Optimization and Evaluation of the <scp>bestRAD</scp> Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, <i>Bactrocera dorsalis</i>

The bestRAD technique is a reduced genome representation approach with high-capacity sample multiplexing and physical isolation of biotin-labelled target DNA fragments using streptavidin beads, which should reduce total cost and genotyping errors. While we here formalise the relevance of this approach within the HTS landscape, our foremost aim was to improve its replicability, validity, and transparency. We first optimised the molecular laboratory protocol and shared the associated protocols (e.g., final detailed methodologies, quality control, best practices) under the FAIR principles. Using 84 worldwide individual samples of the Oriental fruit fly, Bactrocera dorsalis, a major invasive pest, we revealed a low rate of PCR duplicates, robustness to DNA quality and quantity, high genotype call rate, insignificant genotyping error rate, high nuclear and mitochondrial genome representativeness, and a high level of genetic information. This in-depth data quality assessment, along with total cost and handling time reduced by an estimated one-third relative to the parent RAD-Seq version, demonstrates that bestRAD is an excellent compromise between cost and quality. While we generated high-quality genomic resources for B. dorsalis, we also share details and recommendations for the bestRAD technique that can be readily used in any laboratory and applied to all organisms, even without published genome sequence.

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Publication Details

Journal
Molecular Ecology Resources
Published
2025-04-11
DOI
https://doi.org/10.1111/1755-0998.14114
Citations
1
Primary Topic
Insect behavior and control techniques
Type
article
Field-Weighted Citation Impact
1.67

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article

Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis

Sabine Nidelet, Emeline Charbonnel, Bernhard Gschloessl, Laure Benoit et al.
1 citations
Molecular Ecology Resources
Insect behavior and control techniques
1.67
article

Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis

Sabine Nidelet, Emeline Charbonnel, Bernhard Gschloessl, Laure Benoit, Marie‐Pierre Chapuis, David Ouvrard, Enrique Ortega‐Abboud, Raphaël Leblois
article en
1 citations

Abstract

The bestRAD technique is a reduced genome representation approach with high-capacity sample multiplexing and physical isolation of biotin-labelled target DNA fragments using streptavidin beads, which should reduce total cost and genotyping errors. While we here formalise the relevance of this approach within the HTS landscape, our foremost aim was to improve its replicability, validity, and transparency. We first optimised the molecular laboratory protocol and shared the associated protocols (e.g., final detailed methodologies, quality control, best practices) under the FAIR principles. Using 84 worldwide individual samples of the Oriental fruit fly, Bactrocera dorsalis, a major invasive pest, we revealed a low rate of PCR duplicates, robustness to DNA quality and quantity, high genotype call rate, insignificant genotyping error rate, high nuclear and mitochondrial genome representativeness, and a high level of genetic information. This in-depth data quality assessment, along with total cost and handling time reduced by an estimated one-third relative to the parent RAD-Seq version, demonstrates that bestRAD is an excellent compromise between cost and quality. While we generated high-quality genomic resources for B. dorsalis, we also share details and recommendations for the bestRAD technique that can be readily used in any laboratory and applied to all organisms, even without published genome sequence.

Molecular Ecology ResourcesVol. 25(8)
Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Université de Montpellier (FR), Institut Agro Montpellier (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Mathématiques, Informatique et Statistique pour l'Environnement et l'Agronomie (FR), Département Santé des Plantes et Environnement (FR), Institut Agro Montpelier (FR), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (FR), Centre de Biologie pour la Gestion des Populations (FR), Institut de Recherche pour le Développement (FR), L'Institut Agro (FR)
Centre Méditerranéen de l’Environnement et de la Biodiversité, Agence Nationale de la Recherche, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Région Occitanie Pyrénées-Méditerranée, FP7 International Cooperation
Openalex Percentile: Top 20%
Insect behavior and control techniques
1.67
DOIOpen Access PDFOpenAlex
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