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Brown JK. Editorial overview: Fungal diversity: Now for something completely different. Curr Opin Microbiol 2023; 73:102294. [PMID: 37018995 DOI: 10.1016/j.mib.2023.102294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- James Km Brown
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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Knight NL, Moslemi A, Begum F, Dodhia KN, Covarelli L, Hills AL, Lopez-Ruiz FJ. Detection of Ramularia collo-cygni from barley in Australia using triplex quantitative and droplet digital PCR. PEST MANAGEMENT SCIENCE 2022; 78:1367-1376. [PMID: 34889505 DOI: 10.1002/ps.6753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Ramularia leaf spot (RLS), caused by Ramularia collo-cygni, is an emerging threat to barley (Hordeum vulgare L.) production. RLS has been reported in Australia, however only minimal information is available regarding its detection and distribution. Due to initial asymptomatic growth in planta, slow growth in vitro and symptomatic similarities to net blotch and physiological leaf spots, detection of this pathogen can be challenging. Quantitative polymerase chain reaction (PCR)-based methods for R. collo-cygni-specific identification and detection have been described, however these assays have been demonstrated to lack specificity. False-positive detections may have serious implications, thus we aimed to design a robust R. collo-cygni-specific PCR method. RESULTS Using the phylogenetically informative RNA polymerase II second largest subunit (rpb2) and translation elongation factor 1-alpha (tef1-α) genes, along with the tef1-α gene of H. vulgare, a triplex assay was developed for both quantitative and droplet digital PCR. The triplex assay detected R. collo-cygni DNA in barley leaves from New South Wales, South Australia, Tasmania, Victoria and Western Australia. No R. collo-cygni DNA was detected in barley seed grown in Western Australia. CONCLUSION The presence of R. collo-cygni DNA has been confirmed in Australian barley crops, suggesting a distribution ranging across the southern barley growing regions of Australia. The R. collo-cygni-specific assay will be a valuable tool to assist with monitoring the distribution and impact of R. collo-cygni in Australia and other regions. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Azin Moslemi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Farhana Begum
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Kejal N Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Lorenzo Covarelli
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Andrea L Hills
- Department of Primary Industries and Regional Development, State government office in Myrup, Esperance, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
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Einspanier S, Susanto T, Metz N, Wolters PJ, Vleeshouwers VG, Lankinen Å, Liljeroth E, Landschoot S, Ivanović Ž, Hückelhoven R, Hausladen H, Stam R. Whole genome sequencing elucidates the species‐wide diversity and evolution of fungicide resistance in the early blight pathogen
Alternaria solani. Evol Appl 2022; 15:1605-1620. [PMID: 36330303 PMCID: PMC9624079 DOI: 10.1111/eva.13350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/28/2022] Open
Abstract
Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI‐resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, shortly after the introduction of SDHIs. Two primary mutations in the SDH complex (SdhB‐H278Y and SdhC‐H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. For this project, we performed whole‐genome sequencing for 48 A. solani isolates from potato fields across Europe to better characterize the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. The isolates can be grouped into seven genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. We found clear evidence for recombination on the genome, and the observed admixtures might indicate a higher adaptive potential of the fungus than previously thought. Yet, we cannot link the observed recombination events to different Sdh mutations. The same Sdh mutations appear in different, non‐admixed genetic backgrounds; therefore, we conclude they arose independently. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes, apparent admixture in the populations, and evidence for recombination indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.
