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 favour 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 colour 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 (SMRT) 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.

中文翻译：

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改进的参考基因组揭示了孔雀鱼（Poecilia reticulata）中新的性相关区域。

理论预测，如果具有性拮抗多态性的基因座与性别决定基因座相关联，则性别可以获得更大的适应性，这可能有利于减少重组在性别决定区域周围的传播。鉴于性相关区域经常重复且高度杂合，很少有完整的 Y 染色体组装可用于测试这些想法。孔雀鱼系统（Poecilia reticulata) 长期以来一直被用作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多但不完全是 Y 连锁的，而且 X 连锁可能在低捕食人群中最常见。最近对孔雀鱼的种群基因组研究对 Y 连锁区域的大小和位置得出了不同的结论。然而，之前的这项工作使用了一个参考基因组，该基因组是由雌性孔雀鱼的短读序列组装而成的。在这里，我们使用长读长 PacBio 单分子实时测序 (SMRT) 和染色体联系信息，展示了来自男性的新孔雀鱼参考基因组组装。我们跨重复和富含 GC 的区域的新组装序列，从而缩小差距并纠正在短读长的雌性孔雀鱼基因组中发现的错误组装。使用这个改进的参考基因组，我们然后采用广泛的人口抽样来检测整个基因组的性别差异。我们确定了两个显示出一致的男性特异性信号的小区域。此外，我们的结果有助于调和过去孔雀鱼性染色体群体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中一个小的 Y 特异性区域和罕见的重组一致。