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Dhakal U, Kim HS, Toomajian C. The landscape and predicted roles of structural variants in Fusarium graminearum genomes. G3 (BETHESDA, MD.) 2024; 14:jkae065. [PMID: 38546739 DOI: 10.1093/g3journal/jkae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/22/2024] [Indexed: 06/06/2024]
Abstract
Structural rearrangements, such as inversions, translocations, duplications, and large insertions and deletions, are large-scale genomic variants that can play an important role in shaping phenotypic variation and in genome adaptation and evolution. We used chromosomal-level assemblies from eight Fusarium graminearum isolates to study structural variants and their role in fungal evolution. We generated the assemblies of four of these genomes after Oxford Nanopore sequencing. A total of 87 inversions, 159 translocations, 245 duplications, 58,489 insertions, and 34,102 deletions were detected. Regions of high recombination rate are associated with structural rearrangements, and a significant proportion of inversions, translocations, and duplications overlap with the repeat content of the genome, suggesting recombination and repeat elements are major factors in the origin of structural rearrangements in F. graminearum. Large insertions and deletions introduce presence-absence polymorphisms for many genes, including secondary metabolite biosynthesis cluster genes and predicted effectors genes. Translocation events were found to be shuffling predicted effector-rich regions of the genomes and are likely contributing to the gain and loss of effectors facilitated by recombination. Breakpoints of some structural rearrangements fall within coding sequences and are likely altering the protein products. Structural rearrangements in F. graminearum thus have an important role to play in shaping pathogen-host interactions and broader evolution through genome reorganization, the introduction of presence-absence polymorphisms, and changing protein products and gene regulation.
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Affiliation(s)
- Upasana Dhakal
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St., Peoria, IL 61604, USA
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2
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Severinsen MM, Westphal KR, Terp M, Sørensen T, Olsen A, Bachleitner S, Studt-Reinhold L, Wimmer R, Sondergaard TE, Sørensen JL. Filling out the gaps - identification of fugralins as products of the PKS2 cluster in Fusarium graminearum. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1264366. [PMID: 38025899 PMCID: PMC10667903 DOI: 10.3389/ffunb.2023.1264366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023]
Abstract
As one of the grain crop pathogenic fungi with the greatest impacts on agricultural economical as well as human health, an elaborate understanding of the life cycle and subsequent metabolome of Fusarium graminearum is of great interest. Throughout the lifetime of the fungus, it is known to produce a wide array of secondary metabolites, including polyketides. One of the F. graminearum polyketides which has remained a mystery until now has been elucidated in this work. Previously, it was suggested that the biosynthetic product of the PKS2 gene cluster was involved in active mycelial growth, the exact mechanism, however, remained unclear. In our work, disruption and overexpression of the PKS2 gene in F. graminearum enabled structural elucidation of a linear and a cyclic tetraketide with a double methyl group, named fugralin A and B, respectively. Further functional characterization showed that the compounds are not produced during infection, and that deletion and overexpression did not affect pathogenicity or visual growth. The compounds were shown to be volatile, which could point to possible functions that can be investigated further in future studies.
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Affiliation(s)
- Manja Mølgaard Severinsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Mikael Terp
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simone Bachleitner
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lena Studt-Reinhold
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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3
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Chiappim W, de Paula Bernardes V, Almeida NA, Pereira VL, Bragotto APA, Cerqueira MBR, Furlong EB, Pessoa R, Rocha LO. Effect of Gliding Arc Plasma Jet on the Mycobiota and Deoxynivalenol Levels in Naturally Contaminated Barley Grains. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:5072. [PMID: 36981981 PMCID: PMC10049212 DOI: 10.3390/ijerph20065072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/22/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Fusarium graminearum and Fusarium meridionale are primary contaminants of barley, capable of producing several mycotoxins, mainly type B trichothecenes and zearalenone. Cold plasma decontamination has been gaining prominence, seeking to control the fungal and mycotoxin contamination of food and feed and to improve product quality. To reach this objective, the present study was divided into two parts. In the first part, F. meridionale and F. graminearum strains were exposed to gliding arc plasma jet (GAPJ). Cell viability tests showed the inactivation of F. meridionale after 15-min treatment, whereas F. graminearum showed to be resistant. In the second part, barley grains were treated by GAPJ for 10, 20, and 30 min, demonstrating a reduction of about 2 log CFU/g of the barley's mycobiota, composed of yeasts, strains belonging to the F. graminearum species complex, Alternaria, and Aspergillus. A decrease in DON levels (up to 89%) was observed after exposure for 20 min. However, an increase in the toxin Deoxynivalenol-3-glucoside (D3G) was observed in barley grains, indicating a conversion of DON to D3G.
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Affiliation(s)
- William Chiappim
- Laboratory of Plasmas and Applications, Department of Physics, Faculty of Engineering and Sciences, São Paulo State University (UNESP), Guaratinguetá 12516-410, Brazil
| | - Vanessa de Paula Bernardes
- Laboratório de Microbiologia de Alimentos I, Departmento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas-UNICAMP, Campinas 13083-862, Brazil
| | - Naara Aparecida Almeida
- Laboratório de Microbiologia de Alimentos I, Departmento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas-UNICAMP, Campinas 13083-862, Brazil
| | - Viviane Lopes Pereira
- Laboratório de Microbiologia de Alimentos I, Departmento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas-UNICAMP, Campinas 13083-862, Brazil
| | - Adriana Pavesi Arisseto Bragotto
- Laboratório de Microbiologia de Alimentos I, Departmento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas-UNICAMP, Campinas 13083-862, Brazil
| | | | - Eliana Badiale Furlong
- Escola de Química e Alimentos, Universidade Federal do Rio Grande, Rio Grande 96203-900, Brazil
| | - Rodrigo Pessoa
- Laboratório de Plasmas e Processos, Departamento de Física, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, Brazil
| | - Liliana Oliveira Rocha
- Laboratório de Microbiologia de Alimentos I, Departmento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas-UNICAMP, Campinas 13083-862, Brazil
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Powell AJ, Kim SH, Cordero J, Vujanovic V. Protocooperative Effect of Sphaerodes mycoparasitica Biocontrol and Crop Genotypes on FHB Mycotoxin Reduction in Bread and Durum Wheat Grains Intended for Human and Animal Consumption. Microorganisms 2023; 11:microorganisms11010159. [PMID: 36677451 PMCID: PMC9861577 DOI: 10.3390/microorganisms11010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
The occurrence of Fusarium Head Blight (FHB) mycotoxins in wheat grains is a major threat to global food safety and security. Humans and animals are continuously being exposed to Fusarium mycotoxins such as deoxynivalenol (DON) and its acetylated derivatives 3ADON and 15ADON through the ingestion of contaminated food or grain-based diet. In this study, a host-specific mycoparasite biocontrol agent (BCA), Sphaerodes mycoparasitica, significantly reduced FHB mycotoxin occurrence in harvested wheat grains from Fusarium graminearum 3ADON chemotype infected plants in greenhouse. Four genotypes of wheat, two common wheat and two durum wheat cultivars with varying FHB resistance levels were used in this study. Principal Coordinate Analysis (PCoA) using Illumina ITS sequences depicted beta diversity changes in Fusarium species indicating that both plant cultivar and BCA treatments influenced the Fusarium species structure and mycotoxin occurrence in grains. Fusarium graminearum complex (cluster A), F. avenaceum and F. acuminatum (cluster B), and F. proliferatum (cluster C) variants were associated with different FHB mycotoxins based on LC-MS/MS analyses. The predominant FHB mycotoxins measured were DON and its acetylated derivatives 3ADON and 15ADON. The BCA reduced the occurrence of DON in grains of all four cultivars (common wheat: 1000-30,000 µg·kg-1.; durum wheat: 600-1000 µg·kg-1) to levels below the Limit of Quantification (LOQ) of 16 µg·kg-1. A relatively higher concentration of DON was detected in the two common wheat genotypes when compared to the durum wheat genotype; however, the percentage reduction in the wheat genotypes was greater, reaching up to 99% with some S. mycoparasitica treatments. Similarly, a higher reduction in DON was measured in susceptible genotypes than in resistant genotypes. This study's findings underscore the potential of a Fusarium-specific S. mycoparasitica BCA as a safe and promising alternative that can be used in conjunction with other management practices to minimize FHB mycotoxins in cereal grain, food and feed intended for human and animal consumption.
