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Edoardo Piombo  _ Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden.
Ahmed Abdelfattah  _  Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, 11418 Stockholm, Sweden.
Samir Droby  _ Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel.
Michael Wisniewski  _ U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA; Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA.
Davide Spadaro  _ Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; AGROINNOVA-Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy.
Leonardo Schena  _ Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy.

 

Globalization 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.

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

Edoardo Piombo  _ Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden.
Ahmed Abdelfattah  _  Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, 11418 Stockholm, Sweden.
Samir Droby  _ Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel.
Michael Wisniewski  _ U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA; Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA.
Davide Spadaro  _ Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; AGROINNOVA-Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy.
Leonardo Schena  _ Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy.

 

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

Globalization 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.

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