Divergence of two cultivated allotetraploid cottons unveiled by single-molecule long-read expression sequencing

Allotetraploid Gossypium hirsutum and G. barbadense are two major cultivated cotton species that have different fiber traits. Research into the molecular basis of those differences is limited by a lack of accurate, complete transcript profiles. Here we adopted joint PacBio Iso-seq and RNA-seq to investigate genome-wide transcript profiles and uncover differences in the expression between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. We obtained 178,867 full-length transcripts covering 60.0% of gene loci in the TM-1 reference annotation, including 7846 transcription factors and 3122 lncRNAs. Moreover, we identified 304 and 610 high-confidence (HC) species-specific transcripts in TM-1 and Hai7124, respectively, along with 4156 and 4381 tissue-specific transcripts. Our results update the reference genome annotation and also provide potential resources for studying the molecular mechanisms of fiber development. We are thus able to promote improvements in cotton fiber quality.