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Rowland BE, Henriquez MA, Nilsen KT, Subramaniam R, Walkowiak S. Unraveling Plant-Pathogen Interactions in Cereals Using RNA-seq. Methods Mol Biol 2023; 2659:103-118. [PMID: 37249889 DOI: 10.1007/978-1-0716-3159-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Over the past two decades, there have been significant advancements in the realm of transcriptomics, or the study of genes and their expression. Modern RNA sequencing technologies and high-performance computing are creating a "big data" revolution that provides new opportunities to explore the interactions between cereals and pathogens that affect grain yield and food safety. These data are being used to annotate genes and gene variants, as well as identify differentially expressed genes and create global gene co-expression networks. Moreover, these data can unravel the complex interactions between pathogen and host and identify genes and pathways involved in these interactions. This information can then be used for disease mitigation and the development of crops with superior resistance.
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Affiliation(s)
- Bronwyn E Rowland
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Kirby T Nilsen
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada.
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
| | - Sean Walkowiak
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada.
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Comparative transcriptome analysis reveals the biocontrol mechanism of Bacillus velezensis E68 against Fusarium graminearum DAOMC 180378, the causal agent of Fusarium head blight. PLoS One 2023; 18:e0277983. [PMID: 36701319 PMCID: PMC9879434 DOI: 10.1371/journal.pone.0277983] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/07/2022] [Indexed: 01/27/2023] Open
Abstract
Fusarium graminearum is the causal agent of Fusarium Head Blight, a serious disease affecting grain crops worldwide. Biological control involves the use of microorganisms to combat plant pathogens such as F. graminearum. Strains of Bacillus velezensis are common biological control candidates for use against F. graminearum and other plant pathogens, as they can secrete antifungal secondary metabolites. Here we study the interaction between B. velezensis E68 and F. graminearum DAOMC 180378 by employing a dual RNA-seq approach to assess the transcriptional changes in both organisms. In dual culture, B. velezensis up-regulated genes related to sporulation and phosphate stress and down-regulated genes related to secondary metabolism, biofilm formation and the tricarboxylic acid cycle. F. graminearum up-regulated genes encoding for killer protein 4-like proteins and genes relating to heavy metal tolerance, and down-regulated genes relating to trichothecene biosynthesis and phenol metabolism. This study provides insight into the molecular mechanisms involved in the interaction between a biocontrol bacterium and a phytopathogenic fungus.
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Ayada H, Dhioui B, Mazouz H, El Harrak A, Jaiti F, Ouhmidou B, Diouri M, Moumni M. In silico comparative genomic analysis unravels a new candidate protein arsenal specifically associated with Fusarium oxysporum f. sp. albedinis pathogenesis. Sci Rep 2022; 12:19098. [PMID: 36351932 PMCID: PMC9646873 DOI: 10.1038/s41598-022-21858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
Fusarium oxysporum f. sp albedinis (Foa) is a devastating fungus of date palms. To unravel the genetic characteristics associated with its pathogenesis, the two available genomes of Foa 133 and Foa 9 were compared with 49 genomes of 29 other pathogenic formae speciales belonging to Fusarium oxysporum species complex (FOSC). Foa 133 and Foa 9 have genomes of 56.23 Mb and 65.56 Mb with 17460 and 19514 putative coding genes. Of these genes, 30% lack functional annotation with no similarity to characterized proteins. The remaining genes were involved in pathways essential to the fungi's life and their adaptation. Foa secretome analysis revealed that both Foa strains possess an expanded number of secreted effectors (3003 in Foa 133 and 2418 in Foa 9). Those include effectors encoded by Foa unique genes that are involved in Foa penetration (Egh16-like family), host defense mechanisms suppression (lysM family) and pathogen protection (cysteine-rich protein family). The accessory protein SIX6, which induces plant cell death, was also predicted in Foa. Further analysis of secreted CAZymes revealed an arsenal of enzymes involved in plant cell wall degradation. This arsenal includes an exclusively Foa-specific CAZyme (GH5-7). Transcription factors and membrane transporters (MFS) involved in fungicide efflux have been predicted in Foa, in addition to a variety of secondary metabolites. These comprise mycotoxins as well as chrysogin, the latter provides Foa with resistance against adverse environmental conditions. Our results revealed new Foa proteins that could be targeted in future research in order to manage Bayoud disease.
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Affiliation(s)
- Hafida Ayada
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco.
| | - Boutayna Dhioui
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco
| | - Hamid Mazouz
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco
| | - Abdelhay El Harrak
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco
| | - Fatima Jaiti
- Biodiversity, Environment and Plant Protection Team, Faculty of Sciences and Technologies, Moulay Ismail University of Meknès, Meknès, Morocco
| | - Bouchra Ouhmidou
- Microbial biotechnology and bioactive molecules laboratory, Faculty of Sciences and Technologies, Sidi Mohammed Ben Abdellah University of Fez, Fez, Morocco
| | - Mohammed Diouri
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco
| | - Mohieddine Moumni
- Biotechnology and Bioresources Valorization Laboratory, Biology Department, Faculty of Sciences, Moulay Ismail University of Meknès, Meknès, Morocco.
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Kulik T, Molcan T, Fiedorowicz G, van Diepeningen A, Stakheev A, Treder K, Olszewski J, Bilska K, Beyer M, Pasquali M, Stenglein S. Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto. Front Microbiol 2022; 13:885978. [PMID: 35923405 PMCID: PMC9339996 DOI: 10.3389/fmicb.2022.885978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- *Correspondence: Tomasz Kulik,,
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Warsaw, Poland
| | - Grzegorz Fiedorowicz
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kinga Treder
- Department of Agriculture Systems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marco Beyer
- Agro-Environmental Systems, Environmental Monitoring and Sensing Unit, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
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Maphosa MN, Steenkamp ET, Kanzi AM, van Wyk S, De Vos L, Santana QC, Duong TA, Wingfield BD. Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum. J Fungi (Basel) 2022; 8:jof8070657. [PMID: 35887414 PMCID: PMC9316270 DOI: 10.3390/jof8070657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.
