118 results on '"Warris, Sven"'
Search Results
2. Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes
- Author
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Möhlmann, Tim W. R., Vogels, Chantal B. F., Göertz, Giel P., Pijlman, Gorben P., ter Braak, Cajo J. F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, and Koenraadt, Constantianus J. M.
- Published
- 2020
3. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
- Author
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Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel
- Published
- 2021
- Full Text
- View/download PDF
4. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
- Author
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Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel
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- 2021
- Full Text
- View/download PDF
5. Development and evaluation of two TaqMan assays for generic detection of Dickeya species
- Author
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Zijlstra, Carolien, De Haas, Lia Groenenboom –, Krijger, Marjon, Verstappen, Els, Warris, Sven, de Haan, Eisse, and van der Wolf, Jan
- Published
- 2020
- Full Text
- View/download PDF
6. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
- Author
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van de Vossenberg, Bart T. L. H., Warris, Sven, Nguyen, Hai D. T., van Gent-Pelzer, Marga P. E., Joly, David L., van de Geest, Henri C., Bonants, Peter J. M., Smith, Donna S., Lévesque, C. André, and van der Lee, Theo A. J.
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- 2019
- Full Text
- View/download PDF
7. Fusarium in the age of genomics
- Author
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Waalwijk, Cees, Vanheule, Adriaan, Audenaert, Kris, Zhang, Hao, Warris, Sven, van de Geest, Henri, and van der Lee, Theo
- Published
- 2017
- Full Text
- View/download PDF
8. Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges
- Author
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Möhlmann, Tim W.R., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, Koenraadt, Constantianus J.M., Möhlmann, Tim W.R., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, and Koenraadt, Constantianus J.M.
- Abstract
Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis, endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterised. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into 6-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens.
- Published
- 2022
9. Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges
- Author
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Möhlmann, Tim W. R., primary, ter Braak, Cajo J. F., additional, te Beest, Dennis E., additional, Hendriks, Marc, additional, Nijhuis, Els H., additional, Warris, Sven, additional, Drolet, Barbara S., additional, van Overbeek, Leo, additional, and Koenraadt, Constantianus J. M., additional
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- 2021
- Full Text
- View/download PDF
10. Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics
- Author
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Tracanna, Vittorio, primary, Ossowicki, Adam, additional, Petrus, Marloes L. C., additional, Overduin, Sam, additional, Terlouw, Barbara R., additional, Lund, George, additional, Robinson, Serina L., additional, Warris, Sven, additional, Schijlen, Elio G. W. M., additional, van Wezel, Gilles P., additional, Raaijmakers, Jos M., additional, Garbeva, Paolina, additional, and Medema, Marnix H., additional
- Published
- 2021
- Full Text
- View/download PDF
11. Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10X metagenomics
- Author
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Tracanna, Vittorio, Ossowicki, Adam, Petrus, Marloes L.C., Overduin, Sam, Terlouw, Barbara R., Lund, George, Robinson, Serina L., Warris, Sven, Schijlen, Elio G.W.M., van Wezel, Gilles P., Raaijmakers, J.M., Garbeva, Paolina, Medema, Marnix H., Tracanna, Vittorio, Ossowicki, Adam, Petrus, Marloes L.C., Overduin, Sam, Terlouw, Barbara R., Lund, George, Robinson, Serina L., Warris, Sven, Schijlen, Elio G.W.M., van Wezel, Gilles P., Raaijmakers, J.M., Garbeva, Paolina, and Medema, Marnix H.
- Abstract
Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10x metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype.
- Published
- 2021
12. Species identity, life history, and geographic distance influence gut bacterial communities in lab-reared and European field-collected Culicoides biting midges
- Author
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Möhlmann, Tim W.R., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, Koenraadt, Constantianus J.M., Möhlmann, Tim W.R., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, and Koenraadt, Constantianus J.M.
