Supplementary Information for Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars Mingzhou Li1,2,13, Shilin Tian3,13, Long Jin1,13, Guangyu Zhou3,13, Ying Li1,13, Yuan Zhang3,13, Tao Wang1, Carol KL Yeung3, Lei Chen4, Jideng Ma1, Jinbo Zhang3, Anan Jiang1, Ji Li3, Chaowei Zhou1, Jie Zhang1, Yingkai Liu1, Xiaoqing Sun3, Hongwei Zhao3, Zexiong Niu3, Pinger Lou1, Linjin Xian1, Xiaoyong Shen3, Shaoqing Liu3, Shunhua Zhang1, Mingwang Zhang1, Li Zhu1, Surong Shuai1, Lin Bai1, Guoqing Tang1, Haifeng Liu1, Yanzhi Jiang1, Miaomiao Mai1, Jian Xiao1, Xun Wang1, Qi Zhou5, Zhiquan Wang6, Paul Stothard6, Ming Xue7, Xiaolian Gao8, Zonggang Luo9, Yiren Gu10, Hongmei Zhu3, Xiaoxiang Hu11, Yaofeng Zhao11, Graham S. Plastow6, Jinyong Wang4, Zhi Jiang3, Kui Li12, Ning Li11, Xuewei Li1 & Ruiqiang Li2,3 1 Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, China. 2 Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, and School of Life Sciences, Peking University, Beijing, China. 3 Novogene Bioinformatics Institute, Beijing, China. 4 Chongqing Academy of Animal Science, Chongqing, China. 5 Ya’an Vocational College, Ya’an, China. 6 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada. 7 National Animal Husbandry Service, Ministry of Agriculture of China, Beijing, China. 8 Department of Biology and Biochemistry, University of Houston, Houston, USA. 9 Department of Animal Science, Southwest University at Rongchang, Chongqing, China. 10 Sichuan Animal Science Academy, Chengdu, China. 11 State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China. 12 Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China. 13 These authors contributed equally to this work. Correspondence should be addressed to X.L. (email: [email protected]) or to R.L. (email: [email protected]). 0 Nature Genetics: doi:10.1038/ng.2811 Table of contents Supplementary Figs. 1-36 ...................................................................................................... 5 Supplementary Fig. 1. The distribution areas of the original Tibetan wild boar in China. 5 Supplementary Fig. 2. Comparison of Tibetan wild boar and domestic Duroc pig. ......... 6 Supplementary Fig. 3. Synteny between the Tibetan wild boar and Duroc pig genomes. .......................................................................................................................................... 7 Supplementary Fig. 4. Distribution of 19-mer frequency. ................................................ 8 Supplementary Fig. 5. The GC content and CpG frequency for 10 kb, non-overlapping sliding windows across the Tibetan wild boar genome and five other mammalian genomes. .......................................................................................................................... 8 Supplementary Fig. 6. GC content against the sequencing depth of Tibetan wild boar genome. ............................................................................................................................ 9 Supplementary Fig. 7. Depth distribution of fraction bases. ............................................ 9 Supplementary Fig. 8. Distribution of heterozygosity density in the Tibetan wild boar diploid genome. ............................................................................................................... 10 Supplementary Fig. 9. Comparison of gene parameters among the Tibetan wild boar and five other mammalian genomes. .............................................................................. 10 Supplementary Fig. 10. Divergence distribution of classified families of transposable elements. ........................................................................................................................ 11 Supplementary Fig. 11. Length distribution of InDels in the Tibetan wild boar whole genome and in coding sequence (CDS) regions............................................................. 12 Supplementary Fig. 12. Orthology assignment of the Tibetan wild boar, Duroc pig and human genomes. ............................................................................................................ 13 Supplementary Fig. 13. Sequence depth distribution between single- and multi-copy genes in the Tibetan wild boar genome. ......................................................................... 14 Supplementary Fig. 14. Orthology delineation among the protein-coding gene family repertoires of the Tibetan wild boar and five other mammals. ......................................... 14 Supplementary Fig. 15. Venn diagrams showing the distribution of shared and unique gene families. .................................................................................................................. 15 Supplementary Fig. 16. Distribution of pairwise amino acid identity of orthologs between the Tibetan wild boar and five other mammals. ............................................................... 15 Supplementary Fig. 17. Venn diagram showing the distribution of olfactory-related gene repertoires among six mammals. .................................................................................... 16 Supplementary Fig. 18. Identification and comparison of olfactory receptor genes among six mammals using conserved olfactory receptor-specific motifs. ................................... 17 Supplementary Fig. 19. Phylogenetic analysis of the olfactory-related gene repertoires. ........................................................................................................................................ 18 Supplementary Fig. 20. Amino acid identity of olfactory-related genes between Duroc pig, Tibetan wild boar and four other mammals. ............................................................. 18 Supplementary Fig. 21. Average protein similarity of olfactory-related genes and total genes between Duroc pig, Tibetan wild boar and four other mammals. .......................... 19 Supplementary Fig. 22. Comparison of ω values between PSGs in Tibetan wild boar and Duroc pig. ....................................................................................................................... 20 Supplementary Fig. 23. Tibetan wild boar and Duroc pig KA/KS (ω) in functional gene categories. ...................................................................................................................... 21 Supplementary Fig. 24. PSGs in Tibetan wild boar involved in the pathway ‘mTOR 1 Nature Genetics: doi:10.1038/ng.2811 signaling’ and ‘vascular smooth muscle contraction’. ...................................................... 22 Supplementary Fig. 25. Comparison of the proportions of PSGs in Tibetan wild boar and Duroc pig. ....................................................................................................................... 23 Supplementary Fig. 26. PSGs in Duroc pig involved in the pathway of ‘extracellular matrix (ECM)-receptor interaction’. ................................................................................. 23 Supplementary Fig. 27. Inactivation events of six identified pseudogenes related to ‘response to drug’ in the Tibetan wild boar genome. ....................................................... 24 Supplementary Fig. 28. Genetic structure analysis for 103 sequenced individuals using FRAPPE with K = 2 to 9. ................................................................................................. 25 Supplementary Fig. 29. Genome-wide distribution of SNPs. ........................................ 26 Supplementary Fig. 30. Box plot of θπ ratio (θπ, domestic / θπ, Tibetan) and FST values for regions of Tibetan wild boars and Chinese domestic pigs that have undergone positive selection versus the whole genome. ............................................................................... 26 Supplementary Fig. 31. Distribution of selection statistics (Tajima’s D). ....................... 27 Supplementary Fig. 32. LD patterns between the selected regions and whole genome of Tibetan wild boars and Chinese domestic pigs. .............................................................. 28 Supplementary Fig. 33. Analysis of the phylogenetic relationship of Tibetan wild boars (n = 30) and neighboring domestic pigs (n = 15) using SNPs in regions with strong selective sweep signals. ................................................................................................................ 29 Supplementary Fig. 34. Genes embedded in naturally selected regions in Tibetan wild boars related to ‘vitamin B6 binding’ and ‘response to hypoxia’. ..................................... 30 Supplementary Fig. 35. Genes examined in the ‘saliva secretion’ functional category (GO-BP: 0046541) showed signatures of selective sweeps in Chinese domestic pigs. .. 31 Supplementary Fig. 36. Vacuum chewing (Domestic Duroc pig). ................................. 32 Supplementary Tables 1-8, 10-16, 18-22, 24-27 and 29-36 ................................................ 33 Supplementary Table 1. Genome sequencing strategy for the Tibetan wild boar.......... 33 Supplementary Table 2. Estimation of the Tibetan wild boar genome size using K-mer analysis. .........................................................................................................................