Comparative single-cell RNA sequencing reveals cellular types involving gossypol synthesis in upland cotton (Gossypium hirsutum L.) roots

Cotton (Gossypium spp.) is one of the most important cash crops globally for natural fiber and essential vegetable oil sources. As the most vital second metabolite, gossypol and related sesquiterpene aldehydes in cotton function as phytoalexins against pathogens and pests but pose human health concerns. Elucidation of the gossypol biosynthetic pathway started decades ago, and the root was considered the main organ to synthase the gossypol. However, until now, the root cell types involving gossypol synthesis remain known rarely. Here, we used a single-cell RNA-seq of > 20 000 single cells to document the gene expression landscape in the root of upland cotton involving distinct gland phenotyping species. In this research, the major cell types were identified in cotton initially. Moreover, we constructed a single-cell atlas and characterized the distinct gene expression patterns involving gossypol synthesis. The results indicated root cap types were the main cell type in response to gossypol synthesis.