Introduction
The exponential increase in the availability of whole genomes over the
past decade has largely been derived from short-read sequences. However,
while short reads can be assembled into larger contigs and scaffolds,
sequencing gaps and repetitive regions often prevent full contiguous
assembly and correct ordering (Fierst, 2015). Many genomes assembled
from short reads remain highly fragmented and are best considered draft
versions. Long-read sequencing technologies can overcome some issues
associated with gaps and repetitive regions, but they suffer from higher
sequencing error rates (Bleidorn, 2015; Rhoads & Au, 2015). Chromosome
conformation capture sequencing, or Hi-C, is a method to study
three-dimensional folding of chromosomes that offers an elegant solution
to these challenges. Specifically, the Hi-C method detects closely
linked sections (approximately 10-100 Kb) of DNA via chromatin contacts
(van Berkum et al., 2010), producing highly accurate information on
chromosome-scale genomic position (Cairns et al., 2016). When the Hi-C
approach is coupled with an existing short-read draft genome,
scaffolding is dramatically improved by additional anchor points
interspersed throughout the short-read assembly (Li et al., 2018).
The availability of high-quality whole genomes facilitates an enhanced
understanding of genomic organization, the mechanisms that lead to
deviations from ‘common’ architectural patterns, and the potential
outcomes of such deviations. For example, a new, highly-contiguous
genome assembly for the honey bee, Apis mellifera L.
(Hymenoptera: Apidae), supported the detection of inversions associated
with local adaptation in high altitude populations (Christmas et al.,
2019). Comparative genomics has also contributed to a growing
recognition of genomic islands of divergence and speciation (Gagnaire et
al., 2013; Renaut et al., 2013). Numerous recent studies highlight the
ecological roles that divergent regions within genomes may have and how
they are formed (e.g., Bay & Ruegg, 2017; Ma et al., 2018; Renaut et
al., 2013; Tavares et al., 2018).
Neo-sex chromosomes and the degeneration of male sex chromosomes (e.g.,
Muller’s ratchet), present other aspects of genomic speciation that can
be explored using high-quality genome assemblies. For example,
assessments of neo-sex chromosome formation and prevalence, and the
subsequent deterioration of male sex chromosomes, can provide insight
into the mechanisms and consequences of their evolution. High-quality
insect genomes are increasingly valuable because they present numerous
complex sex-determination mechanisms that can affect their stability
through recombination, mutation, and drift (Blackmon et al., 2016).
Recent research has highlighted the interaction between sex chromosomes
and reproductive isolation (Bracewell et al., 2017), and insect genomes
with newly derived neo-sex chromosomes may be better suited for studying
male sex chromosome degeneration than mammal genomes.
Genomic resources for mountain pine beetle, Dendroctonus
ponderosae Hopkins (Coleoptera: Curculionidae), have grown considerably
in recent years (Cullingham et al., 2018; Keeling et al., 2012; Keeling
et al., 2013c). Much of this research and data growth has been in
response to ongoing massive population outbreaks in western North
America driven by climate change, which have resulted in severe forest
disturbances and losses (e.g., Raffa et al., 2008; Saab et al., 2014;
Sambaraju & Goodsman, 2021). Genetics and genomics were quickly
recognized as tools to help model and manage outbreaks by better
understanding population dynamics (Goodsman et al., 2016; James et al.,
2016); signatures of selection (Batista et al., 2016; Janes et al.,
2014); the processes of olfaction (Andersson et al., 2013; Andersson et
al., 2019; Chiu et al., 2019b; Keeling et al., 2013b), pheromone
biosynthesis (Aw et al., 2010; Chiu et al., 2018, 2019a; Keeling et al.,
2013a; Keeling et al., 2016; Nadeau et al., 2017), host colonization
(Chiu et al., 2019c; Robert et al., 2013) and overwintering (Robert et
al., 2016); and the coevolution between the beetle, its hosts, and its
symbiotic microorganisms (James et al., 2011).
While recent focus has been on applied pest management outcomes forD. ponderosae , there are numerous theoretical benefits as well,
and the two often complement each other. For example, the draft mountain
pine beetle genome (Keeling et al., 2013c) revealed considerable synteny
with Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae),
the most closely related genome assembly at the time. That work
highlighted the important roles that specific gene families and the
neo-XY chromosomal system may have in contributing to the ecological
success of the mountain pine beetle (Keeling et al., 2013c). That study
also noted the lack of linkage map data to further refine our knowledge
of the location and formation of the neo-XY system. Traditionally,
linkage maps have been used to quantify effect sizes that certain loci
have on traits of interest (e.g., quantitative trait loci) (Berlin et
al., 2017), which can greatly accelerate breeding programs and our
understanding of evolutionary processes and outcomes. However, linkage
maps can also assist in genome assembly of non-model organisms
(Bartholomé et al., 2014) and provide insight into comparative analyses
of genomic architecture (i.e., synteny, collinearity, chromosomal
rearrangements, etc.) (Barth et al., 2019; Butler et al., 2017).
The karyotype of Dendroctonus spp. (Coleoptera: Curculionidae)
varies from 5 autosome pairs (AA) + neo-XY to 14 AA +
Xyp (Zúñiga et al., 2002), with males being the
heterogametic sex in all cases. In D. ponderosae and D.
jeffreyi Hopkins, the karyotype is 11 AA + neo-XY. Neo-sex chromosomes
result from the fusion of a sex chromosome with an autosome. Three otherDendroctonus spp. have a neo-XY karyotype: D. adjunctusBlandford (6 AA + neo-XY), D. approximatus Dietz (5 AA + neo-XY),
and D. brevicomis LeConte (5 AA + neo-XY). It is not known
whether the neo-XY chromosomes in these species are orthologous to those
in D. ponderosae and D. jefferyi . In D. ponderosae ,
the neo-X is believed to have originated from an ancestral 12 AA +
Xyp karyotype through the fusion of the ancestral-X
chromosome with one copy of the largest autosome (Lanier, 1981). The
ancestral-Y (yp) chromosome was lost, to be replaced by
the other copy of the fused autosome, becoming neo-Y. However, several
species in this genus have the basal 14 AA + Xypkaryotype (Zúñiga et al., 2002), suggesting that the large autosome that
became part of the neo-sex chromosomes in D. ponderosae may
itself have been the fusion of three ancestral autosomes. Thus, a large
portion of the genome content of D. ponderosae is in the sex
chromosomes. Apart from understanding the genome architecture,
delineating the sex chromosomes and the genes they contain will help us
to understand how D. ponderosae has become one of the most
important pest species in its genus, and a keystone species in western
North American pine forests.
Here we provide chromosome-level male and female genome assemblies based
on new proximity ligation and linkage mapping data to further support
research on mountain pine beetle, which continues to exert major
ecological and economic effects on pine forests in Canada and the USA.
We additionally use whole-genome pool-seq and SNP data to assess
signatures of natural selection and investigate genomic linkage in the
context of rapid population, geographic, and host range expansions, as
well as neo-sex chromosome evolution. Our results broadly characterize
the neo-sex chromosomes and indicate that local adaptation in Canadian
mountain pine beetle populations appears to be largely mediated by one
autosomal region and the ancestral-X portion of the neo-X chromosome.