Dynamic evolution of great ape Y chromosomes.
Dynamic evolution of great ape Y chromosomes.
复制标题
类人猿Y染色体的动态进化。
DOI：
10.1073/pnas.2001749117
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发表时间：
2020-10-20
影响因子：
11.1
通讯作者：
Makova KD
中科院分区：
文献类型：
--
作者：
Cechova M;Vegesna R;Tomaszkiewicz M;Harris RS;Chen D;Rangavittal S;Medvedev P;Makova KD
男性特有的Y染色体携带着对精子产生很重要的基因。由于Y是重复的，它的DNA序列只在少数物种中被破译，它的进化仍然难以捉摸。在这里，我们比较了类人猿（人类、黑猩猩、倭黑猩猩、大猩猩和猩猩）的Y染色体，发现它们的许多重复序列和多拷贝基因可能已经存在于它们的共同祖先中。Y重复增加了染色体内接触，这可能有助于基因和基因调控元件的保存。黑猩猩和倭黑猩猩，经历了高精子竞争，经历了许多DNA变化和基因丢失的Y。我们的研究对于理解Y染色体在非人类类人猿繁殖中的作用具有重要意义，所有这些类人猿都是濒危物种。哺乳动物雄性特异性Y染色体在性别决定和雄性生育力中起着关键作用。然而，由于其重复和单倍体的性质，它经常缺席的基因组组装和仍然是谜。类人猿的Y染色体代表了一个特殊的谜题：它们的基因内容在人类和大猩猩之间比在人类和黑猩猩之间更相似，尽管人类和黑猩猩有一个更近的共同祖先。为了解决这个难题，我们构建了一个数据集，包括所有现存的大型猿属的Y。我们从短序列和长序列读取中生成了倭黑猩猩和猩猩Y的组装体，并将它们与公开的人类、黑猩猩和大猩猩Y组装体进行了比对。分析这个数据集，我们发现包括黑猩猩和倭黑猩猩在内的Pan属经历了加速的替代率。Pan还表现出较高的基因死亡率。这些观察结果与Pan中高水平的精子竞争一致。此外，我们推断，类人猿的共同祖先已经拥有了与大多数人类和黑猩猩回文同源的多拷贝序列。尽管如此，每个物种也获得了不同的扩增子序列。我们还检测到回文之间和回文内部的染色质接触增加（来自Hi-C数据），可能促进基因转换和结构重排。我们的研究结果突出了Y染色体进化的动态模式，并为研究濒危类人猿物种的雄性特异性扩散开辟了道路。
The male-specific Y chromosome harbors genes important for sperm production. Because Y is repetitive, its DNA sequence was deciphered for only a few species, and its evolution remains elusive. Here we compared the Y chromosomes of great apes (human, chimpanzee, bonobo, gorilla, and orangutan) and found that many of their repetitive sequences and multicopy genes were likely already present in their common ancestor. Y repeats had increased intrachromosomal contacts, which might facilitate preservation of genes and gene regulatory elements. Chimpanzee and bonobo, experiencing high sperm competition, underwent many DNA changes and gene losses on the Y. Our research is significant for understanding the role of the Y chromosome in reproduction of nonhuman great apes, all of which are endangered. The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.
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影响因子：
64.8
作者：
Hughes, Jennifer F.;Skaletsky, Helen;Brown, Laura G.;Pyntikova, Tatyana;Graves, Tina;Fulton, Robert S.;Dugan, Shannon;Ding, Yan;Buhay, Christian J.;Kremitzki, Colin;Wang, Qiaoyan;Shen, Hua;Holder, Michael;Villasana, Donna;Nazareth, Lynne V.;Cree, Andrew;Courtney, Laura;Veizer, Joelle;Kotkiewicz, Holland;Cho, Ting-Jan;Koutseva, Natalia;Rozen, Steve;Muzny, Donna M.;Warren, Wesley C.;Gibbs, Richard A.;Wilson, Richard K.;Page, David C.
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Page, David C.
影响因子：
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作者：
Cechova, Monika;Harris, Robert S.;Makova, Kateryna D.
通讯作者：
Makova, Kateryna D.
影响因子：
64.8
作者：
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影响因子：
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作者：
Bhowmick, Bejon Kumar;Satta, Yoko;Takahata, Naoyuki
通讯作者：
Takahata, Naoyuki
影响因子：
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作者：
Hallast P;Maisano Delser P;Batini C;Zadik D;Rocchi M;Schempp W;Tyler-Smith C;Jobling MA
通讯作者：
Jobling MA