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Fulton JC, Yu PL, Smith KE, Huguet-Tapia JC, Hudson O, Meeks A, Quesada T, McKeever K, Brawner JT. Comparative Genomics of Fusarium circinatum Isolates Used to Screen Southern Pines for Pitch Canker Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:477-487. [PMID: 35266808 DOI: 10.1094/mpmi-10-21-0247-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pitch canker, caused by the fungal pathogen Fusarium circinatum, is a global disease affecting many Pinus spp. Often fatal, this disease causes significant mortality in both commercially grown and natural pine forests and is an issue of current and growing concern. F. circinatum isolates collected from three locations in the U.S. state of Florida were shown to be virulent on both slash and loblolly pine, with two of the isolates causing equivalent and significantly larger lesions than those caused by the third isolate during pathogenicity trials. In addition, significant genetic variation in lesion length in the pedigreed slash pine population was evident and rankings of parents for lesion length were similar across isolates. Experimental data demonstrate that both host and pathogen genetics contribute to disease severity. High-quality genomic assemblies of all three isolates were created and compared for structural differences and gene content. No major structural differences were observed among the isolates; however, missing or altered genes do contribute to genomic variation in the pathogen population. This work evaluates in planta virulence among three isolates of F. circinatum, provides genomic resources to facilitate study of this organism, and details comparative genomic methods that may be used to explore the pathogen's contribution to disease development.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Katherine E Smith
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, U.S.A
- United States Department of Agriculture Forest Service, Southern Institute of Forest Genetics, Saucier, MS, U.S.A
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Owen Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Tania Quesada
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, U.S.A
| | - Kathleen McKeever
- United States Department of Agriculture Forest Service, Resistance Screening Center, Asheville, NC, U.S.A
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
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Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication. J Fungi (Basel) 2022; 8:jof8060581. [PMID: 35736064 PMCID: PMC9225563 DOI: 10.3390/jof8060581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
In order to reveal the genetic variation signals of Auricularia heimuer that have occurred during their domestication and to find potential functional gene families, we constructed a monokaryotic pan-genome of A. heimuer representing four cultivated strains and four wild strains. The pan-genome contained 14,089 gene families, of which 67.56% were core gene families and 31.88% were dispensable gene families. We screened substrate utilization-related genes such as the chitinase gene ahchi1 of the glycoside hydrolase (GH) 18 family and a carbohydrate-binding module (CBM)-related gene from the dispensable families of cultivated populations. The genomic difference in the ahchi1 gene between the wild and cultivated genomes was caused by a 33 kb presence/absence variation (PAV). The detection rate of the ahchi1 gene was 93.75% in the cultivated population, significantly higher than that in the wild population (17.39%), indicating that it has been selected in cultivated strains. Principal component analysis (PCA) of the polymorphic markers in fragments near the ahchi1 gene was enriched in cultivated strains, and this was caused by multiple independent instances of artificial selection. We revealed for the first time the genetic basis of the ahchi1 gene in domestication, thereby providing a foundation for elucidating the potential function of the ahchi1 gene in the breeding of A. heimuer.
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12
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Yuan Z, Wu Q, Xu L, Druzhinina IS, Stukenbrock EH, Nieuwenhuis BPS, Zhong Z, Liu ZJ, Wang X, Cai F, Kubicek CP, Shan X, Wang J, Shi G, Peng L, Martin FM. Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism. THE ISME JOURNAL 2022; 16:1294-1305. [PMID: 34916613 PMCID: PMC9038928 DOI: 10.1038/s41396-021-01176-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022]
Abstract
Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.
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Affiliation(s)
- Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China. .,Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Qi Wu
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Liangxiong Xu
- grid.411411.00000 0004 0644 5457School of Life Sciences, Huizhou University, Huizhou, 516007 China
| | - Irina S. Druzhinina
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China ,grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Eva H. Stukenbrock
- grid.9764.c0000 0001 2153 9986Botanical Institute, Christian-Albrechts Universität zu Kiel, 24118 Kiel, Germany ,grid.419520.b0000 0001 2222 4708Environmental Genomics Research Group, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Bart P. S. Nieuwenhuis
- grid.5252.00000 0004 1936 973XDivision of Evolutionary Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Zhenhui Zhong
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Zhong-Jian Liu
- grid.256111.00000 0004 1760 2876Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinyu Wang
- grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Feng Cai
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Christian P. Kubicek
- grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Xiaoliang Shan
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Jieyu Wang
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Guohui Shi
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Long Peng
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Francis M. Martin
- grid.29172.3f0000 0001 2194 6418Université de Lorraine, INRAe, UMR 1136 Interactions Arbres/Microorganismes, INRAe-Grand Est-Nancy, 54280 Champenoux, France
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13
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Konkin D, Hsueh YC, Kirzinger M, Kubaláková M, Haldar A, Balcerzak M, Han F, Fedak G, Doležel J, Sharpe A, Ouellet T. Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL. BMC Genomics 2022; 23:228. [PMID: 35321662 PMCID: PMC8944066 DOI: 10.1186/s12864-022-08433-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background The tall wheatgrass species Thinopyrum elongatum carries a strong fusarium head blight (FHB) resistance locus located on the long arm of chromosome 7 (7EL) as well as resistance to leaf and stem rusts, all diseases with a significant impact on wheat production. Towards understanding the contribution of Th. elongatum 7EL to improvement of disease resistance in wheat, the genomic sequence of the 7EL fragment present in the wheat Chinese Spring (CS) telosomic addition line CS-7EL was determined and the contribution and impact of 7EL on the rachis transcriptome during FHB infection was compared between CS and CS-7EL. Results We assembled the Th. elongatum 7EL chromosome arm using a reference-guided approach. Combining this assembly with the available reference sequence for CS hexaploid wheat provided a reliable reference for interrogating the transcriptomic differences in response to infection conferred by the 7EL fragment. Comparison of the transcriptomes of rachis tissues from CS and CS-7EL showed expression of Th. elongatum transcripts as well as modulation of wheat transcript expression profiles in the CS-7EL line. Expression profiles at 4 days after infection with Fusarium graminearum, the causal agent of FHB, showed an increased in expression of genes associated with an effective defense response, in particular glucan endo-1,3-beta-glucosidases and chitinases, in the FHB-resistant line CS-7EL while there was a larger increase in differential expression for genes associated with the level of fungal infection in the FHB-susceptible line CS. One hundred and seven 7EL transcripts were expressed in the smallest 7EL region defined to carry FHB resistance. Conclusion 7EL contributed to CS-7EL transcriptome by direct expression and through alteration of wheat transcript profiles. FHB resistance in CS-7EL was associated with transcriptome changes suggesting a more effective defense response. A list of candidate genes for the FHB resistance locus on 7EL has been established. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08433-8.
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Affiliation(s)
- David Konkin
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Ya-Chih Hsueh
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan Kirzinger
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Marie Kubaláková
- Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Aparna Haldar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences No1, Beijing, China
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, CZ-77900, Olomouc, Czech Republic
| | - Andrew Sharpe
- Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
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14
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Rocher F, Alouane T, Philippe G, Martin ML, Label P, Langin T, Bonhomme L. Fusarium graminearum Infection Strategy in Wheat Involves a Highly Conserved Genetic Program That Controls the Expression of a Core Effectome. Int J Mol Sci 2022; 23:ijms23031914. [PMID: 35163834 PMCID: PMC8836836 DOI: 10.3390/ijms23031914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Fusarium graminearum, the main causal agent of Fusarium Head Blight (FHB), is one of the most damaging pathogens in wheat. Because of the complex organization of wheat resistance to FHB, this pathosystem represents a relevant model to elucidate the molecular mechanisms underlying plant susceptibility and to identify their main drivers, the pathogen’s effectors. Although the F. graminearum catalog of effectors has been well characterized at the genome scale, in planta studies are needed to confirm their effective accumulation in host tissues and to identify their role during the infection process. Taking advantage of the genetic variability from both species, a RNAseq-based profiling of gene expression was performed during an infection time course using an aggressive F. graminearum strain facing five wheat cultivars of contrasting susceptibility as well as using three strains of contrasting aggressiveness infecting a single susceptible host. Genes coding for secreted proteins and exhibiting significant expression changes along infection progress were selected to identify the effector gene candidates. During its interaction with the five wheat cultivars, 476 effector genes were expressed by the aggressive strain, among which 91% were found in all the infected hosts. Considering three different strains infecting a single susceptible host, 761 effector genes were identified, among which 90% were systematically expressed in the three strains. We revealed a robust F. graminearum core effectome of 357 genes expressed in all the hosts and by all the strains that exhibited conserved expression patterns over time. Several wheat compartments were predicted to be targeted by these putative effectors including apoplast, nucleus, chloroplast and mitochondria. Taken together, our results shed light on a highly conserved parasite strategy. They led to the identification of reliable key fungal genes putatively involved in wheat susceptibility to F. graminearum, and provided valuable information about their putative targets.
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Affiliation(s)
- Florian Rocher
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Tarek Alouane
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Géraldine Philippe
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Marie-Laure Martin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Saclay, Université Evry, 91190 Gif sur Yvette, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190 Gif sur Yvette, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Philippe Label
- UMR 547 Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant, INRAE, Université Clermont Auvergne, 63178 Aubière, France;
| | - Thierry Langin
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Ludovic Bonhomme
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
- Correspondence:
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15
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Liu X, Fang X, Yu F, Wang S, Zhang Z, Li K, Ye W, Lee YW, Mohamed SR, Dong F, Xu J, Shi J. Improved Whole-Genome Sequence of Fusarium meridionale, the Fungal Pathogen Causing Fusarium Head Blight in Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:85-89. [PMID: 34533972 DOI: 10.1094/mpmi-07-21-0182-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Members of the Fusarium graminearum species complex (FGSC) cause extensive yield losses in cereal production worldwide, and food safety concerns due to the accumulation of Fusarium toxins in infected grains. Among these pathogens, F. meridionale is responsible for Fusarium head blight of wheat and rice, ear and stalk rot of maize, and pod blight of soybean. Here, we present an improved genome assembly of F. meridionale strain SR5 isolated from rice in China based on PacBio long-read sequencing and Illumina short-read sequencing technology. The assembled genome of SR5 has a total size of 36.82 Mb, an N50 scaffold length of 7.82 Mb, nine scaffolds, and encodes 12,409 predicted genes. These high-quality data expand FGSC genomic resources and provide a valuable resource for better understanding their genetic diversity and the molecular basis of pathogenesis, which will facilitate the development of an effective control strategy.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Xin Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Xin Fang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Fangwei Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement/Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shuang Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kainan Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yin-Won Lee
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
- School of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sherif Ramzy Mohamed
- Department of Food Toxicology and Contaminant, National Research Centre of Egypt, Giza 12411, Egypt
| | - Fei Dong
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jianhong Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jianrong Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory for Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture and Rural Affairs/Key Laboratory for Agro-product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs/Collaborative Innovation Center for Modern Grain Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
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16
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Jiao W, Xu M, Zhou R, Fu Y, Li Z, Xue C. Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin. PLoS One 2021; 16:e0261487. [PMID: 34914789 PMCID: PMC8675698 DOI: 10.1371/journal.pone.0261487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/03/2021] [Indexed: 12/01/2022] Open
Abstract
Elsinochromes (ESCs) are virulence factors produced by Elsinoë arachidis which is the cause of peanut scab. However, the biosynthesis pathway of ESCs in E. arachidis has not been elucidated and the potential pathogenic mechanism of E. arachidis is poorly understood. In this study, we report a high-quality genome sequence of E. arachidis. The size of the E. arachidis genome is 33.18Mb, which is comparable to the Ascomycota genome (average 36.91 Mb), encoding 9174 predicted genes. The self-detoxification family including transporters and cytochrome P450 enzymes were analysis, candidate effectors and cell wall degrading enzymes were investigated as the pathogenicity genes by using PHI and CAZy databases. Additionally, the E. arachidis genome contains 24 secondary metabolism gene clusters, in which ESCB1 was identified as the core gene of ESC biosynthesis. Taken together, the genome sequence of E. arachidis provides a new route to explore its potential pathogenic mechanism and the biosynthesis pathway of ESCs.
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Affiliation(s)
- Wenli Jiao
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Mengxue Xu
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Rujun Zhou
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
| | - Yiwei Fu
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zibo Li
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Caiyun Xue
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
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17
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Xi K, Shan L, Yang Y, Zhang G, Zhang J, Guo W. Species Diversity and Chemotypes of Fusarium Species Associated With Maize Stalk Rot in Yunnan Province of Southwest China. Front Microbiol 2021; 12:652062. [PMID: 34759893 PMCID: PMC8575069 DOI: 10.3389/fmicb.2021.652062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Maize stalk rot caused by Fusarium species is one of the most important fungal diseases of maize throughout the world. The disease is responsible for considerable yield losses and has also been associated with mycotoxin contamination of the crop. In this study, a survey of maize stalk rot was performed in seven locations of Yunnan Province in China during the cropping season of 2015 and 2016. Based on morphological and molecular characteristics, 204 isolates belonging to 12 Fusarium spp. from symptomatic stalks of maize were identified. Among the isolated strains, 83 were identified as Fusarium meridionale (40.5%), 46 as Fusarium boothii (22.5%), 34 as Fusarium temperatum (16.5%), 12 as Fusarium equiseti (5.9%), 10 as Fusarium asiaticum (4.9%), six as Fusarium proliferatum (3.0%), four as Fusarium verticillioides (2.0%), four as Fusarium incarnatum (2.0%), two as Fusarium avenaceum (1.0%), one as Fusarium cerealis (0.5%), one as Fusarium graminearum (0.5%), and one as Fusarium cortaderiae (0.5%). Fusarium cortaderiae was the first report on the causal agent of maize stalk rot disease in China. These isolates were divided into five chemotypes: nivalenol (NIV), deoxynivalenol (DON), beauvericin (BEA), zearalenone (ZEN), and fumonisin (FUM). Phylogenetic analysis based on partial sequences of the translation elongation factor 1α (TEF1-α) showed a high degree of interspecific polymorphisms among the isolates. Pathogenicity analysis on maize stalks indicated that all the 12 species of Fusarium were able to cause the disease symptoms with different aggressiveness. This study on population, pathogenicity, and toxigenic chemotypes of Fusarium species associated with maize stalk rot in Yunnan Province of southwest China, will help design an effective integrated control strategy for this disease.
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Affiliation(s)
- Kaifei Xi
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Liuying Shan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yini Yang
- The Central Agricultural Broadcasting and Television School, Beijing, China
| | - Guoqing Zhang
- General Office of the Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jun Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wei Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing, China
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18
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Tralamazza SM, Abraham LN, Reyes-Avila CS, Corrêa B, Croll D. Histone H3K27 methylation perturbs transcriptional robustness and underpins dispensability of highly conserved genes in fungi. Mol Biol Evol 2021; 39:6424003. [PMID: 34751371 PMCID: PMC8789075 DOI: 10.1093/molbev/msab323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications are key regulators of gene expression and underpin genome integrity. Yet, how epigenetic changes affect the evolution and transcriptional robustness of genes remains largely unknown. Here, we show how the repressive histone mark H3K27me3 underpins the trajectory of highly conserved genes in fungi. We first performed transcriptomic profiling on closely related species of the plant pathogen Fusarium graminearum species complex. We determined transcriptional responsiveness of genes across environmental conditions to determine expression robustness. To infer evolutionary conservation, we used a framework of 23 species across the Fusarium genus including three species covered with histone methylation data. Gene expression variation is negatively correlated with gene conservation confirming that highly conserved genes show higher expression robustness. In contrast, genes marked by H3K27me3 do not show such associations. Furthermore, highly conserved genes marked by H3K27me3 encode smaller proteins, exhibit weaker codon usage bias, higher levels of hydrophobicity, show lower intrinsically disordered regions, and are enriched for functions related to regulation and membrane transport. The evolutionary age of conserved genes with H3K27me3 histone marks falls typically within the origins of the Fusarium genus. We show that highly conserved genes marked by H3K27me3 are more likely to be dispensable for survival during host infection. Lastly, we show that conserved genes exposed to repressive H3K27me3 marks across distantly related Fusarium fungi are associated with transcriptional perturbation at the microevolutionary scale. In conclusion, we show how repressive histone marks are entangled in the evolutionary fate of highly conserved genes across evolutionary timescales.
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Affiliation(s)
- Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland.,Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
| | | | - Benedito Corrêa
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
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19
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Wyrębek J, Molcan T, Myszczyński K, van Diepeningen AD, Stakheev AA, Żelechowski M, Bilska K, Kulik T. Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. Front Microbiol 2021; 12:714651. [PMID: 34531839 PMCID: PMC8439580 DOI: 10.3389/fmicb.2021.714651] [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: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.
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Affiliation(s)
- Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Alexander A Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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20
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Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum. BMC Genomics 2021; 22:630. [PMID: 34461830 PMCID: PMC8404269 DOI: 10.1186/s12864-021-07931-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/11/2021] [Indexed: 01/15/2023] Open
Abstract
Background Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus. Results In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (pG), however, four SNPs were associated with major quantitative trait loci (QTLs) with pG ranging from 12 to 48%. The QTL with the highest pG was involved in DON production and associated with a SNP most probably located within the Tri4 gene. Conclusions The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07931-5.
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Munkvold GP, Proctor RH, Moretti A. Mycotoxin Production in Fusarium According to Contemporary Species Concepts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:373-402. [PMID: 34077240 DOI: 10.1146/annurev-phyto-020620-102825] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributedamong species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts.
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Affiliation(s)
- Gary P Munkvold
- Department of Plant Pathology and Microbiology and Seed Science Center, Iowa State University, Ames, Iowa 50010, USA;
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, Illinois 61604, USA;
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy;
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22
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Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures. Int J Mol Sci 2021; 22:ijms22126257. [PMID: 34200775 PMCID: PMC8230406 DOI: 10.3390/ijms22126257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Fusarium graminearum, the primary cause of Fusarium head blight (FHB) in small-grain cereals, demonstrates remarkably variable levels of aggressiveness in its host, producing different infection dynamics and contrasted symptom severity. While the secreted proteins, including effectors, are thought to be one of the essential components of aggressiveness, our knowledge of the intra-species genomic diversity of F. graminearum is still limited. In this work, we sequenced eight European F. graminearum strains of contrasting aggressiveness to characterize their respective genome structure, their gene content and to delineate their specificities. By combining the available sequences of 12 other F. graminearum strains, we outlined a reference pangenome that expands the repertoire of the known genes in the reference PH-1 genome by 32%, including nearly 21,000 non-redundant sequences and gathering a common base of 9250 conserved core-genes. More than 1000 genes with high non-synonymous mutation rates may be under diverse selection, especially regarding the trichothecene biosynthesis gene cluster. About 900 secreted protein clusters (SPCs) have been described. Mostly localized in the fast sub-genome of F. graminearum supposed to evolve rapidly to promote adaptation and rapid responses to the host's infection, these SPCs gather a range of putative proteinaceous effectors systematically found in the core secretome, with the chloroplast and the plant nucleus as the main predicted targets in the host cell. This work describes new knowledge on the intra-species diversity in F. graminearum and emphasizes putative determinants of aggressiveness, providing a wealth of new candidate genes potentially involved in the Fusarium head blight disease.
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23
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Fumero MV, Yue W, Chiotta ML, Chulze SN, Leslie JF, Toomajian C. Divergence and Gene Flow Between Fusarium subglutinans and F. temperatum Isolated from Maize in Argentina. PHYTOPATHOLOGY 2021; 111:170-183. [PMID: 33079019 DOI: 10.1094/phyto-09-20-0434-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fusarium subglutinans and F. temperatum are two important fungal pathogens of maize whose distinctness as separate species has been difficult to assess. We isolated strains of these species from commercial and native maize varieties in Argentina and sequenced >28,000 loci to estimate genetic variation in the sample. Our objectives were to measure genetic divergence between the species, infer demographic parameters related to their split, and describe the population structure of the sample. When analyzed together, over 30% of each species' polymorphic sites (>2,500 sites) segregate as polymorphisms in the other. Demographic modeling confirmed the species split predated maize domestication, but subsequent between-species gene flow has occurred, with gene flow from F. subglutinans into F. temperatum greater than gene flow in the reverse direction. In F. subglutinans, little evidence exists for substructure or recent selective sweeps, but there is evidence for limited sexual reproduction. In F. temperatum, there is clear evidence for population substructure and signals of abundant recent selective sweeps, with sexual reproduction probably less common than in F. subglutinans. Both genetic variation and the relative number of polymorphisms shared between species increase near the telomeres of all 12 chromosomes, where genes related to plant-pathogen interactions often are located. Our results suggest that species boundaries between closely related Fusarium species can be semipermeable and merit further study. Such semipermeability could facilitate unanticipated genetic exchange between species and enable quicker permanent responses to changes in the agro-ecosystem, e.g., pathogen-resistant host varieties, new chemical and biological control agents, and agronomic practices.
