Whole-genome SNP analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto

dc.creatorKulik, Tomasz
dc.creatorMolcan, Tomasz
dc.creatorFiedorowicz, Grzegorz
dc.creatorvan Diepeningen, Anne
dc.creatorStakheev, Alexander
dc.creatorTreder, Kinga
dc.creatorOlszewski, Jacek
dc.creatorBilska, Katarzyna
dc.creatorBeyer, Marco
dc.creatorPasquali, Matias
dc.creatorStenglein, Sebastian Alberto
dc.date2022-07
dc.date.accessioned2023-08-31T00:07:12Z
dc.date.available2023-08-31T00:07:12Z
dc.identifierhttp://hdl.handle.net/11336/203099
dc.identifierKulik, Tomasz; Molcan, Tomasz; Fiedorowicz, Grzegorz; van Diepeningen, Anne; Stakheev, Alexander; et al.; Whole-genome SNP analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto; Frontiers Media S.A.; Frontiers in Microbiology; 13; 7-2022; 1-9
dc.identifier1664-302X
dc.identifierCONICET Digital
dc.identifierCONICET
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/8543114
dc.descriptionRecent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, a few among them may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.
dc.descriptionFil: Kulik, Tomasz. Department Of Botany And Nature Protection, University; Polonia
dc.descriptionFil: Molcan, Tomasz. Department Of Bioinformatics, Institute Of Biochemistry; Polonia
dc.descriptionFil: Fiedorowicz, Grzegorz. Department Of Botany And Nature Protection, University; Polonia
dc.descriptionFil: van Diepeningen, Anne. Biointeractions & Plant Health, Wageningen Plant Res; Países Bajos
dc.descriptionFil: Stakheev, Alexander. Shemyakin And Ovchinnikov Institute Of Bioorganic Chem; Rusia
dc.descriptionFil: Treder, Kinga. Department Of Agriculture Systems, University Of Warmia; Polonia
dc.descriptionFil: Olszewski, Jacek. Experimental Education Unit; Polonia
dc.descriptionFil: Bilska, Katarzyna. Department Of Botany And Nature Protection, University; Polonia
dc.descriptionFil: Beyer, Marco. Agro-environmental Systems, Luxembourg Institute; Luxemburgo
dc.descriptionFil: Pasquali, Matias. Department Of Food, University Of Milan; Italia
dc.descriptionFil: Stenglein, Sebastian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Cientifico Tecnolológico Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología. Laboratorio de Biología Funcional y Biotecnología; Argentina
dc.formatapplication/pdf
dc.formatapplication/pdf
dc.languageeng
dc.publisherFrontiers Media S.A.
dc.relationinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fmicb.2022.885978
dc.relationinfo:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fmicb.2022.885978/full
dc.rightsinfo:eu-repo/semantics/openAccess
dc.rightshttps://creativecommons.org/licenses/by/2.5/ar/
dc.subjectFUSARIUM GRAMINEARUM SENSU STRICTO
dc.subjectF. GRAMINEARUM COMPLEX
dc.subjectWHOLE-GENOME SEQUENCING
dc.subjectPLANT PATHOGEN
dc.subjectIDENTIFICATION
dc.subjecthttps://purl.org/becyt/ford/4.1
dc.subjecthttps://purl.org/becyt/ford/4
dc.subjecthttps://purl.org/becyt/ford/1.6
dc.subjecthttps://purl.org/becyt/ford/1
dc.titleWhole-genome SNP analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto
dc.typeinfo:eu-repo/semantics/article
dc.typeinfo:ar-repo/semantics/artículo
dc.typeinfo:eu-repo/semantics/publishedVersion


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