A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol.

The pigment gland is a morphological characteristic of Gossypium and its related genera. Gossypium bickii (G) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G was generated, and comparative genomics analysis showed that G was closest to Gossypium australe (G), followed by A- and D-genome species. Two large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypium genomes and were unique to the G and G genomes. Compared with the G genome, two large fragment inversions in chromosomes 12 and 13 were detected in G. According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G was formed by hybridization between Gossypium sturtianum (C) and a common ancestor of G and Gossypium nelsonii (G). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G were verified to be consistent with its phenotype, and nine genes that were related to the process of pigment gland formation were identified. A novel gene, GbiCYP76B6, regulated by GoPGF, was found to affect gossypol biosynthesis. These findings offer insights into the origin and evolution of G and its mechanism of pigment gland formation and gossypol biosynthesis.