The comparison of alternative splicing among the multiple tissues in cucumber

Abstract

Background: Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored.

Results: To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts.

Conclusions: Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.

Keywords: Alternative splicing; Cucumber; Tissue-specific; Tissues.

Fig. 1

Statistics of different AS events

Fig. 2

GO enrichment of genes with more AS events

Fig. 3

GO enrichment of genes with only IR events

Fig. 4

Numbers of different AS event types in the ten tissues

Fig. 5

The cluster of AS event profiles of ten tissues

Fig. 6

GO enrichment analysis of genes with tissue-specific AS events in ten tissues. The colour square represents $-{log}_{10}^{p-\mathit{\text{value}}}$ for the enrichment of GO terms. Red indicates that the term is significantly enriched, and black represents no enrichment in the term. a Molecular function. b Biological process

Fig. 7

Clustering of genes by IR patterns. a The hierarchical clustering of IR genes. The red line was drawn at the height of 0.95, and these genes were classified into 12 parts. b Features of IR genes and p-values by Kruskal–Wallis rank sum test. c The length of the retained introns. d GC percentage of the retained introns. e Exon number of genes. f FPKM of major isoforms