Phylogeny of species within the genus Fragaria revealed by next generation sequencing of multiple low copy nuclear markers

While the utilization of next generation sequencing technologies is rapidly growing, the application of this approach to phylogenetic analysis has been fairly limited to date. We are conducting large scale phylogenetic analyses of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. Our aim is to clarify phylogenetic relationships among Fragaria species and to elucidate the sub-genome composition of the polyploid species. Twenty-four single-copy or low-copy nuclear genes distributed across the genome were selected, and amplicons were sequenced from ninety six genomic DNA samples representing species from diploid to decaploid. Individual gene trees and species trees were reconstructed by different tree-building methods. Our results support the monophyly of Fragaria, and illuminate phylogenetic relationships among diploid species. Our findings also suggest the presence of three types of sub-genomes within the octoploid strawberry genome, and support the prior implications of ancestry for three diploid species: F. vesca and/or F. mandshurica, and F. iinumae. We developed a bioinformatics pipeline that is useful for large scale phylogenetic analysis of other polyploid species, and demonstrate the power of high throughput sequencing technology to enable robust phylogeny estimation from multiple nuclear genes.