Genome Assembly
The draft mountain pine beetle genomes were assembled a decade ago from paired-end and mate-pair Illumina sequences during the early development of long-read sequencing and proximity ligation sequencing technologies. Since then, analytical tools have improved and new assembly tools have been developed to incorporate long-read and proximity ligation sequencing technologies (Amarasinghe et al., 2020). An upsurge of chromosome-level assemblies is currently being published using these new approaches and tools, including for many insects. We used proximity ligation sequencing and the improved analytical tools, along with linkage map information to enhance the draft mountain pine beetle genome assemblies. Most of the assembly content was present in chromosome-sized scaffolds. Linkage map information provided critical complementary information that highlighted inconsistencies in the proximity ligation-based assemblies. Although we saw no evidence of draft scaffolds being incorrectly associated with each other, we found several instances of incorrect local ordering and orientation. This typifies the recurring challenges of this approach. However, bioinformatic tools to reduce these errors continue to develop and improve (e.g., Nakabayashi & Morishita, 2020).
At present, genomes are published for only two other bark beetle species (Curculionidae: Scolytinae): the coffee borer beetle, Hypothenemus hampei (Ferrari) (Vega et al., 2015), and the European spruce bark beetle, Ips typographus L. (Powell et al., 2020). Although the latter was completed with long-read PacBio sequences, our use of the complementary approaches of proximity ligation sequencing and linkage map data for scaffolding existing draft genomes resulted in more contiguous assemblies. However, gene content was similarly complete between assemblies (95.6% for I. typographus versus 95.2% and 94.8%, for the female and male mountain pine beetle assemblies, respectively, based upon BUSCO v4.1.4 with insecta_odb10, created 2020-09-10).