- Abstract
Bacteria are part of the insect gut system and influence many physiological traits oftheir host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis , endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterized. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into six-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens, Bacteria are part of the insect gut system and influence many physiological traits oftheir host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis , endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterized. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into six-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens
- Published
- 2021
13. Functional amplicon sequencing of suppressive soil
- Author
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Tracanna, Vittorio, Ossowicki, Adam, Petrus, Marloes L.C., Overduin, Sam, Terlouw, Barbara R., Lund, George, Robinson, Serina L., Warris, Sven, Schijlen, Elio G.W.M., Van Wezel, Gilles P., Raaijmakers, Jos M., Garbeva, Paolina, Medema, Marnix H., Tracanna, Vittorio, Ossowicki, Adam, Petrus, Marloes L.C., Overduin, Sam, Terlouw, Barbara R., Lund, George, Robinson, Serina L., Warris, Sven, Schijlen, Elio G.W.M., Van Wezel, Gilles P., Raaijmakers, Jos M., Garbeva, Paolina, and Medema, Marnix H.
- Abstract
Functional amplicon sequencing of suppressive soil of NRPS A-domain, Functional amplicon sequencing of suppressive soil of NRPS A-domain
- Published
- 2021
14. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes
- Author
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Gauthier, Jérémy, BOULAIN, Hélène, van Vugt, Joke J.F.A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed Amine, Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagne, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske, Marbouty, Martial, Cônsoli, Fernando Luis, Vet, Louise E.M., Cônsoli, Fernando, Dupas, Stéphane, Hua Van, Aurélie, Le Goff, Gaëlle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James, Vet, Louise, Smid, Hans, Kaiser-Arnault, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth, Drezen, Jean-Michel, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), France Génomique (UMS CNRS 3628 - INRAE 1396 - Inserm 026), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Collège doctoral [Sorbonne universités], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nice Sophia Antipolis (... - 2019) (UNS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0303 health sciences ,food.ingredient ,Host (biology) ,[SDV]Life Sciences [q-bio] ,fungi ,Duurzame gewasbescherming ,Parasitism ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,Virus ,Wespen ,Parasitoid wasp ,Parasitoid ,03 medical and health sciences ,food ,Evolutionary biology ,Bracovirus ,Gene ,030304 developmental biology - Abstract
Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.
- Published
- 2020
- Full Text
- View/download PDF
15. Impact gut bacteria on infection and transmission of pathogenic arboviruses by biting midges and mosquitoes
- Author
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Möhlmann, Tim W.R., Vogels, Chantal B.F., Göertz, Giel P., Pijlman, Gorben P., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, Koenraadt, Constantianus J.M., Möhlmann, Tim W.R., Vogels, Chantal B.F., Göertz, Giel P., Pijlman, Gorben P., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, and Koenraadt, Constantianus J.M.
- Abstract
Tripartite interactions among insect vectors, midgut bacteria, and viruses, maydetermine the ability of insects to transmit pathogenic arboviruses. Here, weinvestigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosusand C. sonorensis biting midges for Schmallenberg virus, and of Aedes aegyptimosquitoes for Zika and chikungunya virus. Gut bacteria were manipulated by treatingthe adult insects with antibiotics., Tripartite interactions among insect vectors, midgut bacteria, and viruses, maydetermine the ability of insects to transmit pathogenic arboviruses. Here, weinvestigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosusand C. sonorensis biting midges for Schmallenberg virus, and of Aedes aegyptimosquitoes for Zika and chikungunya virus. Gut bacteria were manipulated by treatingthe adult insects with antibiotics.
- Published
- 2020
16. Draft genome sequences of three isolates of golubevia sp. basidiomycete fungi isolated from powdery mildew pustules
- Author
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Russ, Lina, Warris, Sven, Lombaers-Van der Plas, Carin, Groenenboom-De Haas, Lia H., Cordewener, Jan H.G., Schijlen, Elio, Köhl, Jürgen, Russ, Lina, Warris, Sven, Lombaers-Van der Plas, Carin, Groenenboom-De Haas, Lia H., Cordewener, Jan H.G., Schijlen, Elio, and Köhl, Jürgen
- Abstract
The genomes of three Golubevia isolates (BC0812, BC0850, and BC0902) that have been shown to reduce conidiation of Blumeria graminis f. sp. tritici were sequenced using a dual-platform approach. The assembled genomes will help to elucidate the molecular mechanisms underlying the biocontrol effect of this understudied group.
