ANALYSIS AND VISUALIZATION OF SINGLE COPY ORTHOLOGS IN ARABIDOPSIS, LETTUCE, SUNFLOWER AND OTHER PLANT SPECIES.

¹ University of California, Davis, Dept. of Vegetable Crops, Davis, CA 95616, USA

Approximately 3,700 of the genes in the Arabidopsis Col-0 genome are single copy. These genes were used to identify conserved orthologs in several other plant species. Using computational approaches we identified 1104 lettuce, 686 sunflower, 1704 tomato, 2016 soybean, 1701 maize and 1290 rice ESTs that are conserved orthologs to these Arabidopsis genes. Each EST sequence from these sets has an unambiguous single strong BLAST hit to the Arabidopsis genome. Reciprocal BLAST searches (Arabidopsis single copy genes versus EST assemblies) showed that more than 80% of BLAST hits had only a single strong hit. It indicated that majority of these conserved orthologs are represented by single genes in multiple plant species. Total number of Arabidopsis genes having similarity (BLAST score 1e-20 or better) at least to one of these selected ESTs is 2205, which is 60% of total number of single copy genes in Arabidopsis. Only 248 sequences were in common between EST collections from different species and Arabidopsis single copy genes. This can be partially explained by the incomplete representation within each EST collection. Analysis and visualization of single copy genes over Arabidopsis chromosomes (http://cgpdb.ucdavis.edu/database/est_vs_ath/arabidopsis_cos_map.html) revealed that these genes were distributed throughout the genome regardless of large scale chromosomal duplications. This indicates that deduction of order of genes in common ancestors is required for informative analyses of synteny.