Dataset Information

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 nontargeted 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, that is, 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 ?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.

SUBMITTER: Bouchemousse S

PROVIDER: S-EPMC7486951 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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

Bouchemousse Sarah S Falquet Laurent L Müller-Schärer Heinz H

Genome biology and evolution 20200701 7

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 nontargeted 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 geneti ...[more]

PMID: 32428241

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Project description:A systematic review focused by plant on non-target impacts from agents deliberately introduced for the biological control of weeds found significant non-target impacts to be rare. The magnitude of direct impact of 43 biocontrol agents on 140 non-target plants was retrospectively categorized using a risk management framework for ecological impacts of invasive species (minimal, minor, moderate, major, massive). The vast majority of agents introduced for classical biological control of weeds (>99% of 512 agents released) have had no known significant adverse effects on non-target plants thus far; major effects suppressing non-target plant populations could be expected to be detectable. Most direct non-target impacts on plants (91.6%) were categorized as minimal or minor in magnitude with no known adverse long-term impact on non-target plant populations, but a few cacti and thistles are affected at moderate (n?=?3), major (n?=?7) to massive (n?=?1) scale. The largest direct impacts are from two agents (Cactoblastis cactorum on native cacti and Rhinocyllus conicus on native thistles), but these introductions would not be permitted today as more balanced attitudes exist to plant biodiversity, driven by both society and the scientific community. Our analysis shows (as far as is known), weed biological control agents have a biosafety track record of >99% of cases avoiding significant non-target impacts on plant populations. Some impacts could have been overlooked, but this seems unlikely to change the basic distribution of very limited adverse effects. Fewer non-target impacts can be expected in future because of improved science and incorporation of wider values. Failure to use biological control represents a significant opportunity cost from the certainty of ongoing adverse impacts from invasive weeds. It is recommended that a simple five-step scale be used to better communicate the risk of consequences from both action (classical biological control) and no action (ongoing impacts from invasive weeds).

Dataset Information

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

Publications

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

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