DOI: 10.6078/d1ch5r
title: Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): a resource for testing evolutionary hypotheses

description: 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=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 D. melanogaster genome and remapping coordinates for a
 large set of transcriptional enhancers (n=3,457), we showed that each
 montium assembly contains orthologs for at least 91 % of D. melanogaster
 enhancers. Importantly, the genic and enhancer contents of our assemblies
 are comparable to that of far more contiguous Drosophila assemblies. The
 alignment of our own D. serrata assembly to a previously published PacBio
 D. serrata 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 montium group
 phylogeny; study the evolution of protein-coding genes and cis-regulatory
 sequences; and determine the genetic basis of ecological and behavioral
 adaptations.
description: This data archive contains repeat-masked assemblies, RepeatMasker
 annotation / summary tables, and liftOver chain files for 23
 <em>montium</em> genomes. It also includes BUSCO assessment
 tables for <em>D. bocki</em>, <em>D. burlai</em>,
 <em>D. jambulina</em>, <em>D. kanapiae</em>,
 <em>D. mayri</em>, <em>D. melanogaster</em>,
 <em>D. pectinifera</em>, <em>D. rufa</em>, and
 <em>D. triauraria</em>. The file Species_Names.tab is a key
 for the species abbreviations used in the filenames. Repeats were
 soft-masked using RepeatMasker. The liftOver chain files were created by
 individually aligning each <em>montium</em> assembly to the
 <em>D. melanogaster</em> genome using a previously described
 whole genome alignment pipeline. Detailed methods are described in a
 forthcoming paper. Given a set of coordinates for annotated features in
 the <em>D. melanogaster</em> genome (in either BED or GFF
 format), and a liftOver chain file, the liftOver utility returns
 coordinates for (putatively) orthologous sequences in an aligned
 <em>montium</em> genome. The liftOver utility can be
 downloaded by following the link to the utilities directory on this
 webpage: http://hgdownload.soe.ucsc.edu/downloads.html. The webpage also
 contains instructions for making the utility executable.
 The un-masked assemblies and raw sequencing data are available
 separately through the <em>Drosophila montium</em> Species
 Group Genomes Project, NCBI BioProject Accession PRJNA554346.