Exploring the Plant Transcriptome through Phylogenetic Profiling  

Abstract

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species-and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

“…The second taxonomic group with large average gene family sizes is the group of the Viridiplantae containing Arabidopsis and rice, both having a history of genome duplications and family expansions as discussed in detail previously (41,42). Next in line are the Metazoa, then the oomycetes (i.e., the Phytophthora spp.…”

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

“…Plant transcription factors can be studied using PlnTFDB (RianoPachon et al, 2007), AGRIS (Palaniswamy et al, 2006), and GRASSIUS (Yilmaz et al, 2009). The complementary platforms Phytome (Hartmann et al, 2006) and SPPG (Vandepoele and Van de Peer, 2005) are hybrid systems integrating gene information from genome sequencing projects with EST data for a comprehensive set of plant species.…”

“…Whereas large-scale cDNA sequencing projects have generated detailed information about gene catalogs expressed in different tissues or during specific developmental stages (Rudd, 2003), the application of genome sequencing combined with highthroughput expression profiling has revealed the existence of thousands of unknown expressed genes conserved within the green plant lineage (Gutierrez et al, 2004;Vandepoele and Van de Peer, 2005). The generation of high-quality complete genome sequences for the model species Arabidopsis thaliana and rice (Oryza sativa) required large international consortia and took several years before completion (Arabidopsis Genome Initiative, 2000;International Rice Genome Sequencing Project, 2005).…”

A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study

“…Comparative biology in which cross-species approaches are used to investigate conservation and diversity in a phylogenetic context also include the comparison of genomewide transcript expression patterns (Bergmann et al, 2004;Rensink et al, 2005;Schranz et al, 2007;Tirosh et al, 2007;Andersen et al, 2008;Vandenbroucke et al, 2008;Schreiber et al, 2009;Parikh et al, 2010). Multispecies global gene expression analysis (phylotranscriptomics) aims to use the evolutionary distance between organisms to its advantage (Vandepoele and Van de Peer, 2005;Kohonen et al, 2007;Fierro et al, 2008;Hashimshony and Yanai, 2010). Cross-species phylotranscriptomics of distinct developmental processes such as pollen or seed development, maturation, and germination require validated cross-species reference genes for normalization of comparative qRT-PCR experiments.…”