- Published
- 2020
17. Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes
- Author
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Möhlmann, Tim W.R., Vogels, Chantal B.F., Göertz, Giel P., Pijlman, Gorben P., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, Koenraadt, Constantianus J.M., Möhlmann, Tim W.R., Vogels, Chantal B.F., Göertz, Giel P., Pijlman, Gorben P., ter Braak, Cajo J.F., te Beest, Dennis E., Hendriks, Marc, Nijhuis, Els H., Warris, Sven, Drolet, Barbara S., van Overbeek, Leo, and Koenraadt, Constantianus J.M.
- Abstract
Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.
- Published
- 2020
18. Draft Genome Sequences of Three Isolates of Golubevia sp. Basidiomycete Fungi Isolated from Powdery Mildew Pustules
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Russ, Lina, primary, Warris, Sven, additional, Lombaers-van der Plas, Carin, additional, Groenenboom-de Haas, Lia H., additional, Cordewener, Jan H. G., additional, Schijlen, Elio, additional, and Köhl, Jürgen, additional
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- 2020
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19. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes
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Gauthier, Jérémy, primary, Boulain, Hélène, additional, van Vugt, Joke J.F.A., additional, Baudry, Lyam, additional, Persyn, Emma, additional, Aury, Jean-Marc, additional, Noel, Benjamin, additional, Bretaudeau, Anthony, additional, Legeai, Fabrice, additional, Warris, Sven, additional, Chebbi, Mohamed Amine, additional, Dubreuil, Géraldine, additional, Duvic, Bernard, additional, Kremer, Natacha, additional, Gayral, Philippe, additional, Musset, Karine, additional, Josse, Thibaut, additional, Bigot, Diane, additional, Bressac, Christophe, additional, Moreau, Sébastien, additional, Periquet, Georges, additional, Harry, Myriam, additional, Montagné, Nicolas, additional, Boulogne, Isabelle, additional, Sabeti-Azad, Mahnaz, additional, Maïbèche, Martine, additional, Chertemps, Thomas, additional, Hilliou, Frédérique, additional, Siaussat, David, additional, Amselem, Joëlle, additional, Luyten, Isabelle, additional, Capdevielle-Dulac, Claire, additional, Labadie, Karine, additional, Merlin, Bruna Laís, additional, Barbe, Valérie, additional, de Boer, Jetske G., additional, Marbouty, Martial, additional, Cônsoli, Fernando Luis, additional, Dupas, Stéphane, additional, Hua Van, Aurélie, additional, Le Goff, Gaëlle, additional, Bézier, Annie, additional, Jacquin-Joly, Emmanuelle, additional, Whitfield, James B., additional, Vet, Louise E.M., additional, Smid, Hans M., additional, Kaiser-Arnault, Laure, additional, Koszul, Romain, additional, Huguet, Elisabeth, additional, Herniou, Elisabeth A., additional, and Drezen, Jean-Michel, additional
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- 2020
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20. Application of high performance computer technology in bioinformatics
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Warris, Sven and Nap, Jan Peter
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Life Sciences &Amp; Renewable Energy ,No Hanze Research Focus Area Applicable ,Bioinformatics ,Science ,Bioinformatica ,Biotechnologie ,Biotechnology ,Computertechnologie - Published
- 2019
21. Application of high performance compute technology in bioinformatics
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de Ridder, D., Nap, J.P., Warris, Sven, de Ridder, D., Nap, J.P., and Warris, Sven
- Abstract
Bioinformatics and computational biology are driven by growing volumes of data in biological systems that also tend to increase in complexity. The research presented in this thesis focuses on the need to analyze such data volumes in such complexity. The results show that the application of high-performance compute technologies, preferably combined with low-cost hardware, is a successful approach to generate new bioinformatics approaches that allow addressing new types of data analyses and research questions in biology. An overview of the technologies and recent developments in biology and computer science relevant for this thesis (Chapter 1) identifies current high-throughput sequencing platforms as a key technology. Sequencing platforms now deliver data sets up to terabytes in size for elucidating genome structure, gene content, gene activity, as well as gene variants. The concepts and technologies from computer science to handle these large amounts of data include (a) grid technologies for compute parallelization while making more efficient use of existing low-cost infrastructure; (b) graphics cards for increased compute power and (c) graph databases for large data volume storage and advanced methods for analyses. This thesis presents novel applications and added value of these three concepts for bioinformatics research. Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge (Chapter 2). They tend to have a minimal free energy (MFE) significantly lower than the MFE of non-small RNA sequences with the same nucleotide composition. Evaluation of many MFEs is, however, too compute-intensive for genome-wide screening. With a local grid infrastructure of desktop computers, MFE distributions of a very large collection of sequence compositions were pre-calculated and used to determine the MFE distribution for any given sequence composition by interpolation. This approach allows on-the-fly calculatio
- Published
- 2019
22. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum
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van de Vossenberg, Bart T.L.H., Warris, Sven, Nguyen, Hai D.T., van Gent-Pelzer, Marga P.E., Joly, David L., van de Geest, Henri C., Bonants, Peter J.M., Smith, Donna S., Lévesque, André C., van der Lee, Theo A.J., van de Vossenberg, Bart T.L.H., Warris, Sven, Nguyen, Hai D.T., van Gent-Pelzer, Marga P.E., Joly, David L., van de Geest, Henri C., Bonants, Peter J.M., Smith, Donna S., Lévesque, André C., and van der Lee, Theo A.J.
- Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
- Published
- 2019
23. Genome sequencing of Golubevia sp isolates
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Russ, Lina, Warris, Sven, Lombaers-Van der Plas, Carin, Groenenboom-De Haas, Lia H., Cordewener, Jan H.G., Schijlen, Elio, Köhl, Jürgen, Russ, Lina, Warris, Sven, Lombaers-Van der Plas, Carin, Groenenboom-De Haas, Lia H., Cordewener, Jan H.G., Schijlen, Elio, and Köhl, Jürgen
- Abstract
Fungal antagonist against powdery mildew in wheat, Fungal antagonist against powdery mildew in wheat
- Published
- 2019
24. Additional file 22: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
- Abstract
Dotplots mapping DBY gene containing GorY scaffold to GorY-Clean contig. (DOCX 70 kb)
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- 2018
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25. Additional file 16: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
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food and beverages - Abstract
The number of duplication or inversion events that were observed on contigs/scaffolds when aligned to human X-degenerate genes. (DOCX 26 kb)
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- 2018
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26. Additional file 3: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
- Abstract
Mapping Report for Ath-Clean BLASR-mapping. (PDF 418 kb)
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- 2018
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27. Additional file 6: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
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Cumulative length distribution of gorilla Y chromosome assemblies. (DOCX 264 kb)
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- 2018
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28. Additional file 9: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
- Abstract
Comparison of published GorY assembly to GorY-Clean in X-degenerate genes. (DOCX 34 kb)
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- 2018
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29. Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, primary, Schijlen, Elio, additional, van de Geest, Henri, additional, Vegesna, Rahulsimham, additional, Hesselink, Thamara, additional, te Lintel Hekkert, Bas, additional, Sanchez Perez, Gabino, additional, Medvedev, Paul, additional, Makova, Kateryna D., additional, and de Ridder, Dick, additional
- Published
- 2018
- Full Text
- View/download PDF
30. pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment
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Warris, Sven, Timal, N.R.N., Kempenaar, Marcel, Poortinga, Arne M., van de Geest, Henri, Varbanescu, Ana L., Nap, Jan Peter, Warris, Sven, Timal, N.R.N., Kempenaar, Marcel, Poortinga, Arne M., van de Geest, Henri, Varbanescu, Ana L., and Nap, Jan Peter
- Abstract
Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. Results The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. Conclusions pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
- Published
- 2018
31. Mining functional annotations across species
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Warris, Sven, primary, Dijkxhoorn, Steven, additional, Sloten, Teije van, additional, and Vossenberg, Bart van de, additional
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- 2018
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32. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
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Warris, Sven, primary, Timal, N. Roshan N., additional, Kempenaar, Marcel, additional, Poortinga, Arne M., additional, van de Geest, Henri, additional, Varbanescu, Ana L., additional, and Nap, Jan-Peter, additional
- Published
- 2018
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33. Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition
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Cochran, Alyssa T., primary, Bauer, Jemma, additional, Metcalf, Jessica L., additional, Lovecka, Petra, additional, Sura de Jong, Martina, additional, Warris, Sven, additional, Mooijman, Paul J. W., additional, van der Meer, Ingrid, additional, Knight, Rob, additional, and Pilon-Smits, Elizabeth A. H., additional
- Published
- 2018
- Full Text
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34. Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni
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Schulze, Stefan, Urzica, Eugen, Reijnders, Maarten J.M.F., Geest, Henri, van de, Warris, Sven, Bakker, Linda V., Fufezan, Christian, Martins dos Santos, Vitor A.P., Schaap, Peter J., Peters, Sander A., Hippler, Michael, Schulze, Stefan, Urzica, Eugen, Reijnders, Maarten J.M.F., Geest, Henri, van de, Warris, Sven, Bakker, Linda V., Fufezan, Christian, Martins dos Santos, Vitor A.P., Schaap, Peter J., Peters, Sander A., and Hippler, Michael
