Genome-Wide Survey of Alternative Splicing in <italic>Actinidia chinensis</italic>

Abstract

Alternative splicing can increase the diversity and complexity of proteome greatly through creating multiple mRNA transcripts from a single gene. RNA-seq data from different organs (leaf, immature fruit, half-ripe fruit and mature fruit) of Actinidia chinensis had been used to identify the alternative splicing events using the A. chinensis genome as reference, and totally 32180 alternative splicing events were discovered from the A. chinensis genome (39040 genes) corresponding to 11651 genes (29% of the total genome). Intron retention events showed the highest frequency (more than 50%) among all the different alternative splicing events. The frequency of events with alternative 3 splice sites was twice than the alternative 5 splice sites. GO enrichment analysis result showed that the alternative splicing gene was mainly enriched in enzyme regulation and nucleotide binding related GO categories. The alternative splicing events in different organs of A. chinensis seemed to preferentially occur in genes with important function. The genes of leaf were associated with the function of actin and microtubule. The genes of immature fruit decided the function of two-component signal system. The genes of half-ripe fruit were connected with phospholipid synthesis process. The genes in mature fruit were associated with signal transduction. In addition, 55.6% of vitamin related genes had been found to have alternative splicing changes, which were significantly higher than the average changes of the genome (the average splicing change level was 29.6%). Those explained that alternative splicing events played an important role in the process of vitamin synthesis. In this paper, through the genome-wide analysis of alternative splicing in A. chinensis , a powerful resource for understanding the complex genome of A. chinensis was provided. The result was also useful to molecular breeding in kiwifruit.