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

Keeling, Christopher I.; Campbell, Erin O.; Batista, Philip D.; Shegelski, Victor A.; Trevoy, Stephen A. L.; Huber, Dezene P. W.; Janes, Jasmine K.; Sperling, Felix A. H.

doi:10.1111/1755-0998.13528

Cited by 16 publications

(17 citation statements)

References 103 publications

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“…The total length of our nuclear assembly (356 Mb) is in the range of other chromosome-length beetle genome assemblies and provides an important resource for this underrepresented order of insects. Our annotation of 12,586 genes is also consistent with other high quality beetle genome assemblies (Fallon et al 2018;Keeling et al 2022;Van Dam et al 2021), and by establishing orthology with the model species, Tribolium castaneum (Herndon et al 2020) we have putative gene functions for over 60% of the genes in our annotation. The putative number of linkage groups proposed here ( 21) is roughly consistent with cytological studies of other Chrysomela (Petitpierre 2011).…”

Section: Discussionsupporting

confidence: 82%

A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis

Bracewell

Stillman

Dahlhoff

et al. 2023

Preprint

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The leaf beetleChrysomela aeneicollishas a broad geographic range across Western North America, but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2900-3450 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here we report a chromosome-scale genome assembly alongside a complete mitochondrial genome, and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology withTribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.

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Section: Discussionsupporting

confidence: 82%

A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis

Bracewell

Stillman

Dahlhoff

et al. 2023

Preprint

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“…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).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2022

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Background Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area. Results Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation. Conclusions Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.

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“…For instance, the two D. frontalis morphotypes A and B exhibit the karyotypes 7AA+XY and 5AA+XY, respectively (11). The analysis of the first sequenced Dendroctonus genome, the MPB, revealed a gene content of ∼13,000, which is significantly lower than in most other beetles and insects (12, 13). This finding has been confirmed by the genome sequencing of the red turpentine beetle (RTB), D. valens (14).…”

Section: Introductionmentioning

confidence: 90%

Genome assembly of the southern pine beetle (Dendroctonus frontalisZimmerman) reveals the origins of gene content reduction inDendroctonus

Copeland,

Landa,

Owoyemi

et al. 2024

Preprint

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Dendroctonus frontalis, also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus, we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non-Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.

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

Cited by 16 publications

References 103 publications

A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis

A chromosome scale genome assembly and evaluation of mtDNA variation in the willow leaf beetleChrysomela aeneicollis

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

Genome assembly of the southern pine beetle (Dendroctonus frontalisZimmerman) reveals the origins of gene content reduction inDendroctonus

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