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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.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1217-x) contains supplementary material, which is available to authorized users.

The comparison of alternative splicing among the multiple tissues in cucumber