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

Abstract

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 Drosophila montium species group, 22 of which are presented here for the first time. The montium group is uniquely positioned for comparative studies. Within the montium 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 montium group and D. melanogaster 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 montium 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=74Large 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 Drosophila montium species group, 22 of which are presented here for the first time. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis -regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.

Highly contiguous assemblies of 101 drosophilid genomes

“… ( A,B ) Assembly contiguity is compared to the D. melanogaster v6.22 reference genome (blue) as well as five recently published, highly contiguous Illumina assemblies (red lines, D. birchii, D. bocki, D. bunnanda, D. kanapiae, D. truncata ; Bronski et al, 2020 ). ( A ) Nx curves, or the (y-axis) size of each contig when contigs are sorted in descending size order, in relation to the (x-axis) cumulative proportion of the genome assembly that is covered.…”

Putative condition-dependent viability selection in wild type stocks ofDrosophila pseudoobscura

“…2019) Drosophila represent recent adaptive radiations with growing potential for ecological genomics. Finally, the montium species group has recently become genome-enabled and is well suited for testing various evolutionary hypotheses (Bronski et al . 2020).…”

Highly contiguous assemblies of 101 drosophilid genomes

“…Nanopore-based assemblies are highly contiguous and complete. ( A,B ) Assembly contiguity is compared to the D. melanogaster v6.22 reference genome (blue) as well as 5 recently published, highly contiguous Illumina assemblies (red lines, D. birchii, D. bocki, D. bunnanda, D. kanapiae, D. truncata ;Bronski et al, 2020 ). ( A ) Nx curves, or the (y-axis) size of each contig when contigs are sorted in descending size order, in relation to the (x-axis) cumulative proportion of the genome assembly that is covered.…”