Floral gene resources from basal angiosperms for comparative genomics research.
BACKGROUND
The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants.


RESULTS
Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms.


CONCLUSIONS
Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.
Albert
Victor A
VA
Natural History Museum, University of Oslo, NO-0318 Oslo, Norway. victor.albert@nhm.uio.no <victor.albert@nhm.uio.no>
Soltis
Douglas E
DE
Carlson
John E
JE
Farmerie
William G
WG
Wall
P Kerr
PK
Ilut
Daniel C
DC
Solow
Teri M
TM
Mueller
Lukas A
LA
Landherr
Lena L
LL
Hu
Yi
Y
Buzgo
Matyas
M
Kim
Sangtae
S
Yoo
Mi-Jeong
MJ
Frohlich
Michael W
MW
Perl-Treves
Rafael
R
Schlarbaum
Scott E
SE
Bliss
Barbara J
BJ
Zhang
Xiaohong
X
Tanksley
Steven D
SD
Oppenheimer
David G
DG
Soltis
Pamela S
PS
Ma
Hong
H
DePamphilis
Claude W
CW
Leebens-Mack
James H
JH
D044822:Biodiversity; D019295:Computational Biology; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020407:Internet; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
D018076:DNA, Complementary