Additional file 1 of Genomic signatures and evolutionary history of the endangered blue-crowned laughingthrush and other Garrulax species
Creators: name: Chen, Hao
name: Huang, Min
name: Liu, Daoqiang
name: Tang, Hongbo
name: Zheng, Sumei
name: Ouyang, Jing
name: Zhang, Hui
name: Wang, Luping
name: Luo, Keyi
name: Gao, Yuren
name: Wu, Yongfei
name: Wu, Yan
name: Xiong, Yanpeng
name: Luo, Tao
name: Huang, Yuxuan
name: Xiong, Rui
name: Ren, Jun
name: Huang, Jianhua
name: Yan, Xueming
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 1: Fig. S1. The genome annotation pipeline of the GCO and GSA. Fig. S2. Distribution of the divergence rate of each type of TE in the GCO and GSA genome. Fig. S3. Venn diagram of gene function annotation results of different protein database. Fig. S4. Syntenic blocks shared between the GCO and GSA scaffolds. Grey lines connect matched gene pairs. Fig. S5. Enrichment analysis of positive selection genes. Fig. S6. The ML tree was constructed based on 66 individuals. Fig. S7. The heatmap of identity-by-state distance from 58 individuals. Fig. S8. The ML tree of the 58 individuals. Fig. S9. ADMIXTURE analysis with ancestral lineages K from 2 to 9. Fig. S10. CV-error of ADMIXTURE analysis. Fig. S11. The phylogenetic relationships among Garrulax species constructed by SNAPP software. Fig. S12. Treemix phylogeny of Garrulax species with TMI as root. Fig. S13. The population inference estimated by smc++. Fig. S14. Population inference in GCO. Fig. S15. Nucleotide polymorphism (π) of each individual from GCO and GSA. Fig. S16. Nucleotide polymorphism (π) of ten GCO individuals. The grey shadow means homozygosis gap region. Fig. S17. Nucleotide polymorphism (π) of 11 GSA individuals. Fig. S18. Distribution of inbreeding coefficient (F) in eight Garrulax species. Fig. S19. Distribution of π value for the eight Garrulax species. Fig. S20. The scope of π value for eight Garrulax species. Fig. S21. The scope of heterozygosity rate value for eight Garrulax species. Fig. S22. LD pattern (left) and ROH number (right) for each Garrulax species based on GSA genome. Fig. S23. The scope of FROH for eight Garrulax species. Fig. S24. Comparison missense and synonymous mutations between GCO and GSA. Fig. S25. Distributions of heterozygosity Hp and zHp. Table S1. Summary of the sequencing data for the de novo genomes. Table S2. Assembly statistics of the GCO and GSA genomes. Table S3. Base contents of the assembled genomes. Table S4. Read coverage of genome assemblies. Table S5. The completeness of the two assembled genomes was assessed by CEGMA and BUSCO. Table S6. Prediction of repeat elements in the two assembled genomes. Table S7. Categories of repeat elements. Table S8. Prediction of gene structure in two genomes. Table S9. Gene structure of genomes of Garrulax species and other avians. Table S10. Functional annotation of the predicted protein-coding genes in the Garrulax genome assemblies. Table S11. Statistics of noncoding RNAs of the GCO and GSA genomes. Table S12. Positive selection genes (PSGs) identified in GCO and GSA. Table S13. The information of 25 species download from NCBI database. Table S14. Expanded and contracted gene families identified by CAFE. Table S15. Sequencing data quality of 66 individuals. Table S16. Detailed sampling information of 66 sequenced individuals. Table S17. Pair individuals with closely relationship of 66 specimens. Table S18. Evidence of gene flow between Garrulax species. Table S19. Genetic diversity of eight Garrulax species based on a reference genome of white-browed laughingthrush. Table S20. Deleterious variants of blue-crowned laughingthrush and white-browed laughingthrush. Table S22. The overlapping windows identified by top 1% FST and zHp value. Table S25. The 218 STRs makersof blue-crowned laughingthrush. Table S26. The 43 STRs were identified on W-related scaffolds to be used as sex confirmation. Table S27. The Z and W chromosomes of 31 avian.