Transcriptome Assembly and Digital Gene Expression Atlas of the Rainbow Trout

                                                       Transcriptome assembly and digital gene expression atlas of the rainbow trout

Background: Transcriptome analysis is a preferred method for gene discovery, marker development and gene expression profiling in non-model organisms. Previously, we generated a transcriptome reference using Sanger-based and 454-pyrosequencing, however, the transcriptome assembly was incomplete and differential gene expression from various tissues was not studied.

Result: Thirteen non-normalized cDNA libraries were sequenced from different tissues using Illumina sequencing.  A total of ~1.167 billion paired-end reads were de novo assembled using Trinity assembler, which yielded 474,524 contigs (>500 bp), of which, 287,593 had significant homology to protein sequences in the NCBI NR protein database. The longest contig of each contig cluster was selected as a reference which yielded 46,457 representative contigs. An EST-Scan of the representative contigs identified 45,291 transcripts with ORF, of which 15,822 were full-length sequences. A digital gene expression atlas was generated by mapping original reads from each tissue to the new transcriptome reference. We identified 7,614 housekeeping and 4,830 tissue-specific genes. Expression of about 17,000-33,000 genes seemed to account for both basic and specialized functions of each tissue, which corresponded to expression of 53%-70% of the total number of genes. Muscle and liver had the least complex transcriptome, with high percentage of their total mRNA contributed by a small number of genes, whereas brain and testis had the most complex transcriptome. The study also identified 4,752 genes with splice variants.

Conclusion: This study provided the most comprehensive assembled and annotated transcriptomic suite of the rainbow trout that is available for functional, structural and comparative genomics research.