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Study of Viral Diversity in Poaceae-Based Communities with Contrasted Plant Richness

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Study of Viral Diversity in Poaceae-Based Communities with Contrasted Plant Richness http://lib.uliege.be https://matheo.uliege.be Study of viral diversity in Poaceae-based communities with contrasted plant richness Auteur : Debue, Virginie Promoteur(s) : Massart, Sébastien Faculté : Gembloux Agro-Bio Tech (GxABT) Diplôme : Master en bioingénieur : chimie et bioindustries, à finalité spécialisée Année académique : 2018-2019 URI/URL : http://hdl.handle.net/2268.2/7676 Avertissement à l'attention des usagers : Tous les documents placés en accès ouvert sur le site le site MatheO sont protégés par le droit d'auteur. Conformément aux principes énoncés par la "Budapest Open Access Initiative"(BOAI, 2002), l'utilisateur du site peut lire, télécharger, copier, transmettre, imprimer, chercher ou faire un lien vers le texte intégral de ces documents, les disséquer pour les indexer, s'en servir de données pour un logiciel, ou s'en servir à toute autre fin légale (ou prévue par la réglementation relative au droit d'auteur). Toute utilisation du document à des fins commerciales est strictement interdite. Par ailleurs, l'utilisateur s'engage à respecter les droits moraux de l'auteur, principalement le droit à l'intégrité de l'oeuvre et le droit de paternité et ce dans toute utilisation que l'utilisateur entreprend. Ainsi, à titre d'exemple, lorsqu'il reproduira un document par extrait ou dans son intégralité, l'utilisateur citera de manière complète les sources telles que mentionnées ci-dessus. Toute utilisation non explicitement autorisée ci-avant (telle que par exemple, la modification du document ou son résumé) nécessite l'autorisation préalable et expresse des auteurs ou de leurs ayants droit. Study of viral diversity in Poaceae-based communities with contrasted plant richness VIRGINE DEBUE TRAVAIL DE FIN D’ETUDES PRESENTE EN VUE DE L’OBTENTION DU DIPLOME DE MASTER BIOINGENIEUR EN CHIMIE ET BIOINDUSTRIES ANNEE ACADEMIQUE 2018-2019 PROMOTEUR : SEBASTIEN MASSART © Toute reproduction du présent document, par quelque procédé que ce soit, ne peut être réalisée qu'avec l'autorisation de l'auteur et de l'autorité académique1 de Gembloux Agro-Bio Tech. Le présent document n'engage que son auteur. 1 Dans ce cas, l'autorité académique est représentée par le(s) promoteur(s) membre du personnel(s) enseignant de GxABT. Study of viral diversity in Poaceae-based communities with contrasted plant richness VIRGINE DEBUE TRAVAIL DE FIN D’ETUDES PRESENTE EN VUE DE L’OBTENTION DU DIPLOME DE MASTER BIOINGENIEUR EN CHIMIE ET BIOINDUSTRIES ANNEE ACADEMIQUE 2018-2019 PROMOTEUR : SEBASTIEN MASSART Acknowledgements First of all, I would like to thank my promoter, Sebastien Massart, for allowing me to do my master thesis in his unit and for allowing me to deepen my knowledge of bioinformatics and phytopathology, for answering my questions and for supervising my work. Thank you for your advice when writing the work. I would also like to warmly thank François Maclot, my supervisor, who has been able to support me throughout this work. Thank you for being so available for answering all my questions. Thank you also for brightening up my laboratory days with your many anecdotes, for giving me many tips and comments to improve the quality of my written work. Let me thank Integrated and Urban Phytopathology Laboratory of the ULiège-Gembloux Agro- Bio Tech University and its staff for welcoming me during my master thesis. And a special thank you to Angelo, for his advice during my manipulations. Thanks also to Arnaud and Lucie for taking the time to answer my questions about bioinformatics. A special thanks to you, my family, who supported me throughout my studies. Thanks to Julien who supported and encouraged me during this period, as well as Laurie, Lucas, Laetitia, Gauthier, Arnaud, Cyril, Kevin, Nicolas, Charles for your support since we joined the faculty. I also wanted to thank the residents of the "Chiée des glands", life has never been so beautiful with you. Thanks also to the AG committee 2015 and the soft team for many moments shared in recent years. Master's thesis performed in the Integrated and Urban Phytopathology Unit of the ULiège- Gembloux Agro-Bio Tech University Abstract Study of plant viruses is essential to address yield loss in crops due to diseases. However, viruses are most often studied in crops while viruses present in wild areas can also have a significant impact if the virus moves from one plot to another according to the different modes of transmission specific to each virus. It is therefore essential to better understand virus behaviour in these non-cultivated areas, and virus adaptation in their environment, through the identification of new virus species, new host plants and study of virus vectors. This