DOI: 10.5061/dryad.g1jwstqvq
title: Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive “needle-eye” sperm phenotype in Drosophila sterile hybrid males

description: Interspecies hybrid sterility has been extensively studied, especially in
 the genus Drosophila. Hybrid sterility is more often found in the
 heterogametic (XX or ZW) sex, a trend called Haldane’s rule. Although this
 phenomenon is pervasive, identification of a common genetic mechanism
 remains elusive, with modest support found for a range of potential
 theories. Here, we identify a single precise morphological phenotype,
 which we call “needle-eye sperm,” that is associated with hybrid sterility
 in three separate species pairs that span the Drosophila genus. The nature
 of the phenotype indicates a common point of meiotic failure in sterile
 hybrid males. We used ten generations of backcross selection paired with
 whole-genome pooled sequencing to genetically map the regions underlying
 the needle-eye sperm phenotype. Surprisingly, the sterility phenotype was
 present in ~50% of males even after ten generations of backcrossing, yet
 the genetic map showed multiple regions associated with sterility,
 indicating multiple regions may have the capacity to be sufficient to
 induce sterility in the F1. Due to the common phenotype among sterile male
 hybrids and the strong effect of individual loci, further exploration of
 the genes uncovered here may identify a universal mechanism for the
 evolution of hybrid sterility. 
description: DNA extraction for each phenotype was performed as a modified
 protocol of the QIAGEN Gel Extraction Kit (Qiagen, Toronto, ON, Canada).
 Each sample was held at 95⁰C for 5 mins in a buffer solution (1M Tris-HCl,
 0.5M EDTA, and 5M NaCl) containing 200µg/mL Protinase K. Isopropanol was
 then added to each sample and incubated overnight at -20 ⁰C. DNA
 purification was performed as directed by the QIAGEN Gel Extraction Kit.
 Purified DNA samples were then sequenced using the Illumina HiSeq 2000
 platform with paired-end 100-bp reads at Génome Québec Innovation Center
 (Montréal, QC, Canada) using a target insert size of 400 bp.
 Assembly of the FASTQ files generated by Illumina sequencing
 technology was performed using two Linux-based <em>de
 novo</em> assemblers: SOAPdenovo 1.05 and its companion program, GapCloser 1.12,
 (Li et al., 2008), and Abyss 1.5.2 (Simpson et al., 2009)
 at Kmer values of 41 to 91. The
 assembly with the highest N50 value was chosen for further
 analysis.
description: These are text files in FASTA format.
description: # Six genome assemblies of Drosophila species for: Identification and
 genetic analysis of a pervasive “needle-eye” sperm phenotype in Drosophila
 sterile hybrid males https://doi.org/10.5061/dryad.vdncjsz1k We used
 Illumina Short-Read Sequencing to obtain draft genome assemblies of six
 genomes. We identify a single precise morphological phenotype, which we
 call "needle-eye sperm," that is associated with hybrid
 sterility in three separate species pairs that span the Drosophila genus.
 ## Description of the data and file structure The assemblies in FASTA
 format and their descriptions are as follows: mauGFP.nt - wildtype *D.
 mauritania* with a GFP-tagged protamine (makes sperm fluoresce green).
 simGFP.nt - same as above, but *D. simulans* BCM10NE.nt - 10th generation
 backcross *mauritiana* males with needle-eye (sterile) sperm BCM10WT.nt -
 10th generation backcross *mauritiana* males with wildtype sperm
 BCS10NE.nt - 10th generation backcross *simulans* males with needle-eye
 (sterile) sperm BCS10WT.nt - 10th generation backcross *simulans* males
 with wildtype sperm ## Sharing/Access information ## Code/Software