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Otero M, Pokhrel A, Seo S, Wendell L, Luangkhot AS, Lawrence KS, Coleman JJ. Evaluation of the Genetic Diversity, Haplotype, and Virulence of Fusarium oxysporum f. sp. vasinfectum Field Isolates from Alabama. PHYTOPATHOLOGY 2024; 114:1587-1595. [PMID: 38619819 DOI: 10.1094/phyto-11-23-0438-r] [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: 04/16/2024]
Abstract
The United States is the third largest producer of cotton and the largest exporter of cotton globally. Fusarium wilt, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum (Fov), was estimated to cause a $21 million cotton yield loss in 2022. Historically, Alabama was an important producer of cotton in the Southeastern United States and was the first state in which Fusarium wilt on cotton was described. To assess the genetic diversity of Fov field isolates in Alabama, 118 field isolates were collected from six counties across the state from 2014 to 2016. Phylogenetic analysis using TEF1 and RPB2 placed the Fov field isolates into 18 haplotypes. Upon profiling the Tfo1 transposon insertion in the NAT gene, it was determined that no race 4 isolates were recovered in Alabama. Representatives of all field isolate haplotypes caused disease on Upland cotton variety Rowden in a hydroponic test tube assay. Two haplotype A isolates were the most aggressive isolates recovered, and haplotype A isolate TF1 was more aggressive than the race 4 isolate 89-1A on Upland cotton and had similar symptom severity on Pima cotton. Karyotype profiling indicted an abundance of small chromosomes characteristic of karyotypes that include accessory chromosomes, with considerable variability between isolates. Collectively, our study indicates that Fov isolates from Alabama are genetically diverse, which may have been promoted by its persistence in cotton fields.
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Affiliation(s)
- Miranda Otero
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Ambika Pokhrel
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Seungyeon Seo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Laura Wendell
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Amber S Luangkhot
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Kathy S Lawrence
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
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Jeewon R, Pudaruth SB, Bhoyroo V, Aullybux AA, Rajeshkumar KC, Alrefaei AF. Antioxidant and Antifungal Properties of Cinnamon, Cloves, Melia azedarach L. and Ocimum gratissimum L. Extracts against Fusarium oxysporum Isolated from Infected Vegetables in Mauritius. Pathogens 2024; 13:436. [PMID: 38921734 PMCID: PMC11206713 DOI: 10.3390/pathogens13060436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Fusarium species, a group of economically destructive phytopathogens, are poorly studied in Mauritius where agriculture holds much significance. Furthermore, the increasing popularity of organic farming has prompted interest in alternatives to chemical fungicides. METHODS After gaining an overview of Fusarium prevalence in Mauritius fields through a survey, the pathogen was isolated from infected crops and identified based on morphological and molecular characteristics. Methanol and water extracts were then prepared from Melia azedarach, Ocimum gratissimum, cinnamon and cloves before determining their phytochemical profiles. Additionally, the antioxidant and antifungal effects of different concentrations of aqueous extracts were assessed. RESULTS The isolate was confirmed as Fusarium oxysporum, and cloves inhibited its growth by up to 100%, especially at 60 and 90 g/L, with the results being significantly higher than those of the synthetic fungicide mancozeb. Over 50% inhibition was also noted for cinnamon and Ocimum gratissimum, and these effects could be linked to the flavonoids, phenols and terpenoids in the extracts. CONCLUSION This study presented the aqueous extracts of cloves, cinnamon and Ocimum gratissimum as potential alternatives to chemical fungicides. It also confirmed the prevalence of Fusarium infection in Mauritius fields, thereby highlighting the need for additional studies on the pathogen.
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Affiliation(s)
- Rajesh Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit 80837, Mauritius
| | - Shaan B. Pudaruth
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Vishwakalyan Bhoyroo
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Aadil Ahmad Aullybux
- Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
| | - Kunhiraman C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Gr., MACS Agharkar Research Institute, G. G. Agarkar Road, Pune 411 004, Maharashtra, India
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
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Nozawa S, Seto Y, Takata Y, Narreto LA, Valle RR, Okui K, Taida S, Alvindia DG, Reyes RG, Watanabe K. Fusarium mindanaoense sp. nov., a New Fusarium Wilt Pathogen of Cavendish Banana from the Philippines Belonging to the F. fujikuroi Species Complex. J Fungi (Basel) 2023; 9:jof9040443. [PMID: 37108898 PMCID: PMC10142649 DOI: 10.3390/jof9040443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
The pathogen causing Fusarium wilt in banana is reported to be Fusarium oxysporum f. sp. cubense (FOC). In 2019, wilt symptoms in banana plants (cultivar: Cavendish) in the Philippines were detected, i.e., the yellowing of the leaves and discoloration of the pseudostem and vascular tissue. The fungus isolated from the vascular tissue was found to be pathogenic to Cavendish bananas and was identified as a new species, F. mindanaoense, belonging to the F. fujikuroi species complex (FFSC); species classification was assessed using molecular phylogenetic analyses based on the tef1, tub2, cmdA, rpb1, and rpb2 genes and morphological analyses. A reciprocal blast search using genomic data revealed that this fungus exclusively included the Secreted in Xylem 6 (SIX6) gene among the SIX homologs related to pathogenicity; it exhibited a highly conserved amino acid sequence compared with that of species in the FFSC, but not with that of FOC. This was the first report of Fusarium wilt in Cavendish bananas caused by a species of the genus Fusarium other than those in the F. oxysporum species complex.
