Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.
Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.
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DOI：
10.1093/gbe/evy085
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发表时间：
2018-04-01
影响因子：
3.3
通讯作者：
Li MH
中科院分区：
文献类型：
--
作者：
Chen ZH;Zhang M;Lv FH;Ren X;Li WR;Liu MJ;Nam K;Bruford MW;Li MH
对X染色体沿着的基因组多样性及其与常染色体多样性的相关性的分析可以促进对形成性连锁基因组结构的进化力量的理解。在灵长类动物和其他模式物种中，X染色体上强烈的选择性扫描和加速的遗传漂变已经被推断出来，但在家养动物中与野生亲属相比，还没有获得这样的洞察力。在这里，我们分析了一个大型绵羊数据集的X染色体变异性，包括来自世界绵羊种群的943只母羊和110只野生和家养绵羊的全基因组的BeadChip阵列。分析全基因组序列，我们观察到一个显着降低X-常染色体的多样性比（0.75）下的中性模型（0.75）相比，预期值（0.6）。特别是，发现一个大的X连锁片段（43.05-79.25 Mb）显示出极低的多样性，最有可能是由于编码基因的高密度，具有高度保守的区域。在一般情况下，我们观察到较高的核苷酸多样性的常染色体上，但在X-连锁片段的平坦的多样性梯度，作为一个函数，增加距离最近的基因，导致降低X：常染色体（X/A）的多样性比，并在灵长类动物和其他模式动物中检测到的正相关性。我们的证据表明，加速遗传漂变，但减少X染色体上的定向选择，以及性别偏见的人口统计学事件，解释低X染色体的绵羊物种的多样性。我们在中东和非中东绵羊种群之间观察到的X连锁和X/A多样性的独特模式可以解释为在国内绵羊最近的驯化后人口扩张过程中的多次迁移，选择和混合，再加上适应新环境的自然选择。此外，我们确定了重要的新基因参与异常的行为表型，代谢和免疫，在绵羊X染色体上的选择。
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.
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