The comparison of alternative splicing among the multiple tissues in cucumber

Abstract

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

Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing

“…For most of the differentially spliced regions, both forms were 440 present, and the difference in relative abundance between forms was often slight, rarely more 441 than five or ten percent ( Supplementary Table S1). Our data supports the growing body of 442 evidence that alternative splicing is cell, tissue, and stage specific in plants (Vitulo et al, 2014;443 Gupta et al, 2015;Li et al, 2016a;Sun et al, 2018), including in roots (Li et al, 2016b). It is 444 likely that alternative splicing plays a role in fine-tuning gene function to meet the needs of 445 different plant tissues or cell types where a gene is expressed.…”

“…SR transcripts 66 themselves are also highly alternatively spliced in plants, with the relative abundance of these 67 alternative transcripts varying according to environmental stresses and hormones (Palusa et al, 68 2007;Gulledge et al, 2012;Filichkin et al, 2015a;Keller et al, 2016;Mei et al, 2017). 69 A growing body of evidence indicates that cell and tissue specific regulation of alternative 70 splicing occurs in plants, but its significance and extent is not well established (Vitulo et al, 71 2014;Li et al, 2016a;Sun et al, 2018). We previously found through analysis of RNA-Seq data 72 from Arabidopsis pollen that the relative abundance of splice variants was similar between 73 leaves and pollen, despite the differences between the two tissues (Loraine et al, 2013).…”

Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

“…9a). Previous studies indicated that alternative spliced transcripts have tissue-specific expression in various plants [61][62][63][64]. For novel splice junctions in B. rapa, 34.4% of alternative spiced transcripts were detected in only one tissue [45].…”

CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers

“…sativus cv. 9930, we assembled transcripts by using TopHat and Cufflinks [16], respectively. These sets of transcripts were then compared with the reference genome annotation file using Cuffcompare.…”