Multi‐omics mapping of chromatin interaction resolves the fine hierarchy of 3D genome in allotetraploid cotton

High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

“…We then polished the contigs using ∼50× Illumina paired-end reads to correct SNPs and small insertions/deletions in the sequencing reads ( Wang et al., 2019 ). The polished contigs were scaffolded into 26 chromosomes using high-throughput chromosome conformation capture (Hi-C) data ( Huang et al., 2022 ; Pei et al., 2022 ), and 99.05% and 97.4% of the contig sequences were anchored to TM-1 and 3-79 ( Supplemental Tables 3 and 4 ), respectively. The final chromosome-scale genomes were 2324 Mb (TM-1 HAU v2) and 2254 Mb (3-79 HAU v3) in length and included 556 and 1662 scaffolds, respectively ( Table 1 ; Supplemental Table 3 ).…”

“…To improve base quality, we aligned Illumina paired-end reads (∼50×) to contigs using BWA–MEM and polished them with Pilon (version 1.23) (--fix bases --mindepth 10 --minmq 30) ( Li, 2013 ; Walker et al., 2014 ). High-quality paired-end Hi-C reads based on DpnII ( Huang et al., 2022 ; Pei et al., 2022 ) for G. hirsutum TM-1 and G. barbadense 3-79 were mapped to the two contig-scale assemblies using Juicer (version 1.6) ( Durand et al., 2016b ). The original contigs were organized into chromosomes with the 3D-DNA pipeline (version 180 419) (-r 2 -i 15000 --build-gapped-map) ( Dudchenko et al., 2017 ).…”