| dc.description.abstract | The increasing availability of genomic data necessitates improved methods for whole-genome comparison. The study of complex phenotypes, especially, will benefit from comparative methods that are comprehensive across whole genomes. Here, I add to the growing amount of genomic insect pest data with a de novo assembly of the southern pine beetle (SPB), Dendroctonus frontalis, transcriptome. The SPB, a wood-boring beetle (WBB), is a major forest pest that is responsible for $1.5 billion of losses in natural and agricultural stands of Loblolly (Pinus taeda L.) and other yellow pine stands throughout the southeastern United States. I show that this transcriptome, assembled with RNAseq data from males, females, and larvae, contains 94.1% of the BUSCOs for the Endopterygota superorder, and indication of a nearly complete gene set. Next, I introduce methods for comparison of gene family changes across the genomes of multiple species of wood-boring beetles, which belong to independently evolved WBB lineages, and non-wood-boring beetles, with two goals: First, I aimed at testing hypotheses regarding the extent of convergent gene family changes associated with the independent evolution of WBBs; Second, I sought to identify candidate gene families contributing to the complex wood-boring phenotype. The comparisons of gene families did not show excess convergent loss or gain in the WBB gene family change pairwise comparisons. However, the methods to tests gene family convergence presented here can be applied to any system with convergent phenotypes, high-quality genomic resources and accurate phylogenetic inferences. Furthermore, I identified several gene families with shared expansions and contractions along the three WBB branches of the beetle phylogeny. The gene families sharing expansions and contractions in WBBs include genes involved in chitin metabolism, organization of the cuticle, cuticle development, immunity, and hormone metabolism. These findings significantly expand the number of genes and biological processes that may contribute to the wood-boring phenotype, beyond well-known examples among chemosensorial families. The integration of available WBB genomic resources with novel data sets, including the SPB gene set, will further improve the ability to understand the genetic underpinning of the wood-boring habit. These efforts should accelerate the discovery of next-generating management strategies for tree-killing outbreaks based on genetic and genomic information. | en |
