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).