Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels
Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels
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DOI：
10.1093/gbe/evaa088
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发表时间：
2020-05
影响因子：
3.3
通讯作者：
Rahulsimham Vegesna;Marta Tomaszkiewicz;O. Ryder;Rebeca Campos-Sánchez;P. Medvedev;Michael Degiorgio;K. Makova
中科院分区：
文献类型：
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作者：
Rahulsimham Vegesna;Marta Tomaszkiewicz;O. Ryder;Rebeca Campos-Sánchez;P. Medvedev;Michael Degiorgio;K. Makova
摘要 Y染色体上的多拷贝扩增基因家族在精子发生中发挥着重要作用。因此，研究濒临灭绝的类人猿物种的遗传变异至关重要。我们利用液滴数字聚合酶链式反应估计了黑猩猩、倭黑猩猩和猩猩群体样本中九个 Y 扩增基因家族的大小（拷贝数），将这些估计值与已发表的人类和大猩猩数据相结合，并生成了类人猿的全基因组睾丸基因表达数据。在进化框架内分析这一综合数据集，我们首先发现基因家族大小存在较高的种间和种内变异，较大的家族与较小的家族相比表现出更高的变异，这种模式与随机遗传漂变一致。其次，对于四个基因家族，我们观察到显着的种间大小差异，有时甚至在姐妹物种（黑猩猩和倭黑猩猩）之间也是如此。第三，尽管拷贝数存在很大差异，但 Y 扩增基因家族的表达水平在物种之间没有显着差异，这表明剂量调节。第四，对于三个基因家族，大小与跨物种的基因表达水平呈正相关，这表明，如果有足够的进化时间，拷贝数会影响基因表达。我们的结果表明，Y 扩增基因家族的大小存在高度变异性，但基因表达水平保持保守，这显着增进了我们对类人猿 Y 染色体进化的理解。
Abstract Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species—chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families’ expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes.