Additional file 1 of Whole-genome resequencing to investigate the genetic diversity and mechanisms of plateau adaptation in Tibetan sheep
Creators: name: Li, Xue
name: Han, Buying
name: Liu, Dehui
name: Wang, Song
name: Wang, Lei
name: Pei, Quanbang
name: Zhang, Zian
name: Zhao, Jincai
name: Huang, Bin
name: Zhang, Fuqiang
name: Zhao, Kai
name: Tian, Dehong
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Whole genome and transcriptome sequencing and analysis results. Table S1. The information of sequencing sample and download data. Table S2. The statistical results of of sequencing data results. Table S3. The statistical results of high-quality sequencing data. Table S4. The results of the read mapping. Table S5. The statistical results of population SNPs in each sample. Table S6. The results of SNPs annotation. Table S7. The statistical results of population InDels in each sample. Table S8. The results of InDels annotation. Table S9. The results of IBS similarity value. Table S10. The results of genetic diversity in each population. Table S11. The statistical results of FST in population. Table S12. The statistical results of unique SNPs in Agrali and Tibetan sheep, separately (partial results). Table S13. The annotation results of unique SNPs in Argali (partial results). Table S14. The annotation results of unique SNPs in Tibetan sheep (partial results). Table S15. The KEGG enrichment results of unique SNPs in Argali (P &lt; 0.05). Table S16. The GO enrichment results of unique SNPs in Argali (P &lt; 0.05). Table S17. The KEGG enrichment results of unique SNPs in Tibetan sheep (P &lt; 0.05). Table S18. The GO enrichment results of unique SNPs in Tibetan sheep (P &lt; 0.05). Table S19. The gene annotation of the top 1% in XP-CLR analysis of Tibetan sheep and Argali (partial results). Table S20. The key genes associated with evolution in selected regions. Table S21. The KEGG enrichment analysis of genes in selective sweep regions of Tibetan sheep and Argali (P &lt; 0.05). Table S22. The GO enrichment analysis of genes in selective sweep regions of Tibetan sheep and Argali (P &lt; 0.05). Table S23. The gene annotation of the top 1% in XP-CLR analysis of Zhashijia sheep and Valley Tibetan sheep (partial results). Table 24. The key genes associated with altitude adaptation in selected regions. Table S25. The KEGG enrichment analysis of genes in selective sweep regions of Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S26. The GO enrichment analysis of genes in selective sweep regions of Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S27. The common genes in unique SNPs and the selective sweep region of Tibetan sheep relative to Argali. Table S28. The KEGG enrichment pathways shared by unique SNPs and the selective sweep region of Tibetan sheep relative to Argali (P &lt; 0.05). Table S29. The GO pathways shared by unique SNPs and the selective sweep region of Tibetan sheep relative to Argali (P &lt; 0.05). Table S30. The results of transcriptome in heart and lung tissues for Zhashijia sheep and Valley Tibetan sheep. Table S31. The KEGG enrichment of differentially expressed genes in heart transcriptome for Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S32. The GO enrichment of differentially expressed genes in heart transcriptome for Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S33. The genes were significantly differentially expressed in the heart transcriptome for Zhashijia sheep and Valley Tibetan sheep (|log2 (HJ/HS)| ≥ 2). Table S34. The KEGG enrichment of differentially expressed genes in lung transcriptome for Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S35. The GO enrichment of of differentially expressed genes in lung transcriptome for Zhashijia sheep and Valley Tibetan sheep (P &lt; 0.05). Table S36. The genes were significantly differentially expressed in the lung transcriptome for Zhashijia sheep and Valley Tibetan sheep (|log2 (LJ/LS)| ≥ 2). Table S37. The common differentially expressed genes in selective sweep of plateau adaptation, heart transcriptome and lung transcriptome. Table S38. The KEGG enrichment of common differentially expressed genes in selective sweep, heart transcriptome and lung transcriptome (P &lt; 0.05). Table S39. The GO enrichment of common differentially expressed genes in selective sweep, heart transcriptome and lung transcriptome (P &lt; 0.05).