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

Yaoxi He, Xin Luo, Bin Zhou, Ting Hu, Xiaoyu Meng, Peter A. Audano, Zev N. Kronenberg, Evan E. Eichler, Jie Jin, Yongbo Guo, Yanan Yang, Xuebin Qi and Bing Su ()
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Yaoxi He: Chinese Academy of Sciences
Xin Luo: Chinese Academy of Sciences
Bin Zhou: Chinese Academy of Sciences
Ting Hu: Chinese Academy of Sciences
Xiaoyu Meng: Chinese Academy of Sciences
Peter A. Audano: University of Washington School of Medicine
Zev N. Kronenberg: University of Washington School of Medicine
Evan E. Eichler: University of Washington School of Medicine
Jie Jin: Nextomics Biosciences
Yongbo Guo: Chinese Academy of Sciences
Yanan Yang: Chinese Academy of Sciences
Xuebin Qi: Chinese Academy of Sciences
Bing Su: Chinese Academy of Sciences

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-12174-w

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