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Affiliation(s)
| | - Tamara Susanto
- Chair of Phytopathology Technical University of Munich Freising Germany
| | - Nicole Metz
- Chair of Phytopathology Technical University of Munich Freising Germany
| | - Pieter J. Wolters
- Plant Breeding Wageningen University and Research Wageningen The Netherlands
| | | | - Åsa Lankinen
- Department of Plant Protection Swedish University of Agricultural Sciences Lomma Sweden
| | - Erland Liljeroth
- Department of Plant Protection Swedish University of Agricultural Sciences Lomma Sweden
| | | | - Žarko Ivanović
- Institute for Plant Protection and Environment Belgrade Serbia
| | - Ralph Hückelhoven
- Chair of Phytopathology Technical University of Munich Freising Germany
| | - Hans Hausladen
- Plant Technology Centre Technical University of Munich Freising Germany
| | - Remco Stam
- Chair of Phytopathology Technical University of Munich Freising Germany
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Fungicide Resistance Evolving in Ramularia collo-cygni Population in Estonia. Microorganisms 2021; 9:microorganisms9071514. [PMID: 34361949 PMCID: PMC8307248 DOI: 10.3390/microorganisms9071514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022] Open
Abstract
Ramularia leaf spot caused by the fungus Ramularia collo-cygni, has recently become widespread in Estonian barley fields. Currently, disease control in barley fields relies on SDHI and DMI fungicides, which might be threatened by R. collo-cygni isolates that are well-adapted to fungicide pressure. In a two-year study, 353 R. collo-cygni isolates were collected from spring barley fields in Estonia. A total of 153 R. collo-cygni isolates were examined for sensitivity to azoles (DMIs; prothioconazole-desthio, epoxiconazole, mefentrifluconazole) and succinate dehydrogenase inhibitors (SDHIs; boscalid, fluxapyroxad). Epoxiconazole was the least effective and a new fungicide mefentrifluconazole was the most effective DMI. Among SDHIs, fluxapyroxad was more effective than boscalid. Also, single R. collo-cygni isolates with high resistance to tested fungicides occurred, which could affect fungicide control of the pathogen. The entire collection of R. collo-cygni was analysed for mutations in fungicide target proteins. Six mutations were identified in CYP51 gene, the most dominant being I381T, I384T, and S459C. Also, numerous point mutations in the SdhC gene were present. The mutation G143A in strobilurin target protein CytB dominates in over 80% of the R. collo-cygni population, confirming the low efficacy of strobilurin fungicides in barley disease control.
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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Drott MT, Satterlee TR, Skerker JM, Pfannenstiel BT, Glass NL, Keller NP, Milgroom MG. The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus. mBio 2020; 11:e00963-20. [PMID: 32665272 PMCID: PMC7360929 DOI: 10.1128/mbio.00963-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/18/2020] [Indexed: 11/20/2022] Open
Abstract
The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of Aspergillus flavus impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of A. flavus sampled from seven states in eastern and central latitudinal transects of the United States. The overall population is subdivided into three genetically differentiated populations (A, B, and C) that differ greatly in their extent of recombination, diversity, and aflatoxin-producing ability. Estimates of the number of recombination events and linkage disequilibrium decay suggest relatively frequent sex only in population A. Population B is sympatric with population A but produces significantly less aflatoxin and is the only population where the inability of nonaflatoxigenic isolates to produce aflatoxin was explained by multiple gene deletions. Population expansion evident in population B suggests a recent introduction or range expansion. Population C is largely nonaflatoxigenic and restricted mainly to northern sampling locations through restricted migration and/or selection. Despite differences in the number and type of mutations in the aflatoxin gene cluster, codon optimization and site frequency differences in synonymous and nonsynonymous mutations suggest that low levels of recombination in some A. flavus populations are sufficient to purge deleterious mutations.IMPORTANCE Differences in the relative frequencies of sexual and asexual reproduction have profound implications for the accumulation of deleterious mutations (Muller's ratchet), but little is known about how these differences impact the evolution of ecologically important phenotypes. Aspergillus flavus is the main producer of aflatoxin, a notoriously potent carcinogen that often contaminates food. We investigated if differences in the levels of production of aflatoxin by A. flavus could be explained by the accumulation of deleterious mutations due to a lack of recombination. Despite differences in the extent of recombination, variation in aflatoxin production is better explained by the demography and history of specific populations and may suggest important differences in the ecological roles of aflatoxin among populations. Furthermore, the association of aflatoxin production and populations provides a means of predicting the risk of aflatoxin contamination by determining the frequencies of isolates from low- and high-production populations.
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Affiliation(s)
- Milton T Drott
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Tatum R Satterlee
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeffrey M Skerker
- Innovative Genomics Institute, The University of California, Berkeley, California, USA
| | | | - N Louise Glass
- Innovative Genomics Institute, The University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, The University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology, The Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, USA
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