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Affiliation(s)
- M Veronica Fumero
- Research Institute on Mycology and Mycotoxicology (IMICO), National Scientific and Technical Research Council-National University of Río Cuarto (CONICET-UNRC), X5800, Río Cuarto, Córdoba, Argentina
| | - Wei Yue
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - María L Chiotta
- Research Institute on Mycology and Mycotoxicology (IMICO), National Scientific and Technical Research Council-National University of Río Cuarto (CONICET-UNRC), X5800, Río Cuarto, Córdoba, Argentina
| | - Sofía N Chulze
- Research Institute on Mycology and Mycotoxicology (IMICO), National Scientific and Technical Research Council-National University of Río Cuarto (CONICET-UNRC), X5800, Río Cuarto, Córdoba, Argentina
| | - John F Leslie
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
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Xie L, Xiao D, Wang X, Wang C, Bai J, Yue Q, Yue H, Li Y, Molnár I, Xu Y, Zhang L. Combinatorial Biosynthesis of Sulfated Benzenediol Lactones with a Phenolic Sulfotransferase from Fusarium graminearum PH-1. mSphere 2020; 5:e00949-20. [PMID: 33239367 PMCID: PMC7690957 DOI: 10.1128/msphere.00949-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
Total biosynthesis or whole-cell biocatalytic production of sulfated small molecules relies on the discovery and implementation of appropriate sulfotransferase enzymes. Although fungi are prominent biocatalysts and have been used to sulfate drug-like phenolics, no gene encoding a sulfotransferase enzyme has been functionally characterized from these organisms. Here, we identify a phenolic sulfotransferase, FgSULT1, by genome mining from the plant-pathogenic fungus Fusarium graminearum PH-1. We expressed FgSULT1 in a Saccharomyces cerevisiae chassis to modify a broad range of benzenediol lactones and their nonmacrocyclic congeners, together with an anthraquinone, with the resulting unnatural natural product (uNP) sulfates displaying increased solubility. FgSULT1 shares low similarity with known animal and plant sulfotransferases. Instead, it forms a sulfotransferase family with putative bacterial and fungal enzymes for phase II detoxification of xenobiotics and allelochemicals. Among fungi, putative FgSULT1 homologues are encoded in the genomes of Fusarium spp. and a few other genera in nonsyntenic regions, some of which may be related to catabolic sulfur recycling. Computational structure modeling combined with site-directed mutagenesis revealed that FgSULT1 retains the key catalytic residues and the typical fold of characterized animal and plant sulfotransferases. Our work opens the way for the discovery of hitherto unknown fungal sulfotransferases and provides a synthetic biological and enzymatic platform that can be adapted to produce bioactive sulfates, together with sulfate ester standards and probes for masked mycotoxins, precarcinogenic toxins, and xenobiotics.IMPORTANCE Sulfation is an expedient strategy to increase the solubility, bioavailability, and bioactivity of nutraceuticals and clinically important drugs. However, chemical or biological synthesis of sulfoconjugates is challenging. Genome mining, heterologous expression, homology structural modeling, and site-directed mutagenesis identified FgSULT1 of Fusarium graminearum PH-1 as a cytosolic sulfotransferase with the typical fold and active site architecture of characterized animal and plant sulfotransferases, despite low sequence similarity. FgSULT1 homologues are sparse in fungi but form a distinct clade with bacterial sulfotransferases. This study extends the functionally characterized sulfotransferase superfamily to the kingdom Fungi and demonstrates total biosynthetic and biocatalytic synthetic biological platforms to produce unnatural natural product (uNP) sulfoconjugates. Such uNP sulfates may be utilized for drug discovery in human and veterinary medicine and crop protection. Our synthetic biological methods may also be adapted to generate masked mycotoxin standards for food safety and environmental monitoring applications and to expose precarcinogenic xenobiotics.
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Affiliation(s)
- Linan Xie
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Dongliang Xiao
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xiaojing Wang
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, People's Republic of China
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Jing Bai
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou City, Jiangsu Province, People's Republic of China
| | - Qun Yue
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Haitao Yue
- Department of Biology and Biotechnology, Xinjiang University, Urumqi, People's Republic of China
| | - Ye Li
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
- National Engineering Lab for Cereal Fermentation Technology, Jiangnan University, Wuxi, People's Republic of China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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25
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Dobbs JT, Kim MS, Dudley NS, Klopfenstein NB, Yeh A, Hauff RD, Jones TC, Dumroese RK, Cannon PG, Stewart JE. Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring. BMC Genomics 2020; 21:764. [PMID: 33148175 PMCID: PMC7640661 DOI: 10.1186/s12864-020-07156-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. RESULTS This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. CONCLUSIONS These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.
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Affiliation(s)
- John T. Dobbs
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331 USA
| | - Nicklos S. Dudley
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Ned B. Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Aileen Yeh
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Robert D. Hauff
- Division of Forestry and Wildlife, Department of Land and Natural Resources, 1151 Punchbowl Street, Room 325, Honolulu, HI 96813 USA
| | - Tyler C. Jones
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - R. Kasten Dumroese
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Philip G. Cannon
- USDA Forest Service, Forest Health Protection, 1323 Club Drive, Vallejo, CA 94592 USA
| | - Jane E. Stewart
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
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Wang X, Peng J, Sun L, Bonito G, Guo Y, Li Y, Fu Y. Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms. Pathogens 2020; 9:pathogens9100834. [PMID: 33065983 PMCID: PMC7650745 DOI: 10.3390/pathogens9100834] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/17/2022] Open
Abstract
Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.
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Affiliation(s)
- Xinxin Wang
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Jingyu Peng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Lei Sun
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Yuxiu Guo
- Life Science College, Northeast Normal University, Changchun 130118, China;
| | - Yu Li
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
| | - Yongping Fu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
- Correspondence:
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27
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Fourie A, de Jonge R, van der Nest MA, Duong TA, Wingfield MJ, Wingfield BD, Barnes I. Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families. Fungal Genet Biol 2020; 143:103433. [PMID: 32652232 DOI: 10.1016/j.fgb.2020.103433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 01/04/2023]
Abstract
Ceratocystis fimbriata is a host specific fungal pathogen of sweet potato (Ipomoea batatas). The closely related species, C. manginecans, is an important pathogen of trees (e.g. Acacia mangium and Mangifera indica) but has never been isolated from tuber crops. The genetic factors that determine the host range and host specificity of these species have not been determined. The aim of this study was to compare the genomes of C. fimbriata and C. manginecans in order to identify species-specific genetic differences that could be associated with host specificity. This included whole-genome alignments as well as comparisons of gene content and transposable elements (TEs). The genomes of the two species were found to be very similar, sharing similar catalogues of CAZymes, peptidases and lipases. However, the genomes of the two species also varied, harbouring species-specific genes (e.g. small secreted effectors, nutrient processing proteins and stress response proteins). A portion of the TEs identified (17%) had a unique distribution in each species. Transposable elements appeared to have played a prominent role in the divergence of the two species because they were strongly associated with chromosomal translocations and inversions as well as with unique genomic regions containing species-specific genes. Two large effector clusters, with unique TEs in each species, were identified. These effectors displayed non-synonymous mutations and deletions, conserved within a species, and could serve as mutational hot-spots for the development of host specificity in the two species.
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Affiliation(s)
- Arista Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht 3584 CH, the Netherlands
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Biotechnology Platform, Agricultural Research Council, Private Bag X05, Onderstepoort 0110, 0002, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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Xu R, Liu X, Peng B, Liu P, Li Z, Dai Y, Xiao S. Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism. Pathogens 2020; 9:pathogens9030232. [PMID: 32245129 PMCID: PMC7157644 DOI: 10.3390/pathogens9030232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cladobotryum dendroides, which causes cobweb disease in edible mushrooms, is one of the major fungal pathogens. Our previous studies focused on the genetic and morphological characterization of this fungus, as well as its pathogenicity and the identification of appropriate fungicides. However, little is known about the genome characters, pathogenic genes, and molecular pathogenic mechanisms of C. dendroides. Herein, we reported a high-quality de novo genomic sequence of C. dendroides and compared it with closely-related fungi. The assembled C. dendroides genome was 36.69 Mb, consisting of eight contigs, with an N50 of 4.76 Mb. This genome was similar in size to that of C. protrusum, and shared highly conserved syntenic blocks and a few inversions with C. protrusum. Phylogenetic analysis revealed that, within the Hypocreaceae, Cladobotryum was closer to Mycogone than to Trichoderma, which is consistent with phenotypic evidence. A significant number of the predicted expanded gene families were strongly associated with pathogenicity, virulence, and adaptation. Our findings will be instrumental for the understanding of fungi-fungi interactions, and for exploring efficient management strategies to control cobweb disease.
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Affiliation(s)
- Rong Xu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xiaochen Liu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Peibin Liu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zhuang Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China;
| | - Yueting Dai
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- Correspondence: (Y.D.); (S.X.); Tel.: +86-431-8453-2989 (Y.D. & S.X.)
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- Correspondence: (Y.D.); (S.X.); Tel.: +86-431-8453-2989 (Y.D. & S.X.)
