Chromosome-level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)

Abstract

Genome sequencing methods and assembly tools have improved dramatically since the 2013 publication of draft genome assemblies for the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). We conducted proximity ligation library sequencing and scaffolding to improve contiguity, and then used linkage mapping and recent bioinformatic tools for correction and further improvement. The new assemblies have dramatically improved contiguity and gaps compared to the originals: N50 values increased 26- to 36-fold, and the number of gaps were reduced by half. Ninety percent of the content of the assemblies is now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Based on linkage mapping information, the 12 largest scaffolds in both assemblies represent all 11 autosomal chromosomes and the neo-X chromosome. These assemblies now have nearly chromosome-sized scaffolds and will be instrumental for studying genomic architecture, chromosome evolution, population genomics, functional genomics, and adaptation in this and other pest insects. We also identified regions in two chromosomes, including the ancestral-X portion of the neo-X chromosome, with elevated differentiation between northern and southern Canadian populations.

Sex chromosome evolution in beetles

“…Those species include: Pogonus chalceus (V an B elleghem et al . 2018), Propylea japonica (Z hang et al 2020), Chrysomela aeneicollis (Bracewell et al submitted), Photinus pyralis (F allon et al 2018), Tribolium castanem, Tribolium confusum (present study), and Dendroctonus ponderosae (K eeling et al . 2022).…”

“…To further explore the evolution of neo-sex chromosomes in beetles, we investigated the mountain pine beetle D. ponderosae (K eeling et al 2022), where females contain twelve pairs of chromosomes (11 autosomes, and a large neo-X chromosome) (L anier and W ood 1968). Importantly, the ancestral part of the neo-X/X chromosome (i.e., the part homologous to the X in T. castaneum ) shows half the coverage in males compared to females ( Figure 3B ); the neo-X (that is, the part homologous to LG2 and LG4 of T. castaneum ), however, only shows a modest coverage reduction in males and is heterogenous across its length ( Figure 3B ).…”

Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens

“…LG10 in RTB also exhibited unique synteny with the P. pyralis LG3a which corresponds to chromosome X. During the review process of this manuscript, a chromosome-level genome assembly of D. ponderosae was reported [37]. We also performed a genome-wide synteny analysis between D. valens and D. ponderosae (Additional file 2: Figure S4).…”

Tolerance to dietary linalool primarily involves co-expression of cytochrome P450s and cuticular proteins in Pagiophloeus tsushimanus (Coleoptera: Curculionidae) larvae using SMRT sequencing and RNA-seq

“…Notably, high-quality genomes of Dendroctonus spp. recently published provide valuable references for interaction studies between the Curculionoidea superfamily and their host terpenoids [47,48]. In this context, some rapidly expanded and positively selected genes related to metabolic capacity, including cytochrome P450 and glutathione S-transferase gene families, were thought to promote Dendroctonus adaptations to oleoresin terpenoids in conifers [48,49].…”