Long-read Assembly of The Chinese Rhesus Macaque Genome And Identification of Ape-specific Structural Variants

September 17, 2019

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 & Bing Su

Nature Communications volume 10, Article number: 4233 (2019)

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.

More info at: https://www.nature.com/articles/s41467-019-12174-w