Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

Simple item page
dc.contributor.authorPiombo, Edoardoen
dc.contributor.authorAbdelfattah, Ahmeden
dc.contributor.authorDroby, Samiren
dc.contributor.authorWisniewski, Michaelen
dc.contributor.authorSpadaro, Davideen
dc.contributor.authorSchena, Leonardoen
dc.contributor.departmentBiological Sciencesen
dc.date.accessioned2021-06-11T15:14:53Zen
dc.date.available2021-06-11T15:14:53Zen
dc.date.issued2021-01en
dc.description.abstractGlobalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding and shotgun metagenomics could be used to simultaneously detect all known pathogens and potentially new ones. This review aims to present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS techniques, particularly metabarcoding, could be useful for the surveillance of soilborne, seedborne and airborne pathogens, as well as for identifying new pathogens and determining the origin of outbreaks. Metabarcoding and shotgun metagenomics still suffer from low precision, but this issue can be limited by carefully choosing primers and bioinformatic algorithms. Advances in bioinformatics will greatly accelerate the use of metagenomics to address critical aspects related to the detection and surveillance of plant pathogens in plant material and foodstuffs.en
dc.description.notesThe Authors wish to thank the European Institute of Innovation and Technology for funding the project "CLEANFRUIT-Standardization of innovative pest control strategies to produce zero residue fruit for baby food and other fruit produce" (EITFood initiative), the Italian Ministry for Education, University and Research for funding the project "A gnotobiotic-based approach to unravel the role of the plant microbiome and develop synthetic communities increasing plant growth and stress tolerance-NATURE" (PRIN2017 programme) and Fondazione Cassa di Risparmio di Cuneo for funding the project, "SMART APPLE-Innovative and SMART technologies for sustainable APPLE production".en
dc.description.sponsorshipEuropean Institute of Innovation and Technology; Italian Ministry for Education, University and ResearchMinistry of Education, Universities and Research (MIUR); Fondazione Cassa di Risparmio di Cuneoen
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3390/microorganisms9010188en
dc.identifier.eissn2076-2607en
dc.identifier.issue1en
dc.identifier.other188en
dc.identifier.pmid33467169en
dc.identifier.urihttp://hdl.handle.net/10919/103786en
dc.identifier.volume9en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectsurveillanceen
dc.subjectplant pathogensen
dc.subjectmetabarcodingen
dc.subjectmetagenomicsen
dc.subjectdetectionen
dc.titleMetagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogensen
dc.title.serialMicroorganismsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
microorganisms-09-00188.pdf
Size:
933.14 KB
Format:
Adobe Portable Document Format
Description:
Published version
Download

Collections

Scholarly Works, Biological Sciences