A compendium of complete primate reference genomes to facilitate conservation, genomics, and ecology

完整的灵长类动物参考基因组汇编，以促进保护、基因组学和生态学

• 批准号: 10675823
• 负责人: Erik Garrison
• 金额: $ 55万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10675823
• 关键词: Acceleration; Biocompatible Materials; Biodiversity; Biology; Cell Line; Collection; Communicable Diseases; Communities; Cytogenetics; DNA; Data; Deposition; Ecology; Ensure; Evolution; Generations; Genes; Genome; Genomics; Graph; Haplotypes; Human; Human Genome; Information Resources; Macaca; Medical Research; Methods; Monkeys; Pan Genus; Pongidae; Population; Primates; Recording of previous events; Research; Research Personnel; Resources; Sequence Alignment; Source; Technology; Validation; Variant; Work; base; genome annotation; genome browser; genome resource; human pangenome; human reference genome; improved; insight; nanopore; nonhuman primate; open data; pan-genome; reference genome; scaffold; vertebrate genome

Our understanding of primate evolution was transformed by the sequencing and assembly of the human reference genome which identified the content and context of genes shared amongst the many different taxa in the primate lineage. Subsequent efforts to assemble the genomes of chimpanzees, macaques, and other nonhuman primates further accelerated our under- standing of these and related species. Problematically, these genomes were of substantially lesser quality than the human genome and often relied on the human genome for long-range scaffolding. Recently however, the advent of long-read sequencing technologies have enabled de novo con- struction of complete, accurate vertebrate genome assemblies. These technological advances have supported renewed assemblies of a handful of apes and monkeys which are vastly improved providing unique insights into the evolution and biology of these species. Nevertheless, complete, accurate, reference quality genomes are lacking for the vast majority of the ~500 extant species of primates. Here we propose to construct complete reference genomes from 50 diverse primate species spanning 75 million years of evolution. Using state-of-the-art long-read sequencing and assem- bly methods we will sequence, assemble, annotate, align, and disseminate these genomes as a resource for the community. Source DNA will be derived from the Integrated Primate Bioma- terials and Information Resource (IPBIR) at the Coriell Institute for Medical Research (Coriell), from a high quality, low-passage, cytogenetically verified collection of cell lines. This resource will greatly enhance the potential for research that will advance our understanding of primate evolutionary history, population genomics, infectious disease, human origins, and primate biodiversity and conservation.

我们对灵长类进化的理解被人类基因组的测序和组装所改变。 参考基因组，它确定了许多不同分类群之间共享的基因的内容和背景， 灵长类动物的血统随后对黑猩猩、猕猴和其他非哺乳动物基因组的组装工作，人类灵长类动物进一步促进了我们对这些和相关物种的了解。问题是，这些 基因组的质量远低于人类基因组，并且通常依赖于人类基因组， 远程脚手架然而，最近，长读段测序技术的出现使基因组测序成为可能。 重新构建完整、准确的脊椎动物基因组组装体。这些技术进步 支持少数猿类和猴子的重新组合，这些猿类和猴子得到了极大的改进， 深入了解这些物种的进化和生物学。尽管如此，完整，准确，参考质量 在现存的约500种灵长类动物中，绝大多数都缺乏基因组。在这里，我们建议构建 来自跨越7500万年进化的50种不同灵长类动物物种的完整参考基因组。使用 最先进的长读序和组装方法，我们将测序，组装，注释，比对， 将这些基因组作为社区资源进行传播。源DNA将来自综合 灵长类生物材料和信息资源（IPBIR），Coriell医学研究所 （Coriell），来自高质量、低传代、细胞遗传学验证的细胞系集合。此资源将 极大地增强了研究的潜力，这将促进我们对灵长类进化历史的理解， 人口基因组学、传染病、人类起源和灵长类生物多样性及保护。