The transposable element-rich genome of the cereal pest Sitophilus oryzae

Nicolas Parisot; Carlos Vargas-Chávez; Clément Goubert; Patrice Baa-Puyoulet; Séverine Balmand; Louis Beranger; Caroline Blanc; Aymeric Bonnamour; Matthieu Boulesteix; Nelly Burlet; Federica Calevro; Patrick Callaerts; Théo Chancy; Hubert Charles; Stefano Colella; André Da Silva Barbosa; Elisa Dell’Aglio; Alex Di Genova; Gérard Febvay; Toni Gabaldón; Mariana Galvão Ferrarini; Alexandra Gerber; Benjamin Gillet; Robert Hubley; Sandrine Hughes; Emmanuelle Jacquin-Joly; Justin Maire; Marina Marcet-Houben; Florent Masson; Camille Meslin; Nicolas Montagné; Andrés Moya; Ana Tereza Ribeiro de Vasconcelos; Gautier Richard; Jeb Rosen; Marie-France Sagot; Arian F. A. Smit; Jessica M. Storer; Carole Vincent-Monegat; Agnès Vallier; Aurélien Vigneron; Anna Zaidman-Rémy; Waël Zamoum; Cristina Vieira; Rita Rebollo; Amparo Latorre; Abdelaziz Heddi

doi:10.1186/s12915-021-01158-2

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The transposable element-rich genome of the cereal pest Sitophilus oryzae

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The transposable element-rich genome of the cereal pest Sitophilus oryzae

Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, …

BMC biology, Vol.19(1), pp.241-28

09/11/2021

DOI: https://doi.org/10.1186/s12915-021-01158-2

PMID: 34749730

Résumé

Biomedical and Life Sciences

Général

Life Sciences

Research Article

Background The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. Results We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. Conclusions Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

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Titre: The transposable element-rich genome of the cereal pest Sitophilus oryzae
Créateurs - sans rôle: Nicolas Parisot - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Carlos Vargas-Chávez - Universitat Pompeu Fabra
Clément Goubert - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Department of Molecular Biology and Genetics, Cornell University, Present Address: Human Genetics, McGill University
Patrice Baa-Puyoulet - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Séverine Balmand - Institut National des Sciences Appliquées de Lyon
Louis Beranger - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Caroline Blanc - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Aymeric Bonnamour - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Matthieu Boulesteix - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon
Nelly Burlet - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon
Federica Calevro - Institut National des Sciences Appliquées de Lyon
Patrick Callaerts - KU Leuven
Théo Chancy - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Hubert Charles - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, ERABLE European Team, INRIA
Stefano Colella - Laboratoire des Symbioses Tropicales et Méditerranéennes
André Da Silva Barbosa - INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris
Elisa Dell’Aglio - Institut National des Sciences Appliquées de Lyon
Alex Di Genova - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, ERABLE European Team, INRIA, Instituto de Ciencias de la Ingeniería, Universidad de O’Higgins
Gérard Febvay - Institut National des Sciences Appliquées de Lyon
Toni Gabaldón - Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Institut Catalan de Recerca i Estudis Avançats (ICREA)
Mariana Galvão Ferrarini - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Alexandra Gerber - Laboratório de Bioinformática, Laboratório Nacional de Computação Científica
Benjamin Gillet - Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon
Robert Hubley - Institute for Systems Biology
Sandrine Hughes - Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon
Emmanuelle Jacquin-Joly - INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris
Justin Maire - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, Present Address: School of BioSciences, The University of Melbourne
Marina Marcet-Houben - Life Sciences, Barcelona Supercomputing Centre (BSC-CNS)
Florent Masson - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)
Camille Meslin - INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris
Nicolas Montagné - Sorbonne Université
Andrés Moya - Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO)
Ana Tereza Ribeiro de Vasconcelos - Laboratório de Bioinformática, Laboratório Nacional de Computação Científica
Gautier Richard - IGEPP, INRAE, Institut Agro, Université de Rennes
Jeb Rosen - Institute for Systems Biology
Marie-France Sagot - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, ERABLE European Team, INRIA
Arian F. A. Smit - Institute for Systems Biology
Jessica M. Storer - Institute for Systems Biology
Carole Vincent-Monegat - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Agnès Vallier - Institut National des Sciences Appliquées de Lyon
Aurélien Vigneron - Institut National des Sciences Appliquées de Lyon
Anna Zaidman-Rémy - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Waël Zamoum - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Cristina Vieira - Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, ERABLE European Team, INRIA
Rita Rebollo - Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203
Amparo Latorre - Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO)
Abdelaziz Heddi - Institut National des Sciences Appliquées de Lyon
Détails de publication: BMC biology, Vol.19(1), pp.241-28
Éditeur: BioMed Central
Note de subvention: Région Auvergne-Rhône-Alpes (http://dx.doi.org/10.13039/501100010115) European Regional Development Fund (http://dx.doi.org/10.13039/501100008530) PROMETEO/2018/133 / Conselleria d’Educació, Generalitat Valenciana PGC2018-099344-B-I00; PID2019-105969GB-I00 / Ministerio de Ciencia, Innovación y Universidades (http://dx.doi.org/10.13039/100014440) IDEX-Lyon PALSE IMPULSION Ministerio de Economía y Competitividad (http://dx.doi.org/10.13039/501100003329) Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement Institut National des Sciences Appliquées de Lyon (http://dx.doi.org/10.13039/501100009081) ANR-10-BLAN-1701; ANR-13-BSV7-0016-01; ANR-17_CE20_0031_01; ANR-17-CE20-0015 / Agence Nationale de la Recherche
Identifiants: 99157293509311
Unité académique: Plant Health Institute of Montpellier - PHIM
Langue: English
Type de ressource: Journal article