Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants
Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants
Abstract Rhesus macaque (Macaca mulatta) is a widely-studied nonhuman primate. Here we present a high-quality de novo genome assembly of the Chinese rhesus macaque (rheMacS) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), the rheMacS genome assembly improves sequence contiguity by 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). To improve gene annotation, we generated more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to the long-read assembly of ape genomes. We show that many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a set of candidate ASSVs that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. This improved rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.
Kronenberg Zev N.、Qi Xuebin、He Yaoxi、Eichler Evan E.、Luo Xin、Audano Peter A.、Guo Yongbo、Hu Ting、Yang Yanan、Zhou Bin、Jin Jie、Meng Xiaoyu、Su Bing
Department of Genome Sciences, University of Washington School of MedicineState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesDepartment of Genome Sciences, University of Washington School of Medicine||Howard Hughes Medical Institute, University of WashingtonState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesDepartment of Genome Sciences, University of Washington School of MedicineState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesNextomics BiosciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Kunming College of Life Science, University of Chinese Academy of SciencesState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences||Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences||Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences
遗传学分子生物学动物学
Kronenberg Zev N.,Qi Xuebin,He Yaoxi,Eichler Evan E.,Luo Xin,Audano Peter A.,Guo Yongbo,Hu Ting,Yang Yanan,Zhou Bin,Jin Jie,Meng Xiaoyu,Su Bing.Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants[EB/OL].(2025-03-28)[2025-04-29].https://www.biorxiv.org/content/10.1101/692749.点此复制
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