Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
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使用多个从头组装全面发现猪基因组中的变异并恢复缺失序列
DOI：
10.1101/gr.207456.116
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发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Li X
中科院分区：
文献类型：
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作者：
Li M;Chen L;Tian S;Lin Y;Tang Q;Zhou X;Li D;Yeung CKL;Che T;Jin L;Fu Y;Ma J;Wang X;Jiang A;Lan J;Pan Q;Liu Y;Luo Z;Guo Z;Liu H;Zhu L;Shuai S;Tang G;Zhao J;Jiang Y;Bai L;Zhang S;Mai M;Li C;Wang D;Gu Y;Wang G;Lu H;Li Y;Zhu H;Li Z;Li M;Gladyshev VN;Jiang Z;Zhao S;Wang J;Li R;Li X
通过重测序发现遗传变异受到以下事实的限制：仅检查与参考基因组相似的序列。由于地理差异和独立的人口统计事件，参考基因组往往不完整，不能代表全部遗传多样性。为了更全面地表征猪（野猪）的遗传变异，我们从欧亚大陆产生了9个具有地理和表型代表性的猪的从头组装。通过将它们与参考猪组装进行比较，我们发现了大量新的SNP和结构变体，以及包含1737个蛋白质编码基因的137.02-Mb序列，这些基因在参考组装中不存在，揭示了选择留下的变体。我们的研究结果说明了全基因组从头测序相对于重测序的力量，并提供了宝贵的遗传资源，使猪在农业生产和生物医学研究中得到有效利用。
Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.