COMPARATIVE GENOMICS OF CHEMOSENSORY GENE FAMILIES AMONG MEMBERS OF THE HELIOTHINAE

Abstract

Insect chemosensory systems play crucial roles in the perception of chemical signals that regulate sexual behaviors and odors that mediate insect-host plant interactions. These processes, mate-finding and acceptance, as well as host plant identification and use, strongly contribute to diversification and speciation among plant-feeding insects, including the Lepidoptera. Chloridea virescens and Chloridea subflexa are an ideal pair species to study the evolution of insect chemosensory systems because they are closely related but show pheromone-based sexual isolation and divergent host plant preferences. My dissertation focuses on the development of genomic tools that enable investigation into genetic mechanisms of host plant and mate recognition, and applies these tools to examine inter- and intraspecific diversity of chemosensory genes among members of the Heliothinae.In chapter 2, I produced a novel Illumina short read C. subflexa genome assembly and an improved, highly contiguous C. virescens genome assembly. Due to quality limitations common to short read assemblies, I used our Heliothine genomes to examine the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa. My work demonstrated that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. Both the potential and pitfalls of reference-assisted assembly are discussed in light of my results. In chapter 3, I manually curated two chemosensory gene families, the odorant receptors (ORs) and odorant binding proteins (OBPs), in C. virescens. In total, I identified 80 ORs, 1 Orco and 49 OBPs. Three types of OBPs were identified according to the number and positions of conserved cysteine residues: 34 classic OBPs, 8 Minus-C OBPs, and 7 Plus-C OBPs. In addition, I used phylogenetic analyses to study evolutionary divergence of OR and OBP gene families among Heliothine moths, which revealed both gene duplications and losses. In chapter 4, I studied the strength and nature of selection on the ORs of field-collected C. virescens and C. subflexa, with focus on the pheromone receptor genes. I characterized the host plant use of these species in central Maryland by comparing the larval densities and infestation rates in 2020 and 2021. Sequencing followed by analysis of selection on field-collected samples indicated that the pheromone receptor, OR6, was under very strong purifying selection in both C. virescens and C. subflexa. AMOVA tests suggested that in C. virescens, host plant-associated population differentiation existed in genes OR6, OR55, OR66 and OR78. Further analyses of genetic divergence analysis focused on OR6 showed that the most highly divergent sites were all in introns. The new genomic tools and analyses of chemosensory gene families described here will serve as a platform for future investigations into the genetic mechanisms underlying host plant specialization and sexual communication among lepidopteran insects.