- Abstract
In contrast to mammals and vascular plants, microalgae show a high diversity in the N-glycan structures of complex N-glycoproteins. Although homologues for β1,2-N-acetylglucosaminyltransferase I (GnTI), a key enzyme in the formation of complex N-glycans, have been identified in several algal species, GnTI-dependent N-glycans have not been detected so far. We have performed an N-glycoproteomic analysis of the hydrocarbon oils accumulating green microalgae Botryococcus braunii. Thereby, the analysis of intact N-glycopeptides allowed the determination of N-glycan compositions. Furthermore, insights into the role of N-glycosylation in B. braunii were gained from functional annotation of the identified N-glycoproteins. In total, 517 unique N-glycosylated peptides have been identified, including intact N-glycopeptides that harbored N-acetylhexosamine (HexNAc) at the nonreducing end. Surprisingly, these GnTI-dependent N-glycans were also found to be modified with (di)methylated hexose. The identification of GnTI-dependent N-glycans in combination with N-glycan methylation in B. braunii revealed an uncommon type of N-glycan processing in this microalgae.
- Published
- 2017
35. Additional file 2: of Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, Geest, Henri Van De, Schijlen, Elio, Höfte, Monica, Saeger, Sarah De, Haesaert, Geert, Waalwijk, Cees, and Lee, Theo Van Der
- Abstract
Structural annotation and transcription of MAT1-1 and rid. A. Architecture of the MAT1 locus in F. poae isolate 2516, located at 3 120 000 bp into chromosome 2. The top track represents the predicted gene model, the second track represents the predicted coding features and the bottom track shows the TopHat mapping of the RNAseq reads. Note the correct splicing of introns for all three alleles. B. The rid (RIP defective) gene in F. poae isolate 2516, located at 2 232 000 bp into chromosome 2. The top track represents the predicted gene models, the second track represents the predicted coding features and the bottom track shows the TopHat mapping of the RNAseq reads. Two separate genes were predicted by the BRAKER1 pipeline. The F. pseudograminearum like gene model is superimposed as the single long coding feature. There is no splicing that supports this model under the conditions tested in this study. (DOCX 109 kb)
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- 2016
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36. Additional file 1: of Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, Geest, Henri Van De, Schijlen, Elio, HĂśfte, Monica, Saeger, Sarah De, Haesaert, Geert, Waalwijk, Cees, and Lee, Theo Van Der
- Abstract
Fragmented BUSCOs in F. poae and F. graminearum. A: Fusarium poae predicted proteins that were identified as fragmented by the BUSCO analysis. The top track corresponds to the predicted gene model, the second track shows the predicted coding features and the bottom track shows the TopHat mapping of the RNAseq reads. Arrows indicate likely sites of miss-annotation (likely fusion of two separate genes). From top to bottom: g7865, g6381, g8721 and g6717. B: Predicted proteins in the F. graminearum set that were identified as fragmented by the BUSCO analysis. The top track corresponds to the predicted gene model, the second track shows the predicted coding features and the bottom track shows the TopHat mapping of the RNAseq reads. Arrows indicate likely sites of miss-annotation From top to bottom: FGRRES_16573 (likely fusion of two neighboring genes), FGRRES_10897 (likely addition of two exons), FGRRES_06268 (likely two exons missed). RNAseq data described in Zhao et al. [38] were used. C: Predicted proteins in the F. poae and F. graminearum set that were identified as fragmented by the BUSCO analysis and are shared between the two species. The top track corresponds to the predicted gene model, the second track shows the predicted coding features and the bottom track shows the TopHat mapping of the RNAseq reads. From top to bottom: g1567/FGRRES_05972, g1914/FGRRES_06308, g8796/FGRRES_09970. The first of the two visualizations corresponds to F. poae, the second corresponds to F. graminearum. (DOCX 754Â kb)
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- 2016
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37. Additional file 6: of Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, Geest, Henri Van De, Schijlen, Elio, HĂśfte, Monica, Saeger, Sarah De, Haesaert, Geert, Waalwijk, Cees, and Lee, Theo Van Der
- Abstract
