Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto.

Autor:	Kulik T; Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland., Molcan T; Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Warsaw, Poland., Fiedorowicz G; Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland., van Diepeningen A; Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands., Stakheev A; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia., Treder K; Department of Agriculture Systems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland., Olszewski J; Experimental Education Unit, Olsztyn, Poland., Bilska K; Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland., Beyer M; Agro-Environmental Systems, Environmental Monitoring and Sensing Unit, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg., Pasquali M; Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy., Stenglein S; National Scientific and Technical Research Council, Godoy Cruz, Argentina.; Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2022 Jul 18; Vol. 13, pp. 885978. Date of Electronic Publication: 2022 Jul 18 (Print Publication: 2022).
DOI:	10.3389/fmicb.2022.885978
Abstrakt:	Recent 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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Kulik, Molcan, Fiedorowicz, van Diepeningen, Stakheev, Treder, Olszewski, Bilska, Beyer, Pasquali and Stenglein.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu