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Nat Commun. 2019 Sep 17;10(1):4233. doi: 10.1038/s41467-019-12174-w.

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants.

He Y1,2,3,4, Luo X1,2,3,4, Zhou B1,2,3,4, Hu T1,2,3,4, Meng X1,2,3,4, Audano PA5, Kronenberg ZN5, Eichler EE5,6, Jin J7, Guo Y1,2,3,4, Yang Y1,2, Qi X1,2,3, Su B8,9,10.

Author information

1
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
2
Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
3
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
4
Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China.
5
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
6
Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
7
Nextomics Biosciences, Wuhan, 430000, China.
8
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. sub@mail.kiz.ac.cn.
9
Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. sub@mail.kiz.ac.cn.
10
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. sub@mail.kiz.ac.cn.

Abstract

We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating 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 ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

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