Transposable element datasheets. Information is listed for every transposable element family found in the genome of isolate 2516 that contains intact (not RIPped) elements. A: Tracks from top to bottom: LTR/TIR, coding region and mapping of RNAseq reads. B: Predicted protein used as bait for blastp, alignment of 15 best hits with the bait and neighbour-joining phylogenetic tree. For the retrotransposons, the pol protein was used. An asterisk denotes the Fusarium poae element in the tree. (PPTX 3451Â kb)
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- 2016
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38. Additional file 7: of Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, Geest, Henri Van De, Schijlen, Elio, HĂśfte, Monica, Saeger, Sarah De, Haesaert, Geert, Waalwijk, Cees, and Lee, Theo Van Der
- Abstract
RIPcal analysis of transposable element families on the core and the supernumerary genome. A comprehensive RIPcal analysis was performed on the core and the supernumerary genome separately. Based on an unbiased approach, 13 families out of 33 show patterns typical for RIP, and this is only detected on the core genome. (PPTX 735Â kb)
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- 2016
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39. Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, primary, Schijlen, Elio, additional, van de Geest, Henri, additional, Vegesna, Rahulsimham, additional, Hesselink, Thamara, additional, te Lintel Hekkert, Bas, additional, Sanchez Perez, Gabino, additional, Medvedev, Paul, additional, Makova, Kateryna D., additional, and de Ridder, Dick, additional
- Published
- 2017
- Full Text
- View/download PDF
40. Identification of methylated GnTI‐dependent N ‐glycans in Botryococcus brauni
- Author
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Schulze, Stefan, primary, Urzica, Eugen, additional, Reijnders, Maarten J. M. F., additional, Geest, Henri, additional, Warris, Sven, additional, Bakker, Linda V., additional, Fufezan, Christian, additional, Martins dos Santos, Vitor A. P., additional, Schaap, Peter J., additional, Peters, Sander A., additional, and Hippler, Michael, additional
- Published
- 2017
- Full Text
- View/download PDF
41. Living apart together : Crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, van de Geest, Henri, Schijlen, Elio, Höfte, Monica, De Saeger, Sarah, Haesaert, Geert, Waalwijk, Cees, van der Lee, Theo, Vanheule, Adriaan, Audenaert, Kris, Warris, Sven, van de Geest, Henri, Schijlen, Elio, Höfte, Monica, De Saeger, Sarah, Haesaert, Geert, Waalwijk, Cees, and van der Lee, Theo
- Abstract
Background: Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. Results: Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. Conclusions: For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
- Published
- 2016
42. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen
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Vanheule, Adriaan, primary, Audenaert, Kris, additional, Warris, Sven, additional, van de Geest, Henri, additional, Schijlen, Elio, additional, Höfte, Monica, additional, De Saeger, Sarah, additional, Haesaert, Geert, additional, Waalwijk, Cees, additional, and van der Lee, Theo, additional
- Published
- 2016
- Full Text
- View/download PDF
43. Metagenomics for biogas production
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Wedema, Ronald, Hofstede, Gert, Warris, Sven, Noback, Michiel, Faber, Folkert, Nap, Jan Peter, and Life Sciences & Renewable Energy
- Subjects
anaerobic digestion ,metagenomics ,anaerobe vergisting ,biogas ,metagenomica - Abstract
Next-generation sequencing technology allows culture- independent analysis of species and genes present in a complex microbial community. Such metagenomics may overcome the inability to culture microbes in isolation. Microbial communities of interest are for example responsible for making biogas. Many applications in metagenomics focus on 16S RNA analysis. We here evaluate the possibility of whole genome analysis (WGS) as approach for metagenomics studies. Samples (Table 1) from three biogas installations fed with different feedstock were used for DNA isolation and WGS analysis. Short (75b) Illumina paired-end DNA sequence reads were generated and assembled into larger continuous stretches (contigs), Acknowledgements Results show that WGS is feasible for complex community analysis. Large groups of organisms (for example the class Methanomicrobia) are present in all samples with a possible role in the biogas production pathway. Assemble reads into contigs •meta-velveth as metagenomics reads assembler Sequence similarity search •proteome reference database from all currently available Bacteria and Achaea genomes Assign hits to taxa •Lowest common ancestor method incorporated in MEGAN4 Such studies will help to identify and use microbial species for future improvements of biogas production dependence on process parameters and feedstock.
