The spatio-temporal landscape of the transcriptome and metabolome of cotton fiber cells during their initiation and late development

Abstract Cotton fibers develop from epidermal cells in the outer integument of ovules. The regulatory process underlying fiber cell development has been extensively studied, little is known about the spatio-temporal profiles of transcriptomes and metabolomes during its development. Here we characterized the dynamics of transcriptome and metabolome during the early developmental stages of cotton fiber cells using a combination of spatial transcriptomic, single-cell transcriptomic, and spatial metabolomic analyses. We identified the key genetic regulators and metabolites that initiate and determine the fate of fiber cells. Both knockdown and gain-of-function analyses of one new identified marker gene BEE3/Gh_A09G062900revealed its important role in the initiation of cotton fiber. We also designed a website for the public visualization of spatial gene expression in cotton that provides important reference datasets of spatio-temporal gene expression and can be used to further decipher the genetic and metabolic regulation of cotton fiber development (http://CottonOvule.cricaas.com.cn/).