Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Natural Accessions

Natural variation is a powerful resource for studying the genetic basis of biological traits. Brachypodium distachyon (Brachypodium) is an excellent model grass with a large collection of inbred, diploid lines. These collections contain extensive phenotypic variation. To provide a genomic foundation for future studies, we are deep sequencing 56 diverse inbred natural accessions in collaboration with the US Department of Energy Joint Genome Institute. Analysis of the first six accessions shows tremendous genetic diversity with SNP frequencies ranging from every 200-600 base pairs. We have generated a set of 2,485,097 nonredundant, high confidence SNPs among these six accessions, including 152,920 SNPs in protein-coding regions. The SNP set in this study contains 96.6% (538 of 557) of SNPs previously used to produce a genetic linkage map, indicating a false negative rate of 3.4%. Deep sequencing also revealed numerous indels (61,582-163,776 small indels (1-30bp) and 2,064-8414 large indels and rearrangements (75bp - 20kbp) per accession), which we are confirming by other methods. In addition to comparing the resequenced reads to the reference genome to identify SNPs and structural variation, we are using de-novo assembly and targeted assembly approaches to identify sequences present in the resequenced genomes that are absent from the reference genome. Data and detailed analysis of these results will be made publicly available.