Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Workshop: Bioinformatics - Genomic Computing Techniques and Applications
The Arabidopsis thaliana and Oryza sativa genomes form a robust core upon which our first expeditions into comparative plant genomics can be based. While a few more genomes will be sequenced within the near future, a large genomics void is left behind for both plants with the larger and concomitantly more repetitive genomes and the more exotic plants of lesser agronomic importance. Reconstructomics utilises the available, but rather overlooked, EST collections to reconstruct partial transcriptomes. These sequences are annotated by using orthologous transfer of annotation from the Arabidopsis and rice genomes in addition to de novo annotation using a suite of current state-of-the-art sequence analysis methods. In excess of two million ESTs from 27 plant species have been clustered into ~500,000 singleton and cluster sequences and have been exhaustively annotated. Using the available Arabidopsis thaliana ESTs and full-length cDNAs as a sequence collection reference, ESTs can be measured to cover ~25% of the total transcriptome and cognately represent in excess of 60% of annotated genes. While this transcriptomic representation is far from perfect, this amount of data is a solid enough base to perform some preliminary expeditions into comparative plant genomics. The collated data from the ten plant species with in excess of 100,000 ESTs has been used to investigate comparative gene content between our reference genomes and the reconstructomes. These analyses provide some insight into the differences in gene content, biases in functional coverage and a glimpse at how gene families might evolve. This presentation concentrates on the more comparative aspects of the reconstructomes. All of the described data is available from the Sputnik website, http://mips.gsf.de/proj/sputnik