Additional file 1 of Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca
Creators: name: Ruiwen Fan
name: Zhongru Gu
name: Xuanmin Guang
name: Marín, Juan Carlos
name: Varas, Valeria
name: González, Benito A.
name: Wheeler, Jane C.
name: Yafei Hu
name: Erli Li
name: Xiaohui Sun
name: Xukui Yang
name: Zhang, Chi
name: Wenjun Gao
name: Junping He
name: Munch, Kasper
name: Corbett-Detig, Russel
name: Barbato, Mario
name: Shengkai Pan
name: Xiangjiang Zhan
name: Bruford, Michael W.
name: Changsheng Dong
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. K-mer distribution. Figure S2. Detailed sampling map of all sequenced individual. Figure S3. Treemix phylogeny and variance plot. Figure S4. Introgression segments into llama (fd). Figure S5. PSMC plot for all four SAC species. Figure S6. MSMC plots for (a) guanaco; (b) llama; (c) vicuña; (d) alpaca. Figure S7. Manhattan plot of selection signatures detected in the comparison between vicuña and alpaca (XP-EHH upper, FST bottom). Figure S8. Manhattan plot of selection signatures detected in the comparison between guanaco and llama (XP-EHH upper, FST bottom). Figure S9. Comparison between region-wide FST and SNP distribution among wild ancestors and domestic relatives for the OR5 and OR2 olfactory receptor family. Figure S10. Comparison between region-wide FST and SNP distribution among wild ancestors and domestic relatives for the HoxD gene clusters and OLA1 gene related to morphology development. Figure S11. SNP distribution among wild ancestors and domestic relatives with evidence of introgression from llama to alpaca on Chr10. Figure S12. SNP distribution among wild ancestors and domestic relatives with evidence of introgression from alpaca to llama: CORIN, FGF21, GNAS, TAGLN. Figure S13. cDNA sequence, expression histogram, Western Blot and protein expression histogram for the alpaca skin FGF5 expression analysis. Figure S14. The phylogeny of South American camelids with segments of high guanaco ancestry removed from alpaca genomes. Table S1. Statistics of the clean data for the de novo genomes. Table S2a-c. Assembly statistics for each species. Table S3. Genome coverage assessed by transcriptome unigenes. Table S4. The BUSCO results of the three new assembled SAC genomes. Table S5. K-mer analysis. Table S6. Aligned sequence data for de novo genomes. Table S6a. Aligned sequence between the de novo genomes and related species: pairwise whole-genome alignment was performed using LASTZ. Table S6b. Synteny analysis for aligned de novo genomes. Table S7a-c. the number of predicted genes for each species. Table S8. Sampling details. Table S9. Resequencing data summary. Table S10. ABBA-BABA statistics. Table S11. Introgressed segments from llama into alpaca using fd and LAI. Table S12. Introgressed segments from alpaca into llama using fd and LAI. Table S13. Introgressed segment and genes showing low and high LAI introgression on the inferred X-chromosome of alpaca. Table S14. Selection signatures detected in comparisons between vicuña and alpaca (XP-EHH). Table S15. Selection signatures detected in comparisons between vicuña and alpaca (FST). Table S16. Selection signatures detected in comparisons between vicuña and alpaca (overlap between methods). Table S17. Selection signatures detected in comparisons between guanaco and llama (XP-EHH). Table S18. Selection signatures detected in comparisons between guanaco and llama (FST). Table S19. Selection signatures detected in comparisons between guanaco and llama (overlap between methods). Table S20. Olfactory receptor gene numbers in South American camelids, compared to the cow. Table S21. PCR and qPCR primers. Table S22. Blood and skin tissue expression counts for de novo sequenced SACs and Chinese alpaca, respectively. Supplementary Note S1 - De novo Genome Sequencing a. Genome size estimation. b. De novo sequencing, assembly and annotation. Supplementary Note S2 - Introgression analysis. Supplementary Note S3- Sample collection, DNA extraction and permits.