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Lewis RW, Okubara PA, Fuerst EP, He R, Gang D, Sullivan TS. Chronic Sublethal Aluminum Exposure and Avena fatua Caryopsis Colonization Influence Gene Expression of Fusarium avenaceum F.a.1. Front Microbiol 2020; 11:51. [PMID: 32117103 PMCID: PMC7010643 DOI: 10.3389/fmicb.2020.00051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/10/2020] [Indexed: 11/21/2022] Open
Abstract
Fusarium avenaceum F.a.1 is a novel strain of a fungal plant pathogen capable of preferentially decaying wild oat (Avena fatua) caryopses compared with those of wheat (Triticum aestivum). Understanding the molecular mechanisms governing weed seed-pathogen interactions is crucial to developing novel weed seed suppression technologies. Additionally, wild oat often competes with wheat in regions undergoing soil acidification, which leads to increases in soluble concentrations of many metals, including aluminum (Al). There is a dearth of information regarding the gene expression responses of Fusarium species to Al toxicity, or how metal toxicity might influence caryopsis colonization. To address this, a transcriptomic approach was used to investigate molecular responses of F.a.1 during wild oat caryopsis colonization in the presence and absence of chronic, sublethal concentrations of Al (400 μM). Caryopsis colonization was associated with induction of genes related to virulence, development, iron metabolism, oxidoreduction, stress, and detoxification, along with repression of genes associated with development, transport, cell-wall turnover, and virulence. Caryopsis colonization during Al exposure resulted in the induction of genes associated with virulence, detoxification, stress, iron metabolism, oxidoreduction, and cell wall turnover, along with repression of genes associated with cell wall metabolism, virulence, development, detoxification, stress, and transcriptional regulation. Aluminum exposure in the absence of caryopses was associated with induction of genes involved in siderophore biosynthesis, secretion, uptake, and utilization, along with several other iron metabolism-related and organic acid metabolism-related genes. The siderophore-related responses associated with Al toxicity occurred concurrently with differential regulation of genes indicating disruption of iron homeostasis. These findings suggest Al toxicity is attenuated by siderophore metabolism in F.a.1. In summary, both caryopsis colonization and Al toxicity uniquely influence transcriptomic responses of F.a.1.
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Affiliation(s)
- Ricky W Lewis
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Patricia A Okubara
- Wheat Health, Genetics, and Quality, USDA-ARS, Pullman, WA, United States
| | - E Patrick Fuerst
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - David Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics. Microorganisms 2020; 8:microorganisms8020305. [PMID: 32098375 PMCID: PMC7075021 DOI: 10.3390/microorganisms8020305] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 01/19/2023] Open
Abstract
Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics.
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Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta. Sci Rep 2020; 10:1586. [PMID: 32005849 PMCID: PMC6994667 DOI: 10.1038/s41598-020-58342-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 01/13/2020] [Indexed: 01/04/2023] Open
Abstract
Ilyonectria robusta causes rusty root rot, the most devastating chronic disease of ginseng. Here, we for the first time report the high-quality genome of the I. robusta strain CD-56. Time-course (36 h, 72 h, and 144 h) dual RNA-Seq analysis of the infection process was performed, and many genes, including candidate effectors, were found to be associated with the progression and success of infection. The gene expression profile of CD-56 showed a trend of initial inhibition and then gradually returned to a profile similar to that of the control. Analyses of the gene expression patterns and functions of pathogenicity-related genes, especially candidate effector genes, indicated that the stress response changed to an adaptive response during the infection process. For ginseng, gene expression patterns were highly related to physiological conditions. Specifically, the results showed that ginseng defenses were activated by CD-56 infection and persisted for at least 144 h thereafter but that the mechanisms invoked were not effective in preventing CD-56 growth. Moreover, CD-56 did not appear to fully suppress plant defenses, even in late stages after infection. Our results provide new insight into the chronic pathogenesis of CD-56 and the comprehensive and complex inducible defense responses of ginseng root to I. robusta infection.
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Tralamazza SM, Rocha LO, Oggenfuss U, Corrêa B, Croll D. Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex. Genome Biol Evol 2019; 11:3106-3122. [PMID: 31609418 PMCID: PMC6836718 DOI: 10.1093/gbe/evz225] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.
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Affiliation(s)
- Sabina Moser Tralamazza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
| | - Liliana Oliveira Rocha
- Food Engineering Faculty, Department of Food Science, University of Campinas, Av. Monteiro Lobato, Brazil
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
| | - Benedito Corrêa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
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Foroud NA, Baines D, Gagkaeva TY, Thakor N, Badea A, Steiner B, Bürstmayr M, Bürstmayr H. Trichothecenes in Cereal Grains - An Update. Toxins (Basel) 2019; 11:E634. [PMID: 31683661 PMCID: PMC6891312 DOI: 10.3390/toxins11110634] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023] Open
Abstract
Trichothecenes are sesquiterpenoid mycotoxins produced by fungi from the order Hypocreales, including members of the Fusarium genus that infect cereal grain crops. Different trichothecene-producing Fusarium species and strains have different trichothecene chemotypes belonging to the Type A and B class. These fungi cause a disease of small grain cereals, called Fusarium head blight, and their toxins contaminate host tissues. As potent inhibitors of eukaryotic protein synthesis, trichothecenes pose a health risk to human and animal consumers of infected cereal grains. In 2009, Foroud and Eudes published a review of trichothecenes in cereal grains for human consumption. As an update to this review, the work herein provides a comprehensive and multi-disciplinary review of the Fusarium trichothecenes covering topics in chemistry and biochemistry, pathogen biology, trichothecene toxicity, molecular mechanisms of resistance or detoxification, genetics of resistance and breeding strategies to reduce their contamination of wheat and barley.
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Affiliation(s)
- Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada.
| | - Danica Baines
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada.
| | - Tatiana Y Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection (VIZR), St. Petersburg, Pushkin 196608, Russia.
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada.
| | - Barbara Steiner
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
| | - Maria Bürstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
| | - Hermann Bürstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
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One Small RNA of Fusarium graminearum Targets and Silences CEBiP Gene in Common Wheat. Microorganisms 2019; 7:microorganisms7100425. [PMID: 31600909 PMCID: PMC6843203 DOI: 10.3390/microorganisms7100425] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/06/2019] [Indexed: 12/24/2022] Open
Abstract
The pathogenic fungus Fusarium graminearum (F. graminearum), causing Fusarium head blight (FHB) or scab, is one of the most important cereal killers worldwide, exerting great economic and agronomic losses on global grain production. To repress pathogen invasion, plants have evolved a sophisticated innate immunity system for pathogen recognition and defense activation. Simultaneously, pathogens continue to evolve more effective means of invasion to conquer plant resistance systems. In the process of co-evolution of plants and pathogens, several small RNAs (sRNAs) have been proved in regulating plant immune response and plant-microbial interaction. In this study, we report that a F. graminearum sRNA (Fg-sRNA1) can suppress wheat defense response by targeting and silencing a resistance-related gene, which codes a Chitin Elicitor Binding Protein (TaCEBiP). Transcriptional level evidence indicates that Fg-sRNA1 can target TaCEBiP mRNA and trigger silencing of TaCEBiP in vivo, and in Nicotiana benthamiana (N. benthamiana) plants, Western blotting experiments and YFP Fluorescence observation proofs show that Fg-sRNA1 can suppress the accumulation of protein coding by TaCEBiP gene in vitro. F. graminearum PH-1 strain displays a weakening ability to invasion when Barley stripe mosaic virus (BSMV) vector induces effective silencing Fg-sRNA1 in PH-1 infected wheat plants. Taken together, our results suggest that a small RNA from F. graminearum can target and silence the wheat TaCEBiP gene to enhance invasion of F. graminearum.
