Six genome assemblies of Drosophila species for: Identification and genetic analysis of a pervasive “needle-eye” sperm phenotype in Drosophila sterile hybrid males

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 sterili..., 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 de novo 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., These are text files in FASTA format., # 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 (steril...

种间杂交不育已被广泛研究，尤其在果蝇属（Drosophila）中。杂交不育更常出现于异配（XX或ZW）性别，这一趋势被称为霍尔丹法则（Haldane’s rule）。尽管该现象普遍存在，但目前仍未明确其通用遗传机制，仅对一系列潜在理论存在有限的支持证据。本研究鉴定出一种单一且精准的形态表型，我们将其命名为“针状眼精子”（needle-eye sperm），该表型与跨越果蝇属的三个独立物种对的杂交不育相关。该表型的特征表明，不育杂交雄性存在共同的减数分裂失败位点。我们通过十代回交选择结合全基因组混池测序，对针状眼精子表型的遗传区域进行了定位。令人意外的是，即使经过十代回交，仍有约50%的雄性表现出不育表型，但遗传图谱显示多个与不育相关的区域……
针对每种表型的DNA提取采用了QIAGEN凝胶回收试剂盒（QIAGEN，加拿大多伦多安大略省）的改良方案。将每份样品置于含有200μg/mL蛋白酶K（Proteinase K）的缓冲液（1M Tris-HCl、0.5M EDTA和5M NaCl）中，95℃保温5分钟。随后向每份样品中加入异丙醇，于-20℃孵育过夜。DNA纯化按照QIAGEN凝胶回收试剂盒的说明书进行。纯化后的DNA样品在加拿大魁北克基因组创新中心（加拿大魁北克省蒙特利尔）使用Illumina HiSeq 2000平台进行测序，采用双端100bp读长，目标插入片段长度为400bp。
利用两款基于Linux平台的从头组装软件对Illumina测序产生的FASTQ文件进行组装：SOAPdenovo 1.05及其配套程序GapCloser 1.12（Li等，2008），以及Abyss 1.5.2（Simpson等，2009），Kmer取值范围为41至91。选择N50值最高的组装结果用于后续分析。本数据集为FASTA格式的文本文件。# 六种果蝇基因组组装文件：用于鉴定和遗传分析果蝇不育杂交雄性中普遍存在的“针状眼”精子表型
https://doi.org/10.5061/dryad.vdncjsz1k
本研究利用Illumina短读长测序技术获取了六个基因组的草图组装结果。我们鉴定出一种单一且精准的形态表型，命名为“针状眼精子”，该表型与跨越果蝇属的三个独立物种对的杂交不育相关。
## 数据与文件结构说明
本研究的FASTA格式组装文件及其说明如下：
mauGFP.nt：带有GFP标记鱼精蛋白的野生型毛里求斯果蝇（D. mauritania），可使精子发出绿色荧光。
simGFP.nt：同上，但为拟暗果蝇（D. simulans）。
BCM10NE.nt：经十代回交的毛里求斯果蝇雄性，携带针状眼（不育）精子表型。
BCM10WT.nt：经十代回交的毛里求斯果蝇雄性，携带野生型精子表型。
BCS10NE.nt：经十代回交的拟暗果蝇雄性，携带针状眼（不育……