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

Abstract

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.

Chromosome structural rearrangements in invasive haplodiploid ambrosia beetles revealed by the genomes ofEuwallacea fornicatusandEuwallacea similis(Coleoptera, Curculionidae, Scolytinae)

“…Moreover, most annotations were largely complete with >97% complete single copy BUSCOs (Table 3). The number of genes annotated for both Euwallacea species were slightly lower than those annotated in Dendroctonus assemblies (Copeland et al, 2024; Liu et al, 2022) and much lower than the annotations of H. hampei (Navarro-Escalante et al, 2021), I. nitidus (Wang et al, 2023) , I. typographus (Powell et al, 2021) and T. bicolor .…”

“…Most chromosomes shared 1:1 conserved synteny and several blocks are either translocated within or across scaffolds. Further, despite the difference in chromosomal numbers between D. ponderosae (2n = 12) and D. valens (2n = 14) (Six & Bracewell, 2015), synteny across assemblies are largely conserved, identified herein and previously (Copeland et al, 2024;Liu et al, 2022). Between the two haplodiploid inbreeding Euwallacea species, the assemblies are less syntenic than the diploid outbreeding species.…”

“…They are among the smallest Scolytinae genomes published and contain the highest number of pseudo-chromosomal scaffolds. Additionally, 17 -81% fewer protein coding genes were predicted for these Euwallacea assemblies compared to previously published Scolytinae genomes (Copeland et al, 2024;Liu et al, 2022;Navarro-Escalante et al, 2021;Powell et al, 2021;Wang et al, 2023).…”