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35
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Nielsen MR, Sondergaard TE, Giese H, Sørensen JL. Advances in linking polyketides and non-ribosomal peptides to their biosynthetic gene clusters in Fusarium. Curr Genet 2019; 65:1263-1280. [DOI: 10.1007/s00294-019-00998-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/24/2022]
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36
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Villani A, Proctor RH, Kim HS, Brown DW, Logrieco AF, Amatulli MT, Moretti A, Susca A. Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes. BMC Genomics 2019; 20:314. [PMID: 31014248 PMCID: PMC6480918 DOI: 10.1186/s12864-019-5567-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/25/2019] [Indexed: 11/29/2022] Open
Abstract
Background The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC. Results We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages. Conclusion Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5567-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessandra Villani
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Robert H Proctor
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Hye-Seon Kim
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Daren W Brown
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Antonio F Logrieco
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Maria Teresa Amatulli
- Institute of Sciences of Food Production, National Research Council, Bari, Italy.,Thales Alenia Space Italia, Torino, Italy
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council, Bari, Italy.
| | - Antonia Susca
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
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37
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Flynn CM, Broz K, Jonkers W, Schmidt-Dannert C, Kistler HC. Expression of the Fusarium graminearum terpenome and involvement of the endoplasmic reticulum-derived toxisome. Fungal Genet Biol 2019; 124:78-87. [PMID: 30664933 DOI: 10.1016/j.fgb.2019.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/29/2018] [Accepted: 01/14/2019] [Indexed: 12/26/2022]
Abstract
The sesquiterpenoid deoxynivalenol (DON) is an important trichothecene mycotoxin produced by the cereal pathogen Fusarium graminearum. DON is synthesized in specialized subcellular structures called toxisomes. The first step in DON synthesis is catalyzed by the sesquiterpene synthase (STS), Tri5 (trichodiene synthase), resulting in the cyclization of farnesyl diphosphate (FPP) to produce the sesquiterpene trichodiene. Tri5 is one of eight putative STSs in the F. graminearum genome. To better understand the F. graminearum terpenome, the volatile and soluble fractions of fungal cultures were sampled. Stringent regulation of sesquiterpene accumulation was observed. When grown in trichothecene induction medium, the fungus produces trichothecenes as well as several volatile non-trichothecene related sesquiterpenes, whereas no volatile terpenes were detected when grown in non-inducing medium. Surprisingly, a Δtri5 deletion strain grown in inducing conditions not only ceased accumulation of trichothecenes, but also failed to produce the non-trichothecene related sesquiterpenes. To test whether Tri5 from F. graminearum may be a promiscuous STS directly producing all observed sesquiterpenes, Tri5 was cloned and expressed in E. coli and shown to produce primarily trichodiene in addition to minor, related cyclization products. Therefore, while Tri5 expression in F. graminearum is necessary for non-trichothecene sesquiterpene biosynthesis, direct catalysis by Tri5 does not explain the sesquiterpene deficient phenotype observed in the Δtri5 strain. To test whether Tri5 protein, separate from its enzymatic activity, may be required for non-trichothecene synthesis, the Tri5 locus was replaced with an enzymatically inactive, but structurally unaffected tri5N225D S229T allele. This allele restores non-trichothecene synthesis but not trichothecene synthesis. The tri5N225D S229T allele also restores toxisome structure which is lacking in the Δtri5 deletion strain. Our results indicate that the Tri5 protein, but not its enzymatic activity, is also required for the synthesis of non-trichothecene related sesquiterpenes and the formation of toxisomes. Toxisomes thus not only may be important for DON synthesis, but also for the synthesis of other sesquiterpene mycotoxins such as culmorin by F. graminearum.
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Affiliation(s)
- Christopher M Flynn
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Saint Paul, MN, USA
| | - Karen Broz
- USDA ARS Cereal Disease Laboratory, Saint Paul, MN, USA
| | | | - Claudia Schmidt-Dannert
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Saint Paul, MN, USA
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Catharina L, Carels N. Specific enzyme functionalities of Fusarium oxysporum compared to host plants. Gene 2018; 676:219-226. [PMID: 29981422 DOI: 10.1016/j.gene.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/14/2018] [Accepted: 07/01/2018] [Indexed: 11/29/2022]
Abstract
The genus Fusarium contains some of the most studied and important species of plant pathogens that economically affect world agriculture and horticulture. Fusarium spp. are ubiquitous fungi widely distributed in soil, plants as well as in different organic substrates and are also considered as opportunistic human pathogens. The identification of specific enzymes essential to the metabolism of these fungi is expected to provide molecular targets to control the diseases they induce to their hosts. Through applications of traditional techniques of sequence homology comparison by similarity search and Markov modeling, this report describes the characterization of enzymatic functionalities associated to protein targets that could be considered for the control of root rots induced by Fusarium oxysporum. From the analysis of 318 F. graminearum enzymes, we retrieved 30 enzymes that are specific of F. oxysporum compared to 15 species of host plants. By comparing these 30 specific enzymes of F. oxysporum with the genome of Arabidopsis thaliana, Brassica rapa, Glycine max, Jatropha curcas and Ricinus communis, we found 7 key specific enzymes whose inhibition is expected to affect significantly the development of the fungus and 5 specific enzymes that were considered here to be secondary because they are inserted in pathways with alternative routes.
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Affiliation(s)
- Larissa Catharina
- Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil, 4036, Prédio da Expansão, 8° andar, sala 814, CEP: 21040-361 Rio de Janeiro, Brazil.
| | - Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Av. Brasil, 4036, Prédio da Expansão, 8° andar, sala 814, CEP: 21040-361 Rio de Janeiro, Brazil.
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Stakheev AA, Samokhvalova LV, Mikityuk OD, Zavriev SK. Phylogenetic Analysis and Molecular Typing of Trichothecene-Producing Fusarium Fungi from Russian Collections. Acta Naturae 2018; 10:79-92. [PMID: 30116619 PMCID: PMC6087817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/21/2022] Open
Abstract
We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1α) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. A study of 60 strains of different origins using DNA markers confirmed, and in the case for several strains, clarified their taxonomic characteristics. As a result, a strain of F. commune (F-900) was identified in Russia for the first time. Furthermore, the strain F-846 proved to be phylogenetically distinct from any of the known Fusarium species. F. equiseti strains from Northwest Russia were found to belong to the North European group (I), whereas a strain from the North Caucasus - to the South European one (II). Partial TRI14 sequences from 9 out of 12 species were determined for the first time. Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. Specific chemotypes of trichothecene B producers were characterized using two primer sets. The chemotyping results were verified by HPLC.
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Affiliation(s)
- A. A. Stakheev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16\10, Moscow, 117997, Russia
| | - L. V. Samokhvalova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16\10, Moscow, 117997, Russia
| | - O. D. Mikityuk
- All-Russian Research Institute of Phytopathology, Institut Str. 5, B. Vyazyomy, Moscow region, 143050 , Russia
| | - S. K. Zavriev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic chemistry of the Russian Academy of Sciences, Miklukho-Maklaya Str. 16\10, Moscow, 117997, Russia
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40
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Plissonneau C, Hartmann FE, Croll D. Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome. BMC Biol 2018; 16:5. [PMID: 29325559 PMCID: PMC5765654 DOI: 10.1186/s12915-017-0457-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Background Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence. Results We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes. Conclusions The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0457-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Bretignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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