thorough
understanding of processes that shape
genes and genomic features, and of the
many similarities and differences between
model monocots (for example, Oryza)
and eudicots (for example, Arabidopsis),
requires a perspective based on evo-
lutionary lineages. Such perspectives
can be obtained only through analysis
of an appropriately broad sampling of
genomes, including lineages branching
from the most basal node on the
angiosperm tree [21]. But which basal
angiosperm(s) should be given the
highest priority for sequencing in the
near future?


Recent phylogenetic analyses [14,15,17,
22] have identified Amborella tricho-
poda, a large shrub known only from
the island of New Caledonia, as the
single 'sister species' to all other living
flowering plants. Amborella therefore
offers the unparalleled potential to
'root' analyses of all angiosperm
features, from gene families to genome
structure, and from physiology to mor-
phology. Furthermore, as the branch-
ing-point for Amborella is situated
'between' gymnosperms and all other
angiosperms, a genome sequence for
Amborella would help characterize
processes that distinguish these two
lineages of extant seed plants. The
nuclear genome sequence of Amborella


would contribute uniquely to efforts to
reconstruct characteristics of the
'ancestral angiosperm'. The importance
of Amborella in this regard is already
widely appreciated [19,23]. Two recent
papers, in fact, point specifically to
basal angiosperms, including Amborella,
as obvious choices for future nuclear
genome sequencing efforts [24,25].

The genome structure of the ancestral
angiosperm is currently much debated:
did a whole-genome duplication pre-
date or coincide with the origin of angio-
sperms (perhaps catalyzing innovation)
or did the whole-genome duplication
reported for several lineages of basal
angiosperms [26] occur after the


Genome Biology 2008, 9-402


B


Angiosperms

Eudicots
(for example, Arabidopsis, Populus,
Vitis, Carica)




SCeratophyllum

<_ Monocots
(for example, Oryza, Zea)


SMagnoliids

Chloranthaceae

Austrobaileyales

Nymphaeales
Amborella --
Gymnosperms -1


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Volume 9, Issue 3, Article 402 Soltis et al. 402.3


Arabidopsis


Oryza
1 ,


Segment


1'


Loss


Inversi


Gene gain in'
monocot-eudicot
lineage or loss in Amborella


Rgure 2
Sequencing the nuclear genome for Amborella will root comparisons of monocot and eudicot genome sequences. (a,b) Sequence-based comparisons of
the Amborella sequence (highlighted in yellow) with (a) Arabidopsis and (b) rice (Oryza) sequences for homologous genome segments (I, I', 2 and 2')
identify homologous genomic regions and genes (shown by colored arrows) that have undergone duplications and presumed gene loss in different
segments. (c) From such comparisons investigators can identify the timings of segmental duplications and inversions, gene gains and losses, and whole-
genome duplications (WGDs) in these three lineages. The large black circle indicates the monocot-eudicot split. The Amborella sequence resolves the
timing of an inversion and a tandem duplication (versus loss of a duplicate) that distinguish homologous Arabidopsis and rice segments. Taken together,
the map comparisons imply that the orientation of the green, blue and red genes in the Amborella sequence matches that in the common ancestor of
monocots and eudicots. We can also infer that the purple gene was present in the common ancestor of monocots and eudicots. However, the
homologous region would have to be sequenced in a gymnosperm to determine whether this gene was gained on the lineage leading to monocots and
eudicots, or was present in the common ancestor of eudicots, monocots and Amborella and lost in the lineage leading to Amborella.


Genome Biology 2008, 9:402


Arabidopsis


Oryza

1 1'


B


Amborella\


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Genome Biolog 2008,


Segment







Genome Biology 2008, Volume 9, Issue 3, Article 402 Soltis et al 402.4


Arabidopsis Chromosome 5








Arabidopsis Chromosome 3


Poplar LG_VIII








Poplar LG_V


Grapevine Chromosome 1 region 1









Grapevine Chromosome 1 region 2


Rice Chromosome 10


Rice Chromosome 4


HI


Rgure 3
Synteny of the Amborella genome with other plant genomes. Illustrated here is a physical map of a 0.65 Mb region of the Amborella nuclear genome
(highlighted in yellow) showing synteny with segments in each of the Arabidopsis, poplar, grapevine, and rice genomes. Two homologous segments are
shown in each case: one above and one below the Amborella map. The physical map is based on high information content fingerprinting of an Amborella
BAC library. Synteny was inferred over 5 Mb tracts of sequenced genomes on the basis of BAC-end sequences matching the reference genomes with
TBLASTX bit scores of greater than 80. Red and green ovals depict BAC-end Amborella sequences with significant hits to known transposable elements
and protein-coding genes, respectively.


