Epigenetics

We collected epigenetics information including chromatin interaction, chromatin accessibility, histone modification and DNA methylation of 6 germplasms from 5 published datasets^[1-5].

Chromatin interaction

We collected Hi-C datasets from 5 germplasms including TM-1 (AD1), ZM4 (AD1), 3-79 (AD2), Shixiya1 (A1) and G. raimondii (D5). Hi-C data were mapped to TM-1 reference genome using BWA-MEM with default parameters and Hi-C format file were created using Juice pipeline. Then, KR normalized matrix were extracted from Hi-C format files at the resolutions of 10kb, 50kb, 100kb using Juicer_tools (version 1.7.6) for visualization. Compartments A/B were firstly identified using eigenvector program in Juicer_tools. TAD-like regions were identified using arrowhead program in Juicer_tools. Users can browse Hi-C heatmaps of all accessions by Jbrowser. Users can search Hi-C interaction frequency, compartment information and TAD regions of all accessions.

Chromatin accessibility

We collected Chromatin accessibility datasets from 4 germplasms including TM-1 (AD1), 3-79 (AD2), Shixiya1 (A1) and G. raimondii (D5). Clean reads were mapped to TM-1 reference genome using Bowtie (version 1.2.0). PCR duplicated reads were removed using Picard tools (version 2.19). Peaks were called using callpeak module of MACS2 software (version 2.1.2) with parameters “--nomodel -q 0.05 --extsize 200 --shift -100 -g 8.84e8 --keep-dup all -B --call-summit”. Users can browse tracks of all accessions in Jbrowser. User can search peaks of all accessions in Chromatin accessibility module by inputting the gene id of interested gene or interested genomic region.

Histone modification

We collected eight kinds of histone modification datasets from 6 germplasms from 5 published datasets, including H3K4me1, H3K4me3, H3K9me2, H3K27me3, H3K9ac, PolII, CENH3 and CH2. Clean reads from all histone modification datasets were mapped to TM-1 reference genome^[6] using Bowtie (version 1.2.0). PCR duplicated reads were removed using Picard tools (version 2.19). Peaks were called using callpeak module of MACS2 software (version 2.1.2) with parameters “--nomodel -q 0.05 --extsize 200 --shift -100 -g 8.84e8 --keep-dup all -B --call-summit”. Users can browse histone modification tracks of all accessions in Jbrowser. User can search histone modification peaks of all accessions in histone modification module by inputting the gene id of interested gene or interested genomic region.

References

[1]	Wang M, Tu L, Lin M, et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication[J]. Nature Genetics, 2017, 49 (4):579.
[2]	Wang M, Wang P, Lin M, et al. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton[J]. Nature Plants, 2018, 4 (2): 90-97.
[3]	Zheng D, Ye W, Song Q, et al. Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton[J]. Plant physiology, 2016, 172 (3): 1760-1771.
[4]	Zheng X, Chen Y, Zhou Y, et al. Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton[J]. Plant Physiology, 2021, 185 (1): 179-195.
[5]	Hu Y, Chen J, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature genetics, 2019, 51 (4): 739-748.
[6]	Huang G, Wu Z, Percy R G, et al. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution[J]. Nature Genetics, 2020, 52 (5).