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Affiliation(s)
- Shunsuke Nozawa
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo 194-8610, Japan
| | - Yosuke Seto
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Yoshiki Takata
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo 194-8610, Japan
| | | | - Reynaldo R. Valle
- BaCaDM Project of College of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo 194-8610, Japan
| | - Keiju Okui
- Unifrutti Japan Corporation, 1-11-1 Marunouchi, Chiyoda-Ku, Tokyo 100-6217, Japan
| | - Shigeya Taida
- Unifrutti Japan Corporation, 1-11-1 Marunouchi, Chiyoda-Ku, Tokyo 100-6217, Japan
| | - Dionisio G. Alvindia
- Philippine Center for Postharvest Development and Mechanization, Science City of Muñoz 3120, Philippines
| | - Renato G. Reyes
- Department of Biology, Central Luzon State University, Science City of Muñoz 3120, Philippines
| | - Kyoko Watanabe
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa-Gakuen, Machida, Tokyo 194-8610, Japan
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Hao Y, Li Y, Ping X, Yang Q, Mao Z, Zhao J, Lu X, Xie B, Yang Y, Ling J. The Genome of Fusarium oxysporum f. sp. phaseoli Provides Insight into the Evolution of Genomes and Effectors of Fusarium oxysporum Species. Int J Mol Sci 2023; 24:ijms24020963. [PMID: 36674475 PMCID: PMC9861946 DOI: 10.3390/ijms24020963] [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: 10/30/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of morphological characters and molecular detection. We further reported the first genome assembly for Fusarium oxysporum f. sp. phaseoli, with 53.7 Mb genome sequence comprising 14,694 genes. Comparative genomic analysis among five Fusarium oxysporum genomes showed that four accessory chromosomes in the five Fusarium oxysporum display similar characteristics, with low sequence similarity (55.35%, vs. overall average of 81.76%), low gene density (2.18 genes/10 kb vs. 3.02 genes/Mb) and highly transposable element density (TEs) (15.01/100 kb vs. 4.89/100 kb), indicating that variable accessory chromosomes are the main source of Fusarium oxysporum evolution. We identified a total of 100 Fusarium oxysporum f. sp. phaseoli-specific effectors in the genome and found 13 specific effector genes located in large insertion or deletion regions, suggesting that insertion or deletion events can cause the emergence of species-specific effectors in Fusarium oxysporum. Our genome assembly of Fusarium oxysporum f. sp. phaseoli provides a valuable resource for the study of cowpea fusarium wilt, and the comparative genomic study of Fusarium oxysporum could contribute to the knowledge of genome and effector-associated pathogenicity evolution in Fusarium oxysporum study.
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Affiliation(s)
- Yali Hao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030810, China
| | - Yan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingxing Ping
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qihong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaofei Lu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Y.); (J.L.)
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Y.); (J.L.)
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Batista ICA, Heck DW, Santos A, Alves G, Ferro CG, Dita M, Haddad F, Michereff SJ, Correia KC, da Silva CFB, Mizubuti ESG. The Population of Fusarium oxysporum f. sp. cubense in Brazil Is Not Structured by Vegetative Compatibility Group or by Geographic Origin. PHYTOPATHOLOGY 2022; 112:2416-2425. [PMID: 35759310 DOI: 10.1094/phyto-02-22-0045-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: 06/15/2023]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), is considered one of the most destructive diseases of bananas in Brazil. In this study, a collection of 194 monosporic isolates from several banana-producing regions located in different climatic zones along a south-to-north transect in Brazil was formed to assess the genetic structure of the population of Foc. The isolates underwent pathogenicity tests, PCR diagnosis for the detection of tropical race 4, and screening of SIX homolog genes that produce putative effector proteins. The vegetative compatibility group (VCG) of 119 isolates was determined by pairing against 17 internationally known VCG-tester strains. A group of 158 isolates was selected for simple sequence repeat (SSR) genotyping. There was moderate diversity of Foc in Brazil. Eight VCGs were identified: 0120, 0122, 0124, 0125, 0128, 01215, 01220, and 01222, of which 78% of isolates belong to a single VCG, whereas 22% of isolates are assigned to multiple VCGs, belonging to complexes of VCGs. The distribution of VCGs is uneven and independent of the banana genotype. The isolates of a VCG shared a similar profile of SIX homologs, but there was no association with geographic region. Four SSR loci were polymorphic, and, on average, 7.5 alleles were detected per locus. Thirty-five multilocus genotypes (MLGs) were identified. There was no association between VCG and MLGs, and no genetic structure of the population of Foc in Brazil was detected.
