Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

文献类型： 外文期刊

第一作者： Lan, Daoliang

作者： Lan, Daoliang;Xiong, Xianrong;Xiong, Yan;Li, Jian;Lan, Daoliang;Fu, Wei;Ji, Wenhui;Xiong, Xianrong;Ying, Shi;Xiong, Yan;Li, Jian;Lan, Daoliang;Fu, Wei;Mipam, Tserang-Donko;Sheng, Peng;Ni, Jiangping;Kong, Xiangdong;Bai, Lijun;Shan, Tongling

作者机构：

关键词： High- and low-altitude; Novel genes; Pangenome; PAV-GWAS; Yak

期刊名称：JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY （ 影响因子：7.0； 五年影响因子：7.3 ）

ISSN： 1674-9782

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： Background The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.Results We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations.Conclusions The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.

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