Supporting data for "A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of Chinese No.1 cotton variety CRI-12"

<i>Gossypium hirsutum</i> L. is the most widely cultivated cotton species, and a high-quality reference genome is necessary for researching the molecular mechanism of agronomic traits in cotton. Here, we adopted the PacBio platform and Hi-C sequencing technologies to assemble a new upland cotton genome of the Chinese No.1 cotton variety CRI-12. We generated a high-quality assembled CRI-12 genome of 2.31 Gb with a contig N50 of 19.65 Mb, which was superior to reported genomes. Comparisons between CRI-12 and other reported genomes revealed 7,966 structural variations (SVs) and 7,378 presence/absence variations (PAVs). The distribution of the haplotypes among A-genome (<i>G. arboreum</i>), D-genome (<i>G. raimondii</i>), and AD-genome (<i>G. hirsutum</i> and <i>G. barbadense</i>) suggested that many haplotypes were lost and recombined in the process of polyploidization. More than half of the haplotypes that correlated with different tolerances were located on chromosome D13, suggesting that this chromosome may be important for wide adaptation. In addition, DNA methylation may provide adaptive advantages in environmental adaptation by whole-genome bisulfite sequencing (WGBS) analysis. This research provides a new reference genome for molecular biology research on <i>Gossypium hirsutum</i> L. and decodes the broad environmental adaptation mechanism in the Chinese No.1 cotton variety CRI-12.