Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species
文献类型： 外文期刊
作者： Chen, Ze-Hui 1 ; Zhang, Min 1 ; Lv, Feng-Hua 1 ; Ren, Xue 1 ; Li, Wen-Rong 4 ; Liu, Ming-Jun 4 ; Nam, Kiwoong 5 ; Bruford 1 ;
作者机构： 1.Chinese Acad Sci, CAS Key Lab Anim Ecol & Conservat Biol, Inst Zool, Beijing, Peoples R China
2.Univ Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China
3.Univ Sci & Technol China, Sch Life Sci, Hefei, Anhui, Peoples R China
4.Xinjiang Acad Anim Sci, Anim Biotechnol Res Ctr, Urumqi, Peoples R China
5.Univ Montpellier, Inst Natl Rech Agron, Diversite Genomes & Interact Microorganismes Inse, Montpellier, France
6.Cardiff Univ, Organisms & Environm Div, Sch Biosci, Cardiff, S Glam, Wales
7.Cardiff Univ, Sustainable Places Res Inst, Cardiff, S Glam, Wales
关键词： X-chromosome evolution; Ovis; genetic drift; selective sweeps; X/A diversity; whole genomes
期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.416； 五年影响因子：4.079 ）
ISSN： 1759-6653
年卷期： 2018 年 10 卷 5 期
页码：
收录情况： SCI
摘要： 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 (similar to 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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