PDF(Pubmed)
Abstract：
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.
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.
摘要：
背景：牦牛的遗传多样性，青藏高原（QTP）的主要家畜，是驯化和育种工作的重要资源。本研究介绍了通过16个牦牛基因组的从头组装获得的第一个牦牛基因组。
结果：我们发现了290Mb的非参考序列和504个新基因。我们的全基因组存在和不存在变异（PAV）分析揭示了5120个PAV相关基因，突出了广泛的品种特异性基因和在牦牛种群中频率不同的基因。基于二元基因PAV数据的主成分分析（PCA）将牦牛分为三个新的群体：野生，domestic,和金川。此外，我们提出了一个“双单倍型基因组杂交模型”，通过整合基因频率来理解品种间的杂交模式，杂合性，和基因PAV数据。PAV-GWAS基因鉴定出一个新基因（BosGru3G009179），该基因可能与金川牦牛的多肋性状有关。此外，整合的转录组和pangenome分析强调了高海拔和低海拔牦牛之间核心基因表达和差异表达基因突变负担的显著差异。跨多个物种的转录组分析显示，牦牛具有最独特的差异表达的mRNAs和lncRNAs（在高海拔和低海拔地区之间），尤其是在心脏和肺部，比较高空和低空适应性时。
结论：牦牛pangenome为功能基因组研究提供了全面的资源和新的见解，支持未来的生物学研究和育种策略。
结果：我们发现了290Mb的非参考序列和504个新基因。我们的全基因组存在和不存在变异（PAV）分析揭示了5120个PAV相关基因，突出了广泛的品种特异性基因和在牦牛种群中频率不同的基因。基于二元基因PAV数据的主成分分析（PCA）将牦牛分为三个新的群体：野生，domestic,和金川。此外，我们提出了一个“双单倍型基因组杂交模型”，通过整合基因频率来理解品种间的杂交模式，杂合性，和基因PAV数据。PAV-GWAS基因鉴定出一个新基因（BosGru3G009179），该基因可能与金川牦牛的多肋性状有关。此外，整合的转录组和pangenome分析强调了高海拔和低海拔牦牛之间核心基因表达和差异表达基因突变负担的显著差异。跨多个物种的转录组分析显示，牦牛具有最独特的差异表达的mRNAs和lncRNAs（在高海拔和低海拔地区之间），尤其是在心脏和肺部，比较高空和低空适应性时。
结论：牦牛pangenome为功能基因组研究提供了全面的资源和新的见解，支持未来的生物学研究和育种策略。
