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(1)) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G(1) was generated, and comparative genomics analysis showed that G(1) was closest to Gossypium australe (G(2)), 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(1) and G(2) genomes. Compared with the G(2) genome, two large fragment inversions in chromosomes 12 and 13 were detected in G(1). According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G(1) was formed by hybridization between Gossypium sturtianum (C(1)) and a common ancestor of G(2) and Gossypium nelsonii (G(3)). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G(1) 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(1) and its mechanism of pigment gland formation and gossypol biosynthesis.