Integrated Isoform-Resolved Transcriptomic Analysis of Gossypium barbadense and Gossypium hirsutum Fibers

Abstract A comprehensive understanding of RNA expression and splicing during cotton fiber development plays a crucial role in explaining the differences in fiber quality between two different cotton species. To date, most cotton transcriptomic studies have utilized short-read sequencing data, which limits the ability to capture full-length mRNAs. In this study, we compiled long-read RNA sequencing data from the PacBio platform, as well as short-read RNA sequencing data from 10 fiber developmental stages, for both Gossypium barbadense and Gossypium hirsutum . We identified 183,767 and 178,994 isoforms in Gossypium barbadense and Gossypium hirsutum , respectively, generating the most comprehensive transcriptomic atlas of cotton to date. Alternative splicing events exhibited stage-specific variations during fiber development, and co-expression network analysis, combined with LASSO regression, identified isoforms highly correlated with each developmental stage. These findings reveal previously uncharacterized aspects of isoform regulation during fiber development and provide valuable resources for further research into the molecular mechanisms underlying fiber quality differences between cotton species.