Y Chromosome Evolution

项目摘要 男性特有的Y染色体对性别决定和生育能力至关重要。然而，由于其高度 重复结构和单倍性，它的序列只在少数哺乳动物物种中被破译， 包括三种猿类--人类、黑猩猩和大猩猩。Y染色体序列的缺失使得 很难获得哺乳动物基因组进化的完整图像，并阻碍了性别研究- 自然种群中的特定动态。在这个项目中，我们选择研究猿Y的进化， 染色体，因为它们在细胞遗传学水平上在物种之间存在巨大差异，并且因为交配和 影响Y染色体的选择和遗传漂变的散布模式在猿类之间有很大的差异。 我们的目标是通过检测Y染色体， 种间分化和种内多样性。在目标1中，我们将研究猿Y染色体的进化 架构应用我们基于最新实验和计算技术的新方法，我们 组装了大猩猩、倭黑猩猩和婆罗洲猩猩的Y染色体。使用这些和公开可用的 在系统发育框架中，我们将研究Y染色体结构的几个特征： 序列差异、基因含量和转座因子积累。谱系特异性 Y染色体进化的加速或减速进化将被确定，其原因将被 在随后的目标中探索。在目标2中，我们将研究影响全局Y染色体的进化力量 通过研究Y染色体的多样性。我们将测试观察到的多样性模式， 从公开可用和内部生成的重新测序数据推断，与随机 遗传漂变或正负选择。在目标3和4中，将确定甄选目标。在 目标3，我们将从短读和长读转录组组装中破译单个基因序列， 构建基因连锁群，并测试作用于个体基因和个体的谱系特异性选择 多拷贝基因家族的基因拷贝。目标4将评估作用于表达式的潜在选择 Y染色体上多拷贝扩增子基因家族的水平和拷贝数。这些基因 在精子发生过程中表达，其缺失与人类男性不育有关。总的来说， 我们的项目将对揭示猿类基因组进化的复杂性具有重要意义。猿Y 染色体组装，比对和转录本目录将作为一个宝贵的资源， 解决了无数长期存在的生物学问题，并设计了遗传标记来追踪 雄性猿类在野外的扩散这一点至关重要，因为所有研究过的猿类物种都濒临灭绝。的技术 为这个项目开发的基因组将与其他研究人员分享，使他们能够研究人类的Y染色体。 其他物种。我们对扩增子基因序列、表达水平和 拷贝数将大大有助于我们了解男性不育的原因。

PROJECT SUMMARY The male-specific Y chromosome is critical for sex determination and fertility. Yet, because of its highly repetitive structure and haploidy, its sequence has only been deciphered for a handful of mammalian species, including just three apes ‒ human, chimpanzee, and gorilla. The lack of Y chromosome sequences has made it difficult to obtain a complete picture of mammalian genome evolution, and has hampered studies of sex- specific dynamics in natural populations. In this project, we have chosen to study evolution of ape Y chromosomes because they differ enormously among species at the cytogenetic level, and because mating and dispersal patterns, which influence selection and genetic drift acting on the Y, vary dramatically among apes. Our goal is to decipher the evolutionary processes shaping ape Y chromosome evolution by examining Y interspecific divergence and intraspecific diversity. In Aim 1 we will study evolution of ape Y chromosome architecture. Applying our novel method based on the latest experimental and computational techniques, we assembled the Y chromosomes of gorilla, bonobo, and Bornean orangutan. Using these and publicly available ape Y assemblies in a phylogenetic framework, we will study several features of Y chromosome architecture: sequence divergence, gene content, and transposable element accumulation. Instances of lineage-specific accelerated or decelerated evolution of Y chromosome evolution will be identified and their causes will be explored in subsequent aims. In Aim 2 we will investigate evolutionary forces affecting global Y chromosome architecture by studying Y chromosome diversity. We will test whether the observed diversity patterns, as inferred from publicly available and in-house generated re-sequencing data, are consistent with random genetic drift or with positive or negative selection. In Aims 3 and 4, the selection targets will be identified. In Aim 3, we will decipher the individual gene sequences from short- and long-read transcriptome assemblies, construct gene phylogenies, and test for lineage-specific selection acting on individual genes and on individual gene copies for multi-copy gene families. Aim 4 will evaluate potential selection acting on the expression levels and copy number of multi-copy ampliconic gene families on the Y chromosome. These genes are expressed during spermatogenesis and their deletions have been implicated in human male infertility. Overall, our project will have important implications for uncovering the intricacies of ape genome evolution. The ape Y chromosome assemblies, alignments, and transcript catalogues will serve as an invaluable resource for addressing a myriad of long-standing biological questions and for designing genetic markers to trace the dispersal of male apes in the wild. This is critical, as all studied ape species are endangered. The techniques developed for this project will be shared with other researchers, enabling them to study Y chromosomes of other species. Our thorough investigation of evolution of ampliconic gene sequence, expression levels, and copy number will significantly contribute to our understanding of the causes of male infertility.