- Published
- 2012
44. Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS
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Warris, Sven, primary, Yalcin, Feyruz, additional, Jackson, Katherine J. L., additional, and Nap, Jan Peter, additional
- Published
- 2015
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45. Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences
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Warris, Sven, primary, Boymans, Sander, additional, Muiser, Iwe, additional, Noback, Michiel, additional, Krijnen, Wim, additional, and Nap, Jan-Peter, additional
- Published
- 2014
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46. Fusariumin the age of genomics
- Author
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Waalwijk, Cees, Vanheule, Adriaan, Audenaert, Kris, Zhang, Hao, Warris, Sven, Geest, Henri, and Lee, Theo
- Abstract
Fusariumis a large genus that includes animal and plant pathogenic species as well as saprophytes. Moreover, specimens from this genus are used in biocontrol as well as for industrial applications. We integrated various disciplines on representatives across the genus. Chromosome numbers (CN) were determined using Germ Tube Burst Method (GTBM), and different sequencing platforms were applied to generate high quality assemblies. In several species, remarkable genome plasticity is observed, including variable CNs and the presence of supernumerary chromosomes that differ markedly from the core chromosomes. It appears that several fusion events between core chromosomes happened during speciation. In F. poae, these supernumerary chromosomes (~8 Mb) exhibit marked differences from the core chromosomes: in the core genome only 2.1% consists of transposable elements (TEs) while TEs make up 25% of the supernumerary chromosomes. The TEs in the core genome show clear signs of repeat-induced point mutation (RIP), while no RIP was found in the supernumerary genome. In addition, no paralogous genes are present on the core, but many are found in the supernumerary genome. Exchange of genetic material occurs between the core and supernumerary genomes. Intact TEs from the supernumerary genome integrate into the core chromosomes, where they are subsequently subjected to RIP. In addition, large blocks of sequence (>200 kb) from the supernumerary genome have recently been translocated to the core genome. The reverse also appears to have occurred: genes from the core seem to have undergone duplication followed by translocation of one of the resulting paralogs to the supernumerary genome, where some paralogs may have undergone further duplications. This exchange of genes between the core and supernumerary genomes bestows significant opportunities for adaptation and evolution on the organism. This is reminiscent to the compartmentalization of genetic material in F. graminearum, where non-conserved regions are found at various places on the four core chromosomes.
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- 2017
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47. Application of high performance compute technology in bioinformatics
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Warris, Sven, primary
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48. Fast selection of miRNA candidates based on largescale pre-computed MFE sets of randomized sequences.
- Author
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Warris, Sven, Boymans, Sander, Muiser, Iwe, Noback, Michiel, Krijnen, Wim, and Nap, Jan-Peter
- Subjects
- *
MICRORNA , *GENOMES , *FREE energy (Thermodynamics) , *NUCLEOTIDES , *NON-coding RNA - Abstract
Background Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Results Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. Conclusion The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification. [ABSTRACT FROM AUTHOR]
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- 2014
- Full Text
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49. Additional file 8: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
- Subjects
3. Good health - Abstract
Coverage and identity of the X-degenerate gene transcripts in GorY and GorY-Clean assemblies. (DOCX 25 kb)
50. Additional file 14: of Correcting palindromes in long reads after whole-genome amplification
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Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De
- Subjects
3. Good health - Abstract
Dotplots mapping Human USP9Y gene to the GorY scaffolds and GorY-Clean contigs. (DOCX 186 kb)
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