State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Nat Commun. 2019 Sep 17;10(1):4233. doi: 10.1038/s41467-019-12174-w.
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.
我们利用长读测序和多平台支架构建方法，呈现了高质量的中国恒河猴（Macaca mulatta）从头基因组组装（rheMacS）。与当前的印度恒河猴参考基因组（rheMac8）相比，rheMacS 将序列连续性提高了 75 倍，封闭了 21940 个剩余组装缺口（60.8 Mbp）。我们通过对来自十个不同组织的长读 RNA 测序生成了两百万多条全长转录本，从而改进了基因注释。我们通过与猿类基因组进行比较，序列解析了 53916 个结构变体（96%为新变体），并鉴定了 17000 个猿类特异性结构变体（ASSVs）。许多 ASSVs 映射到 ChIP-seq 预测的增强子区域内，在这些区域中，猿类和猕猴表现出不同的增强子活性和基因表达。我们进一步对其中一部分进行了特征描述，这些变体可能与猿类或大型猿类特有的表型特征有关，包括无尾、脑容量扩大、提高的手工灵巧性和较大的体型。rheMacS 基因组组装为未来的生物医学和进化研究提供了理想的参考。
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