Additional file 1 of Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae)
Creators: name: Li, Xiaochong
name: Wang, Jinbin
name: Yu, Yanan
name: Li, Guo
name: Wang, Jinpeng
name: Li, Changping
name: Zeng, Zixian
name: Li, Ning
name: Zhang, Zhibin
name: Dong, Qianli
name: Yu, Yiyang
name: Wang, Xiaofei
name: Wang, Tianya
name: Grover, Corrinne E.
name: Wang, Bin
name: Liu, Bao
name: Wendel, Jonathan F.
name: Gong, Lei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. Synteny breaks identified by setting different minimal number of syntenic genes (5, 8, 10, 20, and 30) enclosed in colinear syntenic blocks in paired comparisons (G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii). Fig. S2. Genomic gene synteny identified in G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii genomes. Fig. S3. Characterization of synteny breaks in diploid Gossypieae species. Fig. S4. Reproducibility and resolution of Hi-C data. Fig. S5. Genome-wide Hi-C contact maps constructed in G. arboreum, G. raimondii, and G. kirkii. Fig. S6. Relative distribution of orthologous chromosomes that were not involved in inter-chromosomal rearrangements mediating the descending dysploidy in Gossypioides kirkii. Fig. S7. The chromosomal landscape of genomic and epigenomic features within identified A/B compartments in G. kirkii, G. arboreum, and G. raimondii. Fig. S8. DNA methylation and histone modification near (±2 kb) the gene body of stable (A/B compartment status stable) and switched genes (A/B compartment status switching/transitions). Fig. S9. Representative IGV snapshots illustrating the A/B compartment, epigenetic features (DNA methylation and histone modifications), and gene models around the synteny break in G. arboreum vs. G. kirkii (top) and G. raimondii vs. G. kirkii (bottom). Fig. S10. Profile of TADs identified in G. kirkii, G. arboreum, and G. raimondii, respectively. Fig. S11. No statistically significant co-localization between synteny breaks and TADs interior bodies and intervals. Fig. S12. Fractions of TAD boundaries overlapping with breakpoints of inversion and translocation identified in comparisons of G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii are statistically higher than those randomization controls, which involve groups of shuffled TAD boundaries, shuffled breakpoints, and both TAD boundaries and breakpoints shuffled simultaneously. Fig. S13. Abundance of transposable element (TEs) in boundaries of TAD groups (large and small TADs) in G. kirkii, G. arboreum, and G. raimondii, respectively. Fig. S14. Open-chromatin epigenetic and active transcriptional features of TAD boundaries co-localizing with synteny breaks. Fig. S15. The relationships between genomic rearrangements and epigenetic modifications of syntenic genes for conserved TADs. Table S1. Summary of clean Hi-C reads. Table S2. Summary of uniquely mapped Hi-C reads. Table S3. Summary of valid Hi-C reads. Table S4. Pearson correlations of overall chromosomal distributions in G. kirkii, G. arboreum, and G. raimondii. Table S5. Epigenetic data from public databases.