Global transcriptome diversity of Desi cotton (Gossypium arboreum) using long reads technologies

Gossypium arboreum (AA, 2n = 26), also known as Desi cotton or Asiatic cotton, is an important cultivated cotton species and a putative contributor of the A sub-genome to the modern tetraploid cotton; and inherently tolerant to several biotic and abiotic stresses. Alternative splicing (AS) is a common mechanism in eukaryotes to increase the complexity and diversity of transcriptomes and subsequently proteomes. Analysis of RNA-seq data can result in the discovery of several new transcripts, splice sites and alternative splicing events in the cotton transcriptome. In this study, we sequenced the G. arboreum transcriptome under three different conditions i.e. untreated / healthy, treated with biotic stress through whitefly infestation and treated with abiotic stress via water deprivation. RNA sequencing has been conducted using PacBio IsoSeq sequencing for the discovery and surveying of alternative splicing events. We identified 15419 AS events in G. arboreum that were divided into different structural categories of alternative splicing isoforms including 60 Anti sense, 11959 Full-splice match, 30 Fusion, 177 Genic, 999 Incomplete-splice match, 479 Intergenic, 771 Novel in catalog and 944 Novel not in catalog. Subsequently, randomly selected candidate transcripts were experimentally validated using qRT-PCR. Our comprehensive identification of canonical and non-canonical splicing events, novel and fusion transcripts will aid in improvement of the cotton transcriptome annotation.