Major changes in gene expression between strains of diapausing and non-diapause spruce budworm

To survive harsh winter conditions, many insects enter a state of dormancy called diapause which allows them to withstand extreme temperatures and lack of food. When diapause is induced, insects enter a state of arrested development with a low metabolic rate. Because diapause and environmental conditions are closely linked, variation within and between species in diapause induction, depth, and duration is extremely common. Studies investigating the genetic underpinnings of diapause tend to focus on either different populations and/or environmental variation. We use the eastern spruce budworm (Choristoneura fumiferana) to investigate within-population variation in diapause induction. Typically, C. fumiferana diapauses as second instar larvae, but a small subset of individuals do not diapause and instead continues through development. This non-diapause phenotype can be selected to create a non-diapause strain. Here, we present a chromosome-level assembly of such a non-diapause strain and compare it to an earlier published genome assembly of the diapause strain. Despite the very large life history difference, we did not find evidence of major chromosome rearrangements, indicating that the genetic variation between strains is likely small. Gene expression comparisons between the strains indicate major gene expression changes, where genes associated with glycolysis and environmental signaling processing increase in expression in the diapause strain. Lastly, we found that gene expression diverges halfway through the first instar.