Draft hybrid assembly and annotation of the Drosophila palustris and Drosophila subpalustris genomes

Abstract

Species within the quinaria group of the genus Drosophila are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Drosophila palustris and Drosophila subpalustris are closely related members within the quinaria species group that differ primarily in subtle morphological and behavioral traits. To support future evolutionary genomic studies in drosophilids, we completed new draft hybrid assemblies and annotations of the D. palustris and D. subpalustris genomes. We obtained a fragmented assembly for D. palustris (N50 = 874 Kb) and a near chromosome-scale D. subpalustris assembly (N50 = 27.5 Mbp). Assembly contiguity, repeat content, and gene annotation compared well to other published quinaria group genomes. To demonstrate the utility of our hybrid assemblies, we performed whole genome synteny and phylogenomic comparisons within the quinaria clade. When compared to the chromosome-level Drosophila innubila assembly, the median size of syntenic blocks among quinaria group genomes was approximately 1 Mbp, although this estimate was influenced by assembly contiguity. Phylogenomic analyses estimated that the two major branches of the quinaria group diverged ∼17.9 MYA, with D. palustris and D. subpalustris diverging ∼1-2 MYA. We expect that our D. palustris and D. subpalustris assemblies will provide important additions to studies of genome evolution within Drosophilidae.