Bank vole heart transciptome 454 reads
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate
Background  Understanding the genetic basis of adaptive changes has been a major goal of evolutionary  biology. In complex organisms without sequenced genomes, de novo transcriptome assembly  using a longer read sequencing technology followed by expression profiling using short reads is  likely to provide comprehensive identification of adaptive variation at the expression level and  sequence polymorphisms in coding regions. We performed sequencing and de novo assembly of  the bank vole heart transcriptome in lines selected for high metabolism and unselected controls.  Results  A single 454 Titanium run produced over million reads, which were assembled into 63,581  contigs. Searches against the SwissProt protein database and the ENSEMBL collection of mouse  transcripts detected similarity to 11,181 and 14,051 genes, respectively. As judged by the  representation of genes from the heart-related Gene Ontology categories and UniGenes detected  in the mouse heart, our detection of the genes expressed in the heart was nearly complete (>95%  and almost 90% respectively). On average, 38.7% of the transcript length was covered by our  sequences, with notably higher (45.0%) coverage of coding regions than of untranslated regions  (24.5% of 5' and 32.7% of 3'UTRs). Lower sequence conservation between mouse and bank vole  in untranslated regions was found to be partially responsible for poorer UTR representation. We  detected widespread transcription from noncoding genomic regions, a finding not reported in  previous studies regarding transcriptomes in non-model organisms. We also identified over 19  thousand putative single nucleotide polymorphisms (SNPs), a much higher fraction than expected  by chance exhibited variant frequency differences between selection regimes.  Conclusion  Longer reads and higher sequence yield per run provided by the 454 Titanium technology in  comparison to earlier generations of pyrosequencing proved beneficial for the quality of  assembly. An almost full representation of genes known to be expressed in the mouse heart was  identified. Usage of the extensive genomic resources available for the house mouse, a moderately  (20-40 mln years) divergent relative of the voles, enabled a comprehensive assessment of the  transcript completeness. Transcript sequences generated in the present study allowed the  identification of candidate SNPs associated with divergence of selection lines and constitute a  valuable permanent resource forming a foundation for RNAseq experiments aiming in detection  adaptive changes both at the level of gene expression and sequence variants, that would facilitate  studies of the genetic basis of evolutionary divergence.