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.

人类的测序和组装改变了我们对灵长类进化的理解 参考基因组，它确定了在许多不同的类群中共享的基因的内容和背景 灵长类的血统。随后收集黑猩猩、猕猴和其他非人类灵长类动物的基因组的努力进一步促进了我们对这些物种和相关物种的了解。有问题的是，这些 基因组的质量比人类基因组低得多，通常依赖于人类基因组 远程脚手架。然而，最近长读测序技术的出现使得 构建完整、准确的脊椎动物基因组组合。这些技术进步已经 支持少数类人猿和猴子的更新组装，这些组件得到了极大的改进，提供了独特的 对这些物种的进化和生物学的洞察。尽管如此，完整、准确、参考质量 现存的约500种灵长类动物中，绝大多数缺乏基因组。在这里，我们建议构建 来自50个不同灵长类物种的完整参考基因组，跨越7500万年的进化。vbl.使用 最先进的长读测序和组装方法，我们将对其进行排序、组装、注释、对齐和 将这些基因组作为社区资源进行传播。源DNA将从集成的 科里尔医学研究所灵长类生物材料与信息资源 (Coriell)，来自高质量、低传代、细胞遗传学验证的细胞系收集。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史的理解， 种群基因组学、传染病、人类起源、灵长类生物多样性和保护。