Additional file 1 of Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice
Creators: name: Liu, Ming
name: Yu, Caixia
name: Zhang, Zhichao
name: Song, Mingjing
name: Sun, Xiuping
name: Piálek, Jaroslav
name: Jacob, Jens
name: Lu, Jiqi
name: Cong, Lin
name: Zhang, Hongmao
name: Wang, Yong
name: Li, Guoliang
name: Feng, Zhiyong
name: Du, Zhenglin
name: Wang, Meng
name: Wan, Xinru
name: Wang, Dawei
name: Wang, Yan-Ling
name: Li, Hongjun
name: Wang, Zuoxin
name: Zhang, Bing
name: Zhang, Zhibin
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Mouse samples in this study. a. Geographical sites of the 36 wild mice. b. The definition and relation of wild, wild-derived inbred and classic inbred mice in this study. Figure S2. The CV error variation for different K values of ADMIXTURE analysis on genomes of mice. Figure S3. PCA analysis on mouse genomes. a. The three-dimensional diagram of PCA based on the top three principal components (PC1-PC3). b. The percentage of eigenvalue in the top 10 principal components. Figure S4. Top 20 GO categories of the genes located in low nucleotide diversity regions (top 5%) in classical inbred mice as compared with those in wild mice and wild-derived inbred mice. Figure S5. Top 20 GO categories of the genes located in top 5% Fst regions in classical inbred mice as compared with those of wild mice and wild-derived inbred mice. Figure S6. Top 20 GO categories of the genes located in top 5% XP-CLR regions in classical inbred mice as compared with those of wild mice and wild-derived inbred mice. Figure S7. Top 20 GO categories of the 339 common positive selected genes in classical inbred mice as compared with those of wild mice and wild-derived inbred mice. Figure S8. The ratio of highly expressed genes in different organs and tissues in mice. The ratio of highly expressed genes in the immature brain, brain, liver, heart, and lung are illustrated in Fig. 2f. Figure S9. The ratio of the genes with abnormal behavioral phenotypes in mouse models. Figure S10. The heatmap of the 56 common differently expressed genes (merged from hippocampus and frontal lobe) in the frontal lobe of mice. Figure S11. The differences in relative expression of Vwc2l between classical inbred and wild mice. Each circle indicates one individual mouse, and error bars are standard error of mean (SEM). * indicates p &lt; 0.05. Figure S12. The differences in relative expression of Astn2 between classical inbred and wild mice. Each circle indicates one individual mouse, and error bars are SEM. Figure S13. The mutant mice model of rs27900929 in Astn2 gene. a. The position of rs27900929 in the Astn2 gene. The rectangles indicate exons of Astn2, and the red rectangles indicate the exon specially exist in the isoform b. b. The identification of Astn2 mutant mice. The bands for sequencing is 1085 bp. Red arrow heads indicate the mutant position. Figure S14. The differences in active tameness (actively contacting the hand of operators) between tamed and mutant mice. Each circle indicates one individual mouse, and error bars are SEM. Figure S15. The exponential relationship between accepting time and ratio of Astn2 isoform a/b. Each circle indicates one individual mouse. Passive tameness was the tolerance of the animal to touch from a human hand, as measured by accepting time. Figure S16. The binding pockets of the proteins of the Astn2 isoform a and b. The red color indicates the different area (Exon 4), and the yellow color indicates the large pockets. Isoform a lacks an alpha helix, and there is a binding pocket nearby the alpha helix of isoform b. Figure S17. The frequency and their relationship of tri-, bi- and single allele of SNPs of Astn2 in wild and classical inbred mice by using the criterion that the frequency of the reference allele in the wild mice is less than 20% of that in classical inbred mice. Table S1. The characters of the 36 wild mouse samples. Table S2. The characters of the 36 inbred mouse strains downloaded from Sanger Institute. Table S3. The sequencing characters of the 36 wild mouse samples. Table S4. Number of raw SNPs and their distributions in wild and classical inbred mice. Table S5. Number of raw SNPs and their distributions in wild-derived inbred mice originating from M. musculus. Table S6. Wild-derived inbred mice and their wild relatives. Table S21. Details of the tameness test in tamed and mutant mice. Table S23. Constructed mouse models for tameness test. Table S26. Primers used in this study.