Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton

Abstract The polyploid genome of cotton greatly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such circumstances in cotton can help us explore the genetic mechanisms of the early seedling growth dynamics of cotton. This study, through long-read single-molecule sequencing, compared the transcriptomes of three yield-contrasting genotypes of upland cotton. Our analysis identified a diversity of spliced isoforms in each genotype, of which most were novel compared to previous cotton reference transcriptomes and had significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant expression differences in the root and leaf of each genotype. An array of core isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Divergent spliced isoforms with differential regulation from the GIGANTEA (GI) are expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate rhythmic expression profiles in cotton leaves, which may change the transcriptional regulatory network. Silencing of GI novel spliced isoforms Gh_A02G0645_N17 significantly impacts biomass traits in cotton and contributes to variability in growth and development. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid genome of cotton.