Whole Genome Sequences of 23 Species from the Species Group (Diptera: Drosophilidae): A Resource for Testing Evolutionary Hypotheses.

Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich species group, 22 of which are presented here for the first time. The group is well-positioned for clade genomics. Within the clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the group and is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the group range from 155 Mb to 223 Mb (mean = 196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min = 18 kb, max = 390 kb, mean = 74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5-15%. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96% of known single-copy Dipteran genes (BUSCOs, n = 2,799). Similarly, by aligning our assemblies to the genome and remapping coordinates for a large set of transcriptional enhancers (n = 3,457), we showed that each assembly contains orthologs for at least 91% of enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous assemblies. The alignment of our own assembly to a previously published PacBio assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the group phylogeny; study the evolution of protein-coding genes and -regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.