Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Genomic Sequence Annotation, Deep Allele Sampling, And Whole Genome Sequencing In Fragaria.

Thomas M Davis¹ , Melanie E Shields¹ , Linyuan Li² , Kevin M Folta³ , Jeffrey L Bennetzen⁴ , Vladimir Shulaev⁵

¹  University of New Hampshire, Department of Biological Sciences, Rudman Hall, Durham, NH 03824 USA

²  University of New Hampshire, Department of Mathematics, Kingsbury Hall, Durham, NH 03824 USA

³  University of Florida, Horticultural Sciences Department, Gainesville, FL 32611 USA

⁴  University of Georgia, Department of Genetics, Athens, GA 30602 USA

⁵  Virginia Polytechnic Institute and State University, Bioinformatics Institute, Blacksburg, VA 24061 USA

We have taken a multi-faceted approach to achieve a detailed annotation of genomic (fosmid) sequences from the strawberry model species Fragaria vesca. FGENESH ab initio gene predictions were compared using gene-finding parameters based on six reference genomes. When Blastx and Blastn homology-based gene searches were performed and compared with ab initio predictions, homology-based assessments of start and stop codon locations were matched most closely by the Arabidopsis- and Medicago-based FGENESH predictions, and least closely by Vitis. Over 50% of genes predicted by FGENESH and validated by Blastx have no Fragaria EST support, documenting a substantial need for more EST sequencing, particularly from flower and fruit libraries. A diverse spectrum of repetitive element types were identified, and their copy numbers predicted. In the context of our newly funded USDA-NRI grant, we will implement deep allele sampling at 28 carefully chosen loci in 90 Fragaria germplasm accessions. All interested investigators are invited to submit candidate loci and germplasm accessions for possible use in this study. A mathematical formula has been devised and employed to calculate the number of sequences needed to assure 99% confidence that all alleles are sampled in each plant. Analysis of these data will test the null hypothesis that all octoploid Fragaria share a common genome constitution. An update on the status of a Fragaria whole-genome sequencing effort will be presented. This project is supported in part by grants from the National Research Initiative Plant Genome Program of USDA’s Cooperative State Research, Education and Extension Service.