Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
复制标题
DOI：
10.1093/gbe/evaa187
复制
发表时间：
2020-10-01
影响因子：
3.3
通讯作者：
Weigel D
中科院分区：
文献类型：
--
作者：
Fraser BA;Whiting JR;Paris JR;Weadick CJ;Parsons PJ;Charlesworth D;Bergero R;Bemm F;Hoffmann M;Kottler VA;Liu C;Dreyer C;Weigel D
理论预测，如果具有性别对抗性多态性的位点与性别决定位点相关联，则两性之间可以获得更大的适合度，这有利于在性别决定区域周围减少重组的传播。鉴于性别连锁区域经常是重复的和高度杂合的，很少有完整的Y染色体组合可用于测试这些想法。孔雀鱼系统（Poecilia reticulata）一直被认为是性冲突导致性染色体形成的一个例子。早期的遗传学研究表明，雄性颜色模式基因大部分（但不完全）是y连锁的，而x连锁可能在低捕食种群中最常见。最近对孔雀鱼种群基因组的研究得出了关于y连锁区域的大小和位置的不同结论。然而，这项先前的工作使用了从雌性孔雀鱼的短读序列中组装的参考基因组。在这里，我们利用长读PacBio单分子实时测序和染色体接触信息，提出了一个新的雄性孔雀鱼参考基因组组装。我们的新组装序列跨越了重复和GC-rich区域，从而弥补了短读雌性源孔雀鱼基因组中发现的空白和错误组装。利用这个改进的参考基因组，我们采用广泛的种群抽样来检测基因组中的性别差异。我们确定了两个显示一致的男性特有信号的小区域。此外，我们的结果有助于调和过去对孔雀鱼性染色体的种群基因组研究提出的相互矛盾的结论。我们的结果与雄性孔雀鱼的小y特异性区域和罕见的重组相一致。
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
登录
查看更多内容
影响因子：
2.6
作者：
Dor, Lior;Shirak, Andrey;Ron, Micha
通讯作者：
Ron, Micha
影响因子：
3
作者：
Girgis HZ
通讯作者：
Girgis HZ
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
10.7
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
10.7
作者：
Charlesworth, Deborah;Zhang, Yexin;Yong, Lengxob
通讯作者：
Yong, Lengxob