Genome Biolog 2008, 9-402


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http://genomebiology.com/2008/9/3/402



divergence of Amborella? Was the
common ancestor of Vitis, Populus, and
Arabidopsis an ancient hexaploid that
arose after the monocot-eudicot split?
Did a separate genome-wide duplica-
tion occur early in monocot evolu-
tionary history [8,11]? The answers to
these questions are crucial for under-
standing angiosperm genome evolution
and the diversification of flowering
plants themselves. The Amborella
Genome Project will address funda-
mental questions relating to the early
evolution of gene content and genome
structure in angiosperms (Figure 2),
while providing comprehensive genomic
resources for researchers studying all
aspects of angiosperm biology [27].

In addition, two features of Amborella's
truly extraordinary mitochondrial gen-
ome raise compelling questions that
warrant the sequencing of the
Amborella nuclear genome. First, the
Amborella mitochondrial genome is
extraordinarily rich in 'foreign' genes
acquired by horizontal gene transfer,
far richer than any other plant
mitochondrial genome [28]. These
foreign genes were acquired from a
wide range of donors. These findings
raise important questions that can best
be addressed with a complete nuclear
genome sequence. For instance, is the
Amborella nuclear genome also
exceptionally rich in foreign sequences,
and were these sequences acquired
from the same donors as the foreign
mitochondrial sequences? The
Amborella nuclear genome sequence
will enable subsequent experiments to
determine what roles, if any, foreign
nuclear genes play in Amborella.
Second, the Amborella mitochondrial
genome is exceptionally large, and
much of the extra DNA is of unknown
origin (Rice DW, Richardson AO,
Young GJ, Sanchez-Puerta MV, Zhang
Y, CWD, Knox EB, Munzinger J, Boore
J, JDP, unpublished observations). We
suspect that much of this unknown
DNA was probably acquired from
Amborella's nuclear genome, a
hypothesis that can only be tested once
a complete nuclear sequence is
available.


Genome Biology 2008, Volume 9, Issue 3, Article 402 Soltis et al. 402.5


Ongoing deep transcriptome sequen-
cing and physical mapping [26,29,30]
form the foundation for this important
project. Amborella cDNA sequences
have already rooted gene trees and illu-
minated the timing of gene diver-
sification relative to the origin of the
angiosperms for many gene families
([31-34] and Duarte JR, Wall PK,
Barakat A, Zhang J, Cui L, Landherr LL,
Leebens-Mack J, Ma H, CWD, Kim S, et
al., unpublished observations), and the
potential for further evolutionary
orientation of other gene families is
great. The generation and analysis of a
bacterial artificial chromosomes (BAC)
fingerprint/end sequence physical map
of the relatively small, 870 Mb
Amborella genome [26] is already
yielding new and exciting information
about the genome structure of the
earliest angiosperms and the retention of
some syntenic blocks throughout angio-
sperm history (Figure 3). The physical
map will also serve as a framework for
assembling the sequence of the
Amborella genome.

Given the available genomic infra-
structure, the importance of Amborella
as the sister to all other extant
angiosperms, the large community of
plant biologists who require a universal
evolutionary reference for their studies,
and the availability of cost-effective,
ultra-high-throughput DNA sequencing
technologies, it is our opinion that the
Amborella genome is in an extremely
strong position to warrant complete
sequencing in the near future. Thus, the
stage is set for a large-scale inter-
national Amborella genome sequencing
initiative in support of fundamental and
applied plant sciences, and we enthu-
siastically advocate such an endeavor.


Acknowledgements
This work was supported in part by NSF grant
PGR-0638595, DBI-207202 and NIH grant ROI-
GM-70612.


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