Plant & Animal Genomes XVII Conference

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

Genomic Sequence Annotation And Deep Allele Sampling In Fragaria.

Thomas M Davis¹ , Melanie E Shields¹ , Kevin M Folta² , Denise CM Tombolato² , Jeffrey L. Bennetzen³ , Ana Clara Pontaroli³

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

²  University of Florida, Horticultural Sciences Department, Gainesville, FL 32611 USA

³  University of Georgia, Department of Genetics, Athens, GA 30602 USA

We have taken a multi-faceted approach in performing 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 most closely matched by the Arabidopsis- and Medicago-based FGENESH predictions, and least closely matched by the Vitis-based predictions. Only ~16% of all identified genes had complete Fragaria EST coverage, while over 50% percent of genes predicted by FGENESH and validated by Blastx have no Fragaria EST support at all, documenting a substantial need for more Fragaria 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 inclusion in this study. Analysis of these data will test the null hypothesis that all octoploid Fragaria share a common genome constitution, and will provide a useful marker set for linkage mapping in diploid and octoploid strawberries. 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.