Database

Floral gene resources from basal angiosperms for comparative genomics research

Victor A Albert¹ , Douglas E Soltis² , John E Carlson³ , William G Farmerie⁴ , P Kerr Wall⁵ , Daniel C Ilut⁶ , Teri M Solow⁶ , Lukas A Mueller⁶ , Lena L Landherr⁵ , Yi Hu⁵ , Matyas Buzgo² , Sangtae Kim² , Mi-Jeong Yoo² , Michael W Frohlich⁷ , Rafael Perl-Treves⁸ , Scott E Schlarbaum⁹ , Barbara J Bliss⁵ , Xiaohong Zhang⁵ , Steven D Tanksley⁶ , David G Oppenheimer² , Pamela S Soltis¹⁰ , Hong Ma⁵ , Claude W dePamphilis⁵ and James H Leebens-Mack⁵

¹Natural History Museum, University of Oslo, NO-0318 Oslo, Norway

²Department of Botany, University of Florida, Gainesville, FL 32611, USA

³School of Forest Resources, The Pennsylvania State University, University Park, PA 16802, USA

⁴Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA

⁵Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

⁶Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA

⁷Department of Botany, Natural History Museum, London SW7 5BD, United Kingdom

⁸Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel

⁹Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN 37996, USA

¹⁰Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA

author email corresponding author email

BMC Plant Biology 2005, 5:5doi:10.1186/1471-2229-5-5

Published:	30 March 2005

Abstract

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.

Conclusion

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.