Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Abstract

BackgroundUnderstanding 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.ResultsA 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. Our data might suggest a 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 of the SNPs than expected by chance exhibited variant frequency differences between selection regimes.ConclusionLonger 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 at detection of adaptive changes both at the level of gene expression and sequence variants, that would facilitate studies of the genetic basis of evolutionary divergence.

Determinants of intra-specific variation in basal metabolic rate

“…The existence of an association between the effects of artificial selection on aerobic capacity and the genetics of heart muscle metabolism has also been confirmed by Babik et al (2010) in a non-model rodent—the bank vole ( Myodes glareolus ). Babik et al (2010) used 454 sequencing technology (for review see Wheat 2010) followed by expression profiling of the heart transcriptome in lines of bank voles selected for high metabolism as compared to unselected controls (Sadowska et al 2008).…”

“…They detected a number of putative single nucleotide polymorphisms (SNPs) between selection lines whose variant frequency differences were much higher than those expected by chance. Although the exact causal link between identified SNPs and the underlying response to selection on metabolic rate remains unclear, Babik et al’s (2010) study exemplifies the potential offered by new generation sequencing technologies for studying BMR in animals whose genome sequences are not available (see also Vera et al 2008). …”

“…Babik et al (2010) used 454 sequencing technology (for review see Wheat 2010) followed by expression profiling of the heart transcriptome in lines of bank voles selected for high metabolism as compared to unselected controls (Sadowska et al 2008). They detected a number of putative single nucleotide polymorphisms (SNPs) between selection lines whose variant frequency differences were much higher than those expected by chance.…”

Evolution of basal metabolic rate in bank voles from a multidirectional selection experiment

“…Therefore, the selected lines provide a promising foundation for investigating both underlying molecular mechanisms responsible for differences observed at the organismal level [51,52] and a wide range of possible correlated responses [53 -55].…”

Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

“…This filter parameter is still stricter than that in the bank vole study [14]. Therefore, for a small risk of false positives, we can also use some of these lower confidence SNP's to increase the total set of SNPs by about 50% to around 45,000 SNPs.…”