Abstract
We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.
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Acknowledgements
We thank J. Guan, Y. Liu, Y. Xie, H. Wang and L. Bai for help in preparing the pig tissues. We thank Q. Quan, F. Wang, Y. Tan, Y. Guo and G. Yu for the optimizing chart. We thank S. Zhao and L. Huang for critical review of the manuscript. This work was supported by grants from the National Special Foundation for Transgenic Species of China (2014ZX0800950B, 2009ZX08009-155B and 2011ZX08006-003), the Foundation for Discipline Construction of Sichuan Agricultural University, the Specialized Research Fund of Ministry of Agriculture of China (NYCYTX-009), the Project of Provincial Twelfth Five Years' Animal Breeding of Sichuan Province (2011YZGG15), the National High Technology Research and Development Program of China (863 Program) (2013AA102502), the Postdoctoral Fellowship of Peking-Tsinghua Center for Life Sciences and the China Postdoctoral Science Foundation (2012M520123) to X.L. and M.L., the Chongqing Fund for Distinguished Young Scientists (CSTC2010BA1007) to J.W. and the Fund of Peking University to the Biodynamic Optical Imaging Center (BIOPIC), the Fund of Peking-Tsinghua Center for Life Sciences and the Fund of National Basic Research Program of China (2011CB809201) to R.L.
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M.L., S.T., R.L. and X.L. led the experiments and designed the analytical strategy. M.L., L.J., T.W., J.W., Y. Zhao, Z.W., Y.G., G.T., P.L. and Q.Z. performed animal work and prepared biological samples. X. Shen, S.S., Z.L., S.L. and Z.J. constructed the DNA library and performed sequencing. M.L., S.T., L.J., G.Z., Y. Zhang and Y. Li designed the bioinformatics analysis process. Jinbo Zhang, X. Sun, S.Z., L.X. and H. Zhu performed the genome assembly. M.L., Y. Zhang, S.T., G.Z., J.X., M.M., Y.J., M.Z. and H.L. performed the genome annotation and the orthologous and evolutional analyses. Y. Zhang, M.L., S.T., H. Zhao, L.C., Z.N., L.B. and L.Z. identified rapidly evolving genes and pseudogenes. S.T., M.L., J.L., J.M. and A.J. performed the read mapping and SNP identification. M.L., S.T., G.Z., J.L., X.H., X.W., X.G. and M.X. performed phylogenetic and population genetic analysis and linkage disequilibrium analysis. S.T., M.L., Y. Li, G.Z. and L.J. reconstructed demographic history. M.L., S.T., Y. Liu, C.Z. and Jie Zhang performed identification of regions with significant signatures of selective sweep. M.L., S.T., G.Z., L.J., Y. Li and Y. Zhang wrote the paper. R.L., C.K.L.Y., X.L., P.S., G.S.P., K.L. and N.L. revised the paper.
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Li, M., Tian, S., Jin, L. et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet 45, 1431–1438 (2013). https://doi.org/10.1038/ng.2811
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DOI: https://doi.org/10.1038/ng.2811
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