RNA-Seq Reveals Patterns of Immune Gene Activation in the Livers of Lake Trout Morphotypes in Response to Lamprey Parasitism in the Lab

Sea lamprey cause extensive mortality to lake trout in the Great Lakes, but relatively little is known about their sub-lethal effects.  Laboratory-reared lean and siscowet lake trout that are part of a common garden rearing study, were parasitized by lamprey in the laboratory and the livers were collected. Differences in the hepatic transcriptome between parasitized and nonparastized lean and siscowet lake trout were determined using RNA-Seq.  RNA was extracted from parasitized and nonparasitized lean and siscowet livers and individually sequenced using the Illumina HiSeq platform.  Sequences were pooled to build a de novo assembled reference using the Trinity sequence assembler.  Each sample was individually mapped to the reference to determine gene count (expression) and count levels were statistically analyzed using DESeq2, edgeR, and baySeq. Regulated genes were analyzed using Ingenuity Pathway Analysis. Many of the regulated genes were involved with the immune system including chemokines and Toll-like and interleukin receptors as well as enzymes such as indoleamine 2,3 dioxygenase (IDO) that mediate local effects on innate and adaptive immune responses to inflammation.  IDO, that regulates tryptophan availability through the kynurenine pathway, is also regulated during infection by protozoan parasites in mammals and may be important in immunorecognition.