A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype.

ABSTRACT:

Background

Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes.

Results

We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. Several gene structures have been improved and alternative splicing was described for about 30% of the genes. A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. A quantitative analysis of the isoforms indicated that most of the

SUBMITTER: Vitulo N 

PROVIDER: S-EPMC4108029 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature