Bioinformatics and Genomics Graduate Program, The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park.
Department of Biology, Pennsylvania State University, University Park.
Genome Biol Evol. 2020 Jun 1;12(6):842-859. doi: 10.1093/gbe/evaa088.
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.
Y 染色体上的多拷贝扩增基因家族在精子发生中起着重要作用。因此，研究濒危大猿物种中这些基因的遗传变异至关重要。我们使用液滴数字聚合酶链反应（ddPCR）估计了黑猩猩、倭黑猩猩和猩猩种群样本中九个 Y 扩增基因家族的大小（拷贝数），将这些估计值与人类和大猩猩的已发表数据相结合，并为大猿提供了全基因组睾丸基因表达数据。在进化框架内分析这个综合数据集，我们首先发现基因家族大小的种间和种内变异很大，与较小的家族相比，较大的家族表现出更高的变异，这种模式与随机遗传漂变一致。其次，对于四个基因家族，我们观察到了显著的种间大小差异，有时甚至在姐妹物种——黑猩猩和倭黑猩猩之间。第三，尽管拷贝数有很大的变化，但 Y 染色体扩增基因家族的表达水平在物种之间没有显著差异，表明存在剂量调节。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，在有足够的进化时间的情况下，拷贝数会影响基因表达。我们的研究结果表明 Y 染色体扩增基因家族在大小上具有高度的可变性，但在基因表达水平上具有保守性，这显著推进了我们对大猿 Y 染色体进化的理解。
