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因人类的测序和组装而改变 参考基因组，识别了许多不同分类单元之间共享的基因的内容和背景 灵长类谱系。随后组装黑猩猩、猕猴和其他非人类灵长类动物基因组的努力进一步加速了我们对这些物种和相关物种的了解。有问题的是，这些 基因组的质量远低于人类基因组，并且通常依赖于人类基因组 长距离脚手架。然而最近，长读长测序技术的出现使得 完整、准确的脊椎动物基因组组装的新构建。这些技术进步已经 支持少数猿和猴子的更新组装，这些组装得到了极大的改进，提供了独特的 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 现存约 500 种灵长类动物中的绝大多数都缺乏基因组。这里我们建议构建 来自 50 个不同灵长类物种、跨越 7500 万年进化史的完整参考基因组。使用 我们将使用最先进的长读长测序和组装方法进行测序、组装、注释、比对和组装 传播这些基因组作为社区的资源。源 DNA 将源自集成 Coriell 医学研究所的灵长类生物材料和信息资源 (IPBIR) (Coriell)，来自高质量、低传代、经过细胞遗传学验证的细胞系集合。该资源将 极大地增强研究潜力，促进我们对灵长类进化历史的理解， 群体基因组学、传染病、人类起源以及灵长类动物多样性和保护。