The Contribution of Next Generation Sequencing to Help Define Differences in Lake Trout Morphotypes in Lake Superior

New sequencing technologies have exponentially increased our ability to look at the transcriptomes of organisms.  We have used Next Gen sequencing to compare the transcriptomes of lean and siscowet lake trout; two morphotypes from Lake Superior. The siscowet is common in Lake Superior where they make up most of the lake trout biomass.  This fish is characterized by a short convex snout, high fat content in flesh and viscera, deep body, and a short, thick caudal peduncle. These and other metrics distinguish it from the other principal morphotype, the lean lake trout.  The siscowet is a deepwater form found at depths >80 meters, as opposed to lean lake trout that are more restricted to shallower water. Microsatellite analyses indicate that there are population genetic differences between lake trout morphotypes that suggest reproductive separation and perhaps a genetic basis for the differences in morphology and physiology.  However, since the morphotypes also inhabit different environments, it is unclear whether genetics or the environment is ultimately responsible for these differences.  In a common garden rearing study, we raised siscowet and lean lake trout from fertilized eggs under identical environmental conditions for over 5 years.   From year 1 to the present, significant differences in growth, morphometry (truss analysis) and lipid content have been observed between the communally reared siscowets and leans.  At year one, RNAseq analysis using Roche 454 sequencing showed significant differences in the expression of a number of genes in the liver between morphotypes.  Interestingly, the expression of most of those genes was not significantly different by year 2 and 3.  However, several genes identified by this analysis, including a complement-like C1q protein, continue to be differentially expressed at very high levels.  Sequencing of this gene reveals that the difference between morphotypes is a result of differential processing of the transcript resulting in transcripts that likely code for different proteins. The laboratory reared leans and siscowets have also been used for lamprey parasitism experiments to determine if differences in parasitism occur between morphotypes.  RNAseq analysis using the Illumina platform has revealed genes within the livers of the morphotypes that are up and down-regulated as a result of lamprey parasitism.  While some of the genes are shared between morphotypes, others appear to be morphotype-specific.  The use of Next Gen sequencing approaches to compare morphotype transcriptomes has provided a means to globally assess differences without preconceived ideas of which genes may be regulated.