Additional file 1 of Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioids
Creators: name: Lu, Ying
name: Li, Wenhao
name: Li, Yalin
name: Zhai, Wanying
name: Zhou, Xuming
name: Wu, Zhichao
name: Jiang, Shouwen
name: Liu, Taigang
name: Wang, Huamin
name: Hu, Ruiqin
name: Zhou, Yan
name: Zou, Jun
name: Hu, Peng
name: Guan, Guijun
name: Xu, Qianghua
name: Canário, Adelino V. M.
name: Chen, Liangbiao
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. An eagle’s view of a C. hamastus. Figure S2. Comparison of genome GC Content among 5 notothenioid species. Figure S3. Landscape of the C. hamatus genome at 100 Kb scale. Figure S4. Maximum likelihood trees reconstructed from extracted mitochondrial reads of 52 C. hamastus individuals together with C. myersi and C. rastrospinosus. Figure S5. The phylogeny of the re-sequenced 52 individuals with individual names shown supplementary to Fig. 1C. Figure S6. Characteristics of SNPs identified in the C. hamatus populations. Figure S7. Phylogeny tree depicts the closer relationship between RS1 and the individual of the reference genome (REF). Figure S8. Results of a parallel SNP call from the 52 individuals against an ad-hoc draft genome assembled from only the WGS sequencing reads from a ZD2 individual. Figure S9. Reconstructed phylogenetic tree of ten fishes based on the maximum likelihood method. Figure S10. The demographic histories of C. hamatus populations, RS1, RS2, ZD1, and ZD2, parallelly estimated by Pairwise sequentially Markovian coalescent (PSMC). Figure S11. Corresponding scaled residuals of Fig. 2F from the fit of the TreeMix model to the data. Figure S12. The phylogenetic tree of the trim-35 and trim-39-like homologous genes from three icefish genomes indicating gene family dynamics between the species. Figure S13. Differential survival time after capture by RS1 and RS2. Figure S14. The Venn diagram showing the total number of bacterial species identified in three populations. Figure S15. Principal Component Analysis showing a population-based clustering pattern of the gut microbiota in the three populations. Figure S16. Differentially abundant gut microbiota species specifically associated with RS1, RS2 and ZD1 as determined by LEfSe. Figure S17. The enriched GO list of the positive selection genes identified in C. hamatus, G. aceratus and D. mawsoni, supplementary to Fig. 4G. Figure S18. Phylogenetic analysis and gene evolution of notothenioid fish. Figure S19. Phylogenetic trees of the ZPAX1 and ZPC5 genes contained in the seven Antarctic species. Figure S20. The distribution of dS values of the simulated sequences from the ZPAX1 and ZPC5 trees. Figure S21. The temperature curve along the Ocean depth. Table S1. Statistics of sequencing data. Table S2. BUSCO outputs for the C. hamatus genome. Table S3. Annotated repetitive sequences. Table S4. Statistics of the assemblies for each pseudo-chromosome. Table S5. Functional classification of the protein-coding genes according to different databases. Table S6. Statistics of protein-coding genes predicted by various methods. Table S7. Summary of non-coding RNA genes in C. hamatus genome. Table S8. Collected C. hamatus samples and sequencing statistics. Table S9. SNP calling in 4 populations. Table S10. Tracy-Widom (TW) statistics for the first four eigenvalues form PCA analysis. Table S11. The RS1 specific gene list under selective sweep. Table S12. The RS2 specific gene list under selective sweep. Table S13. The ZD1 specific gene list under selective sweep. Table S14. List of sweep regions of RS1, using an outlier approach in RS2. Table S15. List of sweep regions of RS2, using an outlier approach in RS1. Table S16. List of sweep regions of ZD1, using an outlier approach in RS2. Table S17. The microbial phyla and classes specifically associated with a C. hamatus population. Table S18. The microbial organisms specifically associated with a C. hamatus population. Table S19. ZPAX1 and ZPC5 gene copy number tally in eight notothenioids. Table S20. Data info of genome, annotations and reads used in this study. Data S1-S8 are available from http://ogd.shou.edu.cn/download.html .