Comparative genomics of the chitinase gene family in lodgepole and jack pines: contrasting responses to biotic threats and landscape level investigation of genetic differentiation

Abstract

The sister species, lodgepole pine (Pinus contorta var. latifolia Engelm.) and jack pine (Pinus banksiana Lamb), face pressures from a multitude of biotic agents, including mountain pine beetle (Dendroctonus ponderosae Hopkins, 1902) and their pathogenic fungal associates (e.g., Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf.), mistletoe (Arceuthobium americanum Nutt. ex A.Gray), and the pathogen causing western gall rust (Cronartium harknessii E. Meinecke). Here, we report new stem tissue transcriptome resources developed for lodgepole and jack pines subjected to these biotic stresses. The annotated transcriptomes were compared to determine species-specific responses to the necrotrophic G. clavigera and the biotrophic Cronartium harknessii. We focused on chitinases, a family that includes members with well-documented roles in defense. Putative chitinase family members were identified via annotation, sequence similarity to reference chitinase genes, phylogenetic analyses, and in silico motif characterization. RNA-Seq revealed marked differences in the responses of lodgepole and jack pine chitinases to G. clavigera and Cronartium harknessii. The potential for adaptive variation in chitinases was investigated by assessing the level of genetic differentiation between and within lodgepole and jack pines using single nucleotide polymorphisms within chitinases. These analyses illustrate the potential of combining transcriptomic and genotyping resources to investigate genotype–phenotype correlations for non-model species.