Tissue‐Specific Alternative Splicing in Rainbow Trout

Alternative splicing allows generations of different RNA transcripts from the same genes which produce structurally and functionally different proteins/isoforms. Determining the alternative splice variants answers important questions in the genome biology of any species. Emergence of the next-generation RNA sequencing (RNA-seq) technology offers unprecedented opportunity for genome-wide detection of alternative splicing. However, detection of alternative splicing in non-model species, where a complete reference genome is not available, is one of the most challenging bioinformatics problems.

In this study, a new approach is introduced to detect alternative splicing without the need to a reference genome. The main concept of this method is “Splice Detection through Gap Existence” “SDTGE”. The method is based on the fact that splice variance leads to gap formations when sequence reads with splice variances (e.g., from different tissues) are mapped back to a transcriptome reference that is assembled from all reads.

In this study, thirteen cDNA libraries were sequenced from different tissues of a rainbow trout fish using Illumina platform.  A total of ~1.2 billion reads were de novo assembled using the Trinity RNA-Seq assembler. 15,802 full-length sequences were identified and used as a reference.  The reads were then mapped to these sequences. Using the SDTGE approach, a large number of putative splice variant events were identified.  These data are currently being validated using other in silico and in vitro approaches.  This method is promising in detecting splice variance in non-model species including many of the agriculture species