Improved Annotation of the Peach (Prunus persica) Genome and Identification of Tissue- or Development Stage-Specific Alternative Splicing through the Integration of Iso-Seq and RNA-Seq Data

Abstract

Alternative splicing (AS) is an important way to generate notable regulatory and proteomic complexity in eukaryotes. However, accurate full-length splicing isoform discovery by second-generation sequencing (SGS) technologies is beset with the precise assembly of multiple isoforms from the same gene loci. In recent years, third-generation sequencing (TGS) technologies have been adopted to gain insight into different aspects of transcriptome complexity, such as complete sequences of mRNA, alternative splicing, fusion transcript, and alternative polyadenylation (APA). Here, we combined PacBio Iso-Seq and Illumina RNA-Seq technologies to decipher the full-length transcriptome of peach. In total, 40,477 nonredundant high-quality consensus transcript sequences were obtained from equally pooled libraries from 10 samples of 6 organs, including leaf, shoot, flower, fruit peel, fruit mesocarp, and fruit stone, of which 18,274 isoforms were novel isoforms of known genes and 546 isoforms were novel gene transcripts. We also discovered 148 fusion transcripts, 15,434 AS events, 508 potential lncRNAs, and 4368 genes with APA events. Of these AS events, the most abundant (62.48%) AS type was intron retention (IR). Moreover, the expression levels of different isoforms identified in this study were quantitatively evaluated, and highly tissue- or development stage-specific expression patterns were observed. The novel transcript isoforms and new characteristics of the peach transcriptome revealed by this study will facilitate the annotation of the peach genome and lay the foundations for functional research in the future.