Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species
Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species
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DOI：
10.1093/molbev/msaa187
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发表时间：
2020-12-01
影响因子：
10.7
通讯作者：
Yong, Lengxob
中科院分区：
文献类型：
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作者：
Charlesworth, Deborah;Zhang, Yexin;Yong, Lengxob
孔雀鱼（Poecilia reticulata）的遗传和物理图谱表明，雄性和雌性之间的重组模式存在很大差异。交叉事件在雌性染色体上均匀发生，但在雄性减数分裂中，它们仅限于距每条染色体着丝粒最远的尖端，从而产生非常高的每兆碱基重组率，如哺乳动物性染色体的假常染色体区域。我们使用GC含量来间接推断孔雀鱼染色体上的重组模式，基于重组与偏向GC的基因转换相关的证据，因此具有高重组率的基因组区域应该可以通过高GC含量来检测。我们使用内含子序列和密码子的第三个位置来尽可能地在匹配的序列之间进行比较，并且都可能处于弱选择之下。几乎所有孔雀鱼染色体，包括性染色体 (LG12)，在其组装末端附近都具有非常高的 GC 值，这表明由于雄性减数分裂中强烈的交叉定位而导致高重组率。我们的测试并不表明孔雀鱼 XY 对比常染色体或近亲鸭嘴鱼 (Xihophorus maculatus) 的同源染色体具有更强的交叉定位。因此，我们得出结论，孔雀鱼 XY 对最近并未经历不同重组模式的进化变化，或降低其交叉率，但孔雀鱼进化了 Y 连锁，因为获得了雄性决定因素，该因素也赋予了雄性交叉模式。我们还鉴定了孔雀鱼染色体的着丝粒末端，这在基因组组装中并未确定。
Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and third positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localization in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localization than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of guppy chromosomes, which were not determined in the genome assembly.