The plant calcineurin B-like protein–CBL interacting protein kinase (CBL–CIPK) signaling pathway is a Ca2+-related signaling pathway that responds strongly to both biological and abiotic environmental stimuli. This study identified eight CBL and eighteen CIPK genes from peach for the first time. Their basic properties and gene structure were analyzed, and the CBL and CIPK members from Arabidopsis and apple were combined to study their evolutionary relationships. Using RT-qPCR and RNA-seq data, we detected the expression patterns of PprCBLs and PprCIPKs in different tissues and fruit development stages of peach. Among them, the expression levels of PprCBL1 and PprCIPK18 were stable in various tissues and stages. The expression patterns of other members showed specificity between cultivars and developmental stages. By treating shoots with drought and salt stress simulated using PEG6000 and NaCl, it was found that PprCIPK3, PprCIPK6, PprCIPK15 and PprCIPK16 were strongly responsive to salt stress, and PprCIPK3, PprCIPK4, PprCIPK10, PprCIPK14, PprCIPK15, PprCIPK16 and PprCIPK18 were sensitive to drought stress. Three genes, PprCIPK3, PprCIPK15 and PprCIPK16, were sensitive to both salt and drought stress. We cloned four PprCBL and several PprCIPK genes and detected their interaction by yeast two-hybrid assay (Y2H). The results of Y2H show not only the evolutionary conservation of the interaction network of CBL–CIPK but also the specificity among different species. In conclusion, CBL and CIPK genes are important in peach and play an important role in the response to various abiotic stresses.

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.