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Abstract

BackgroundThe 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.ResultsRandom 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.ConclusionInitial 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.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

“…The E-value cut-offs for inferring sequence similarity vary from 1e-3 [17,24] to 1e-50 [64,65], but 1e-10 to 1e-30 have been widely used [19,32,43,66-69]. To ensure high confidence as previously suggested [64] and to increase the likelihood of inferring biological significance, we used the following thresholds of E-values: (a) E = 0, the two sequences are identical and considered to derive from the same gene; (b) 1e-50 ≤ E < 0, the two sequences are highly similar and likely to be from the same gene family; (c) 1e-5 ≤ E < 1e-50, the two sequences are similar in one or more regions along the whole sequence and likely to contain the same functional domain(s) or motif(s); (d) E < 1e-5, the two sequences are likely to be unrelated genes.…”

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

“…The plastid genome tree provides an improved framework for comparative genomics in angiosperms and emphasizes the importance of including representatives from all of these clades. Current genomic sequencing projects only include representatives of the two most derived sister lineages, monocots and eudicots, but cDNA sequences for basal angiosperms are growing rapidly (31). An organismal context is essential for interpretation of nuclear gene phylogenies and the complex gene duplication history that they often imply.…”

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

“…Until recently, such data were available only for major model species such as A. thaliana and rice, and for several species of basal angiosperms [14]. We report characterization of genes expressed in the flower and inflorescence of two species of buckwheat, the common buckwheat F. esculentum and F. tataricum .…”