Genome Assembly of the Ragweed Leaf Beetle: A Step Forward to Better Predict Rapid Evolution of a Weed Biocontrol Agent to Environmental Novelties

Abstract

Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far, only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of non-targeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first sequenced genome of a phytophagous insect used as a BCA, i.e. the leaf beetle Ophraella communa, a promising BCA of common ragweed, recently and accidentally introduced into Europe. A total 33.98 Gb of raw DNA sequences, representing c. 43-fold coverage, were obtained using the PacBio SMRT-Cell sequencing approach. Among the five different assemblers tested, the SMARTdenovo assembly displaying the best scores was then corrected with Illumina short reads. A final genome of 774 Mb containing 7,003 scaffolds was obtained. The reliability of the final assembly was then assessed by benchmarking universal single-copy orthologous genes (> 96.0% of the 1,658 expected insect genes) and by remapping tests of Illumina short reads (average of 98.6% ± 0.7% without filtering). The number of protein-coding genes of 75,642, representing 82% of the published antennal transcriptome, and the phylogenetic analyses based on 825 orthologous genes placing O. communa in the monophyletic group of Chrysomelidae, confirm the relevance of our genome assembly. Overall, the genome provides a valuable resource for studying potential risks and benefits of this BCA facing environmental novelties.

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

“…The draft assembly of D. carinulata is one of only two currently available reference genomes of biocontrol agents of invasive plants, both in the family Chrysomelidae, subfamily Galerucinae (Bouchemousse, Falquet, & Muller-Scharer, 2020), an inviting opportunity for broader comparative work. The resource we developed here is unique in that it can be used for four intentionally released biocontrol agents (the four Diorhabda spp.…”

Genome assemblies of three closely related leaf beetle species (Galerucellaspp)

“…The demography, host searching behavior and immunology have previously been addressed in several Galerucella species (Zheng et al 2008;Fors et al 2015;Yang et al 2020), but no genome assemblies of Galerucella species are currently available. The closest related species that has an available genome assembly is ragweed leaf beetle (Ophraella communa), which also belongs to the leaf beetle (Chrysomelidae) family (Figure 1) (Bouchemousse et al 2020). Here we report de-novo genome assemblies for G. calmariensis, G. pusilla and G. tenella.…”

Is biocontrol efficacy rather driven by the plant or the antagonist genotypes? A conceptual bioassay approach

“…Ophraella has recently and accidentally been introduced and was first recorded in China in 2001 and Europe in 2013 (Ma et al 2008;Müller-Schärer et al 2014). The few published studies on genetic differentiation among Ophraella populations indicate clear differences among regions and among populations within regions, revealed both by molecular markers and phenotyping (Bordeyne et al 2020;Bouchemousse et al 2020;Nishide et al 2015).…”