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Looking beyond virus detection in RNA sequencing data: Lessons learned from a community-based effort to detect cellular plant pathogens and pests

hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorHAEGEMAN, Annelies
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorFOUCART, Yoika
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorDE JONGHE, Kris
hal.structure.identifierResearch Institute for Agricultural, Fisheries and Food [ILVO]
dc.contributor.authorGOEDEFROIT, Thomas
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorAL RWAHNIH, Maher
hal.structure.identifierNewcastle University [Newcastle]
dc.contributor.authorBOONHAM, Neil
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierJulius Kühn-Institut [JKI]
dc.contributor.authorGAAFAR, Yahya
hal.structure.identifierUSDA-APHIS PPQ
dc.contributor.authorHURTADO-GONZALES, Oscar
hal.structure.identifierNational Institute of Biology [Ljubljana] [NIB]
hal.structure.identifierJozef Stefan International Postgraduate School [Ljubljana, Slovenia]
dc.contributor.authorKOGEJ ZWITTER, Zala
hal.structure.identifierNational Institute of Biology [Ljubljana] [NIB]
dc.contributor.authorKUTNJAK, Denis
hal.structure.identifierAgricultural Institute of Slovenia
dc.contributor.authorLAMOVŠEK, Janja
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLEFEBVRE, Marie
hal.structure.identifierUSDA Animal and Plant Health Inspection Service [USDA-APHIS]
dc.contributor.authorMALAPI, Martha
hal.structure.identifierAgricultural Institute of Slovenia
dc.contributor.authorMAVRIČ PLEŠKO, Irena
hal.structure.identifierUnited States Department of Agriculture [USDA]
dc.contributor.authorÖNDER, Serkan
hal.structure.identifierDepartment of Plant Protection, Agroscope
dc.contributor.authorREYNARD, Jean-Sébastien
hal.structure.identifierChemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
dc.contributor.authorSALAVERT PAMBLANCO, Ferran
hal.structure.identifierDepartment of Plant Protection, Agroscope
dc.contributor.authorSCHUMPP, Olivier
hal.structure.identifierUniversity of California [Davis] [UC Davis]
dc.contributor.authorSTEVENS, Kristian
hal.structure.identifierZespri International Limited
dc.contributor.authorPAL, Chandan
hal.structure.identifierGénétique et Amélioration des Fruits et Légumes [GAFL]
hal.structure.identifierUnité de Pathologie Végétale [PV]
dc.contributor.authorTAMISIER, Lucie
hal.structure.identifierNiğde Ömer Halisdemir University
dc.contributor.authorULUBAŞ SERÇE, Çiğdem
hal.structure.identifierDutch General Inspection Service for Agricultural Seed and Seed Potatoes
dc.contributor.authorVAN DUIVENBODE, Inge
hal.structure.identifierPlant Health and Environment Laboratory, Ministry for Primary Industries
dc.contributor.authorWAITE, David
hal.structure.identifierUSDA-APHIS PPQ
dc.contributor.authorHU, Xiaojun
hal.structure.identifierJulius Kühn-Institut - Federal Research Centre for Cultivated Plants [JKI]
dc.contributor.authorZIEBELL, Heiko
hal.structure.identifierGembloux Agro-Bio Tech, University of Liege
dc.contributor.authorMASSART, Sébastien
dc.date.issued2023-06
dc.identifier.issn2223-7747
dc.description.abstractEnHigh-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
dc.language.isoen
dc.publisherMDPI
dc.subject.enplant pathogen
dc.subject.endiagnostics
dc.subject.enhigh-throughput sequencing
dc.subject.enmetagenomics
dc.subject.enmetatranscriptomics
dc.subject.enRNA-seq
dc.title.enLooking beyond virus detection in RNA sequencing data: Lessons learned from a community-based effort to detect cellular plant pathogens and pests
dc.typeArticle de revue
dc.identifier.doi10.3390/plants12112139
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie
dc.description.sponsorshipEuropePlant Health Bioinformatics Network
bordeaux.journalPlants
bordeaux.page2139
bordeaux.volume12
bordeaux.issue11
bordeaux.peerReviewedoui
hal.identifierhal-04117624
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04117624v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Plants&rft.date=2023-06&rft.volume=12&rft.issue=11&rft.spage=2139&rft.epage=2139&rft.eissn=2223-7747&rft.issn=2223-7747&rft.au=HAEGEMAN,%20Annelies&FOUCART,%20Yoika&DE%20JONGHE,%20Kris&GOEDEFROIT,%20Thomas&AL%20RWAHNIH,%20Maher&rft.genre=article


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