Assaying gene content in Arabidopsis.
Arabidopsis has been popular as a model plant system for decades. Completion of the Arabidopsis genome and the availability of large expressed sequence-tag collections from other dicot species provides an opportunity to assess gene content in Arabidopsis, specifically by identifying genes from dicot test species that are absent from Arabidopsis. I report here results from these sorts of comparisons, carried out in part to assess the extent to which Arabidopsis is representative of dicot genomes and also the degree to which gene loss and novel gene acquisition has accompanied angiosperm speciation. More than 10% of the contigs from each of three dicot test species have no detectable homologue in Arabidopsis. By means of cross comparison among the test species, 154 specific cases of gene loss in the lineage leading to Arabidopsis were identified, including several well characterized enzymes and a group of proteins with strong homologs in the photosynthetic bacterium Synechocystis. These results show that although Arabidopsis is broadly representative of the other dicot genomes, there seems to be substantial variation even among relatively closely related genera. Further, although we cannot yet draw a causative link, variation in actual gene content seems appears to be a feature of angiosperm speciation.
Allen
Keith D
KD
Bioinformatics Department, Paradigm Genetics, 108 TW Alexander Drive, Building 1A, Research Triangle Park, NC 27709-4528, USA. kallen@paragen.com
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics; D030541:Databases, Genetic; D005798:Genes, Bacterial; D017343:Genes, Plant; D018745:Genome, Plant; D019684:Magnoliopsida / Q000145:classification / Q000201:enzymology / Q000235:genetics; D008390:Markov Chains; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
D029681:Arabidopsis Proteins; D010940:Plant Proteins