Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

ASTRA: Integrated Bioinformatics Tools For Ryegrass And White Clover Genomics

CHRISTOPHER G. LOVE¹ , Timothy A. Erwin¹ , Erica G. Logan¹ , Gary Barker² , Nick James³ , Sean May³ , German Spangenberg¹ , David Edwards¹

¹  Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia

²  School of Biological Sciences, University of Bristol, BS8 1UG, UK

³  Nottingham Arabidopsis Stock Centre, Plant Science Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

ASTRA is an integrated database providing detailed annotation of expressed gene sequences (ESTs). Ryegrass and clover ASTRA databases maintain 44 524 perennial ryegrass ESTs and 42 017 white clover ESTs respectively. Each of these sequences has been annotated by comparison to GenBank, SwissProt and Gene Ontology (GO) databases, EST redundancy has been resolved through assembly with CAP3 and sequences have been aligned onto EnsEMBL viewers for comparison with the complete genomes of rice and Arabidopsis thaliana. In addition, SSR Primer and AutoSNP, have been applied for the in silico mining of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Resulting data is accessed through a web interface allowing key-word searches of annotation, GO browsing and sequence interrogation of resident sequences using BLAST. In total 3 214 ryegrass and 5 407 white clover SSRs were identified along with large numbers of SNPs and InDels. The integration of different analysis tools and the resulting data within a central resource allow users to identify novel candidate genes and associated molecular genetic markers that can be applied to germplasm enhancement in these agronomically important forage crops.