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Affiliation(s)
- Izabel C A Batista
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
| | - Daniel W Heck
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
| | - Alessandro Santos
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
| | - Gabriel Alves
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
| | - Camila G Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
| | - Miguel Dita
- Alliance of Bioversity International and CIAT, Cali, Colombia
| | | | | | | | | | - Eduardo S G Mizubuti
- Departamento de Fitopatologia, Universidade Federal de Viçosa, MG 36570-900, Brazil
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6
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Brenes Guallar MA, Fokkens L, Rep M, Berke L, van Dam P. Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range. FRONTIERS IN PLANT SCIENCE 2022; 13:1012688. [PMID: 36340405 PMCID: PMC9627151 DOI: 10.3389/fpls.2022.1012688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2.
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Affiliation(s)
- Megan A. Brenes Guallar
- Bioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, Netherlands
| | - Like Fokkens
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Lidija Berke
- Bioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, Netherlands
| | - Peter van Dam
- Bioinformatics and Software Development Team, Genetwister Technologies B.V., Wageningen, Netherlands
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Redkar A, Sabale M, Schudoma C, Zechmann B, Gupta YK, López-Berges MS, Venturini G, Gimenez-Ibanez S, Turrà D, Solano R, Di Pietro A. Conserved secreted effectors contribute to endophytic growth and multihost plant compatibility in a vascular wilt fungus. THE PLANT CELL 2022; 34:3214-3232. [PMID: 35689625 PMCID: PMC9421472 DOI: 10.1093/plcell/koac174] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/03/2022] [Indexed: 05/04/2023]
Abstract
Fungal interactions with plant roots, either beneficial or detrimental, have a crucial impact on agriculture and ecosystems. The cosmopolitan plant pathogen Fusarium oxysporum (Fo) provokes vascular wilts in more than a hundred different crops. Isolates of this fungus exhibit host-specific pathogenicity, which is conferred by lineage-specific Secreted In Xylem (SIX) effectors encoded on accessory genomic regions. However, such isolates also can colonize the roots of other plants asymptomatically as endophytes or even protect them against pathogenic strains. The molecular determinants of endophytic multihost compatibility are largely unknown. Here, we characterized a set of Fo candidate effectors from tomato (Solanum lycopersicum) root apoplastic fluid; these early root colonization (ERC) effectors are secreted during early biotrophic growth on main and alternative plant hosts. In contrast to SIX effectors, ERCs have homologs across the entire Fo species complex as well as in other plant-interacting fungi, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence and rapid activation of plant immune responses, while ERC deletion in a nonpathogenic isolate led to impaired root colonization and biocontrol ability. Strikingly, some ERCs contribute to Fo infection on the nonvascular land plant Marchantia polymorpha, revealing an evolutionarily conserved mechanism for multihost colonization by root infecting fungi.
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Affiliation(s)
| | - Mugdha Sabale
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | | | - Bernd Zechmann
- Baylor University, Center for Microscopy and Imaging, Waco, Texas 76798, USA
| | - Yogesh K Gupta
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | | | | | - Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnologıa-CSIC (CNB-CSIC), 28049 Madrid, Spain
| | - David Turrà
- Department of Agriculture and Center for Studies on Bioinspired Agro-enviromental Technology, Università di Napoli Federico II, 80055 Portici, Italy
| | - Roberto Solano
- Plant Molecular Genetics Department, Centro Nacional de Biotecnologıa-CSIC (CNB-CSIC), 28049 Madrid, Spain
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Buijs VA, Groenewald JZ, Haridas S, LaButti KM, Lipzen A, Martin FM, Barry K, Grigoriev IV, Crous PW, Seidl MF. Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis. G3 (BETHESDA, MD.) 2022; 12:jkac061. [PMID: 35311955 PMCID: PMC9073689 DOI: 10.1093/g3journal/jkac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/02/2022] [Indexed: 11/14/2022]
Abstract
Members of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch's postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.
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Affiliation(s)
- Valerie A Buijs
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Johannes Z Groenewald
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt M LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Francis M Martin
- Department of Biology, Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine “Interaction Arbres/Microorganismes”, Champenoux F-54280, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Pedro W Crous
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, The Netherlands
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Hill R, Buggs RJA, Vu DT, Gaya E. Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures. Mol Biol Evol 2022; 39:6575681. [PMID: 35484861 PMCID: PMC9051438 DOI: 10.1093/molbev/msac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.
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Affiliation(s)
- Rowena Hill
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Richard J A Buggs
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom
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10
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McTaggart AR, James TY, Shivas RG, Drenth A, Wingfield BD, Summerell BA, Duong TA. Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex. Stud Mycol 2022; 99:100132. [PMID: 35027981 PMCID: PMC8693468 DOI: 10.1016/j.simyco.2021.100132] [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] [Indexed: 11/30/2022] Open
Abstract
The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.
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Affiliation(s)
- A R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - T Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - R G Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, 4350, Australia
| | - A Drenth
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - