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
复制标题
中国恒河猴基因组的长读组装和猿特异性结构变异的鉴定
DOI：
10.1038/s41467-019-12174-w
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发表时间：
2019-09-17
影响因子：
16.6
通讯作者：
Su, Bing
中科院分区：
文献类型：
--
作者：
He, Yaoxi;Luo, Xin;Su, Bing
我们提出了一个高质量的从头基因组组装（rheMacS）的中国猕猴（猕猴mulatta）使用长读测序和多平台支架的方法。与目前的印度恒河猴参考基因组（rheMac 8）相比，rheMacS将序列连续性提高了75倍，关闭了21，940个剩余的组装缺口（60.8 Mbp）。我们通过长读段RNA测序从10种不同组织中产生200多万个全长转录本来改进基因注释。我们对53，916个结构变体（96%是新的）进行了测序，并根据与猿基因组的比较确定了17，000个猿特异性结构变体（ASSV）。许多ASSV在ChIP-seq预测的增强子区域内作图，其中猿和猕猴显示出不同的增强子活性和基因表达。我们进一步描述了一个子集，可能有助于猿或类人猿特定的表型特征，包括无尾，脑容量扩张，改善手动灵活性，和大的身体尺寸。rheMacS基因组组装是未来生物医学和进化研究的理想参考。
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.