Additional file 1 of Structural variant landscapes reveal convergent signatures of evolution in sheep and goats
Creators: name: Yang, Ji
name: Wang, Dong-Feng
name: Huang, Jia-Hui
name: Zhu, Qiang-Hui
name: Luo, Ling-Yun
name: Lu, Ran
name: Xie, Xing-Long
name: Salehian-Dehkordi, Hosein
name: Esmailizadeh, Ali
name: Liu, George E.
name: Li, Meng-Hua
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Results and Supplementary Figures 1–30. Fig. S1. Genomic characterization and synteny landscape for the de novo assembled Asiatic mouflon genome. Fig. S2. Venn diagrams. Fig. S3. The size distribution of SVs exceeding 1 kb by variant types in sheep and goats. Fig. S4. Experimental validation of the SVs identified in this study. Fig. S5. Genomic features of the sheep and goat genomes. Fig. S6. Distribution of short length SVs and transposable elements. Fig. S7. The pattern of linkage disequilibrium (LD) decay in genomes of sheep and goats based on SNPs. Fig. S8. Principal component analysis (PCA) of domestic sheep and domestic goats based on structural variants. Fig. S9. The cross-validation errors for different values of K in admixture analysis of sheep and goats. Fig. S10. Genome-wide selective test for candidate genes associated with the domestication of domestic sheep and domestic goats. Fig. S11. Genome-wide selective test for candidate genes associated with the domestication of domestic goats during two different developmental stages. Fig. S12. Genome-wide selective test for candidate genes associated with the genetic improvement of domestic sheep and domestic goats. Fig. S13. Functional enrichment analysis reveals significant GO terms and KEGG pathways for the candidate selected genes associated with the fertility. Fig. S14. Genome-wide selective test for candidate genes associated with the reproduction traits of domestic sheep and domestic goats based on SNP data. Fig. S15. Genome-wide selective test for candidate genes associated with the wool and cashmere related trait of domestic sheep and domestic goats. Fig. S16. Genome-wide selective test for candidate genes associated with the dairy trait of domestic sheep and domestic goats. Fig. S17. Genome-wide selective test for candidate genes associated with the meat production trait of domestic sheep and domestic goats. Fig. S18. Evolution and function analysis of the deletions in BMPR1B of goats. Fig. S19. Experimental validation of the selected deletions in BMPR1B and BMPR2. Fig. S20. Evolution analysis of the deletions in BMPR1B of sheep. Fig. S21. Linkage disequilibrium and haplotype block analysis of the SVs and SNPs in BMPR1B of sheep. Fig. S22. Evolution and function analysis of the deletions in BMPR2 of sheep. Fig. S23. Evolution and function analysis of the deletions in BMPR2 of goats. Fig. S24. Linkage disequilibrium and haplotype block analysis of the SVs and SNPs in BMPR2 of goats. Fig. S25. The IGV visualization of location and sequence of the deletion in BMPR1B significantly (P &lt; 0.05) associated with litter size in Yunshang black goats. Fig. S26. SV introgression from wild sheep to domestic sheep populations at chromosomes 1–27 and from wild goat to domestic goat populations at chromosomes 1–29. Fig. S27. Genome-wide environmental analysis of 22 environmental variables and structural variants associated with local adaptation in sheep and goats. Fig. S28. The SV numbers identified in the Ovis and Capra are close to saturation with our sample sizes. Fig. S29. Genetic structure of wild and domestic goat populations based on SNPs. Fig. S30. The IGV visualizations of locations and genotypes of the SVs in 5 well-known genes associated with production traits.