will allow to better control disease risks to crops in case of virus transmission to them from wild reservoirs. In this study, prevalence of three plant viruses was examined, i.e. Barley yellow dwarf virus (Luteovirus, Luteoviridae), a new nepovirus (Secoviridae) candidate and a new waikavirus (Secoviridae) candidate three different plant communities (monoculture, pasture and grassland with high ecological value) within the Natural Park of Burdinale Mehaigne (Antheit, Province of Liège, Belgium). Virus prevalence was studied in plant communities as a whole as well as within some specific Poaceae species (Poa trivialis L. and Lolium perenne L.). Virus prevalence was studied using RT-PCR techniques to determine the presence of the virus in plant samples randomly collected from the plots. Co-infections between these three virus species were also analyzed. Bioinformatics analyses were also carried out on nepovirus and waikavirus candidates in order to determine if they represent some new virus species. Results showed a high prevalence (80-90%) of nepoviruses in wild plant communities, while any symptoms were observed. Bioinformatics analyses allowed study phylogeny of different consensus viral sequences established for each plant community. These sequences were then compared with each other but also with reference sequences from NCBI for Nepovirus, Waikavirus and Sequivirus genera (all belonging to Secoviridae family). Bioinformatics study showed that nepovirus is potentially a new virus species similar to Tomato black ring virus and Beet ringspot virus. The waikavirus shows a significant genetic difference with other waikaviruses. A last part of the project was to investigate host range of White clover mosaic virus. This virus, known to only infect Fabaceae plants such as clovers (Trifolium repens L.), was also detected by high throughput sequencing in Lolium perenne L. in a pasture in Héron (Province of Liège). Virus detection by RT-PCR in clovers and ryegrass confirmed sequencing data and allowed to extend host range of this virus species to Poaceae. Keywords: plant virus ecology – metagenomics – wild Poaceae – crops – virus prevalence Résumé L'étude des virus des plantes est essentielle pour remédier aux pertes de rendement des cultures dues aux maladies. Cependant, les virus sont le plus souvent étudiés dans les cultures alors que les virus présents dans les zones sauvages peuvent également avoir un impact significatif si le virus se déplace d'une parcelle à une autre selon les différents modes de transmission propres à chaque virus. Il est donc essentiel de mieux comprendre le comportement viral dans ces zones non cultivées et l'adaptation des virus dans leur environnement, par l'identification de nouvelles espèces virales, de nouvelles plantes hôtes et l'étude des vecteurs de virus. Cela permettra de mieux contrôler les risques de maladies pour les cultures en cas de transmission du virus à partir de réservoirs sauvages. Dans cette étude, la prévalence de trois virus végétaux a été examinée, à savoir le Barley yellow dwarf virus (Luteovirus, Luteoviridae), un nouveau nepovirus (Secoviridae) candidat et un nouveau waikavirus (Secoviridae) candidat dans trois communautés végétales différentes (monoculture, pâturage et prairie à haute valeur écologique) dans le Parc naturel Burdinale Mehaigne (Antheit, Province de Liège, Belgique). La prévalence du virus a été étudiée dans l'ensemble des communautés végétales ainsi que dans certaines espèces spécifiques de Poaceae (Poa trivialis L. et Lolium perenne L.). La prévalence du virus a été étudiée à l'aide de techniques de RT-PCR pour déterminer la présence du virus dans des échantillons de plantes prélevés au hasard sur les placettes. Les co-infections entre ces trois espèces de virus ont également été analysées. Des analyses bio-informatiques ont également été effectuées sur des candidats nepovirus et waikavirus afin de déterminer s'ils représentent de nouvelles espèces virales. Les résultats ont montré une prévalence élevée (80-90%) de nepovirus dans les communautés végétales sauvages, alors que des symptômes ont été observés. Les analyses bio-informatiques ont permis d'étudier la phylogénie de différentes séquences virales consensuelles établies pour chaque communauté végétale. Ces séquences ont ensuite été comparées entre elles, mais aussi avec des séquences de référence provenant de NCBI pour les genres Nepovirus, Waikavirus et Sequivirus (tous appartenant à la famille des Secoviridae). Une étude bio-informatique a montré que le nepovirus est potentiellement une nouvelle espèce de virus similaire au Tomato black ring virus et au Beet ringspot virus. Le waikavirus présente une différence génétique significative avec les autres waikavirus. Une dernière partie du projet consistait à étudier la gamme d'hôtes du White clover mosaic virus. Ce virus, connu pour n'infecter
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