Additional file 2 of Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

Additional file 2: Table S1. Summary information of 495 domestic and 37 wild sheep as well as 209 domestic and 72 wild goats used in this study. Table S2. Statistic for wild and domestic sheep assemblies. Table S3. The distribution of GC content and gene coverage and their correlation in the genome assembly of Asiatic mouflon. Table S4. Summary information of the sequencing and alignment statistics for sheep (n = 532) and goat (n = 281) samples. Table S5. Summary information of ancient goat DNA samples used in this study. Table S6. Summary information of SVs in sheep (n = 532) and goats (n = 281). Table S7. Length distribution of SVs in the predefined ranges in sheep and goats. Table S8. Comparison of the SVs/CNVRs identified in this study and those reported in previous studies. Table S9. The novel SVs/CNVRs that were not detected in previous studies. Table S10. Details of SV validation by PCR and qPCR in sheep. Table S11. The SV hotspot regions overlapping with QTL regions in sheep and goats. Table S12. The number of SVs in the telomere and normal regions in sheep and goat genomes. Table S13. Functional annotation of the SVs detected in the 532 domestic and wild sheep. Table S14. Functional annotation of the SVs detected in the 281 domestic and wild goats. Table S15. SV annotated genes that are common between Ovis and Capra. The SVs associated with the common genes are either specific to or shared between Ovis and Capra species. Table S16. Summary information of the overlapped SVs and QTLs in sheep and goats. Table S17. Log2(fold enrichment) of SVs in QTLs for each individual of sheep. Table S18. Log2(fold enrichment) of SVs in QTLs for each individual of goats. Table S19. Transposable element (TE) annotation in Ovis and Capra SV calling sets. Table S20. Functional annotation of candidate selected regions identified with overlap of top 5% DISV and significant FST for domestication related traits in domestic sheep and domestic goats. Table S21. The most significantly enriched GO terms (FDR < 0.1) and KEGG pathways (FDR < 0.1) for the candidate genes associated with domestication, improvement, wool, milk, meat and reproduction related traits in domestic sheep and domestic goats. Table S22. Common genes under convergent selection between sheep and goats associated with domestication, improvement, wool, milk, meat and reproduction related traits. Table S23. Functionally enriched (FDR < 0.15) GO terms and KEGG pathways for the common genes under convergent selection associated with domestication, improvement, wool, milk, meat and reproduction related traits in sheep and goats. Table S24. Functional annotation of candidate selected regions identified with the top 5% FST value for stage I (from bezoar to ancient goats) and stage II (from ancient goats to native goats) of goat domestication. Table S25. Functional annotation of candidate selected regions identified with the top 5% FST value for improvement related traits in domestic sheep and domestic goats. Table S26. Detailed information on sheep and goat populations involved in the selective tests for structural variants (SVs) associated with particular production traits. Table S27. Functional annotation of candidate selected regions identified with the top 5% PBS value for wool, milk, meat and reproduction related traits in domestic sheep and domestic goats. Table S28. Functional annotation of candidate selected regions identified with the top 1% PBS value for reproduction traits in domestic sheep based on SNP data. Table S29. Functional annotation of candidate selected regions identified with the top 1% PBS value for reproduction traits in domestic goats based on SNP data. Table S30. Convergently selected genes of sheep and goats identified in this study that have been reported previously in human, sheep, goat and other animals. Table S31. Candidate selected genes in the convergent pathways implicated in the female reproduction process in Fig. 5 that have been previously reported with functions in reproductive system by studies in GeneRIF (Gene References Into Functions) and mouse transgenic document in MGI (Mouse Genome Informatics). Table S32. Allele frequency of the deletion (DEL00034481) in the BMPR1B gene in prolific and non-prolific sheep populations. Table S33. Allele frequency of the deletion (DEL00067921) in the BMPR1B gene in prolific and non-prolific goat populations. Table S34. Experimental validation results of BMPR1B gene in prolific and non-prolific sheep. Table S35. Experimental validation results of BMPR2 gene in Asiatic mouflon and the Middle Eastern domestic sheep populations. Table S36. Whole-genome sequencing and phenotypic data of goats used in this GWAS analysis for the litter size trait. Table S37. Genome-wide association signals using SV data for the litter size trait of goats based on the threshold of P < 0.05. Table S38. Overlapped genes between those identified by GWAS analysis of goats in this study and reported previously to be functionally linked to reproduction in human, sheep, goat and other animals. Table S39. Candidate introgression regions identified in domestic sheep based on the allele frequency of specific SVs that shared with wild sheep. Table S40. Candidate introgression regions identified in domestic goats based on the allele frequency of specific SVs that shared with wild goats. Table S41. Genes overlapped with the introgression regions in domestic sheep. Table S42. The most significantly (FDR < 0.1) enriched results of gene ontology terms and KEGG pathways for the introgressed genes identified in domestic sheep and domestic goats. Table S43. Genes overlapped with the introgression regions in domestic goats. Table S44. The sheep and goat samples of the ATAC-seq data used in this study. Table S45. The whole-genome sequencing data of the same sheep samples as the ATAC-seq data. Table S46. Significant signals of SVs identified by genome-wide association study (GWAS) between SVs and environmental variables in sheep and goats. Table S47. The most significantly enriched GO terms (FDR < 0.1) and pathways (FDR < 0.1) for the candidate genes associated with environmental variables in sheep and goats and overlapped genes in both ruminants. Table S48. The sheep and goat samples of the RNA-seq data used in this study.