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Y Chromosome Evolution

Y染色体进化

基本信息

批准号：
10092198
负责人：
KATERYNA MAKOVA
金额：
$ 41.39万
依托单位：
PENNSYLVANIA STATE UNIVERSITY, THE
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-02-01 至 2023-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10092198
关键词：
Address Affect Architecture Biological Catalogs Chickens Chromosomes Code Complement Computational Technique Computing Methodologies Cytogenetics DNA Resequencing DNA Transposable Elements Data Disease Evolution Female Fertility Gene Dosage Gene Family Genes Genetic Drift Genetic Markers Genome Genomics Goals Gorilla gorilla Haploidy Human Individual Investigation Male Infertility Methods Modeling Multigene Family Nature Pan Genus Pan paniscus Partner in relationship Pattern Phylogenetic Analysis Phylogeny Pongidae Pongo pygmaeus Population Population Sizes Process Proteins Publishing Research Research Personnel Resources Sex Chromosomes Shapes Spermatogenesis Structure System Techniques Testing Testis Theoretical model Transcript Y Chromosome Y protein autosome base design digital diverse data human male interest male male fertility mammalian genome novel prototype rapid technique sex sex determination simulation sperm cell trait transcriptome

项目摘要

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.

项目总结