Unrevealing the transcriptome complexity of octoploid strawberry through ONT long read sequencing

Despite the advances in the finding of genome-wide alternatively spliced genes in strawberry, it remains unexplored how AS responds to developmental cues and what relevance of these outcomes have been linked to the gene function. In this study, we have systematically investigated the transcriptome complexity using long-read Oxford Nanopore Technologies along the four successive developmental stages. The full-length cDNA sequencing results unraveled thousands of previously unexplored AS isoforms. Alternative transcription start site (aTSS) and alternative transcription termination site (aTTS) were the two AS types that were more abundant than intron retention. Differentially expressed transcripts unrevealed the key transitional role of the white fruit stage. Isoform switches of transcripts from 757 genes with protein-coding potential change and domain gain or loss as the main consequences were observed. These genes with switched isoforms take part in key processes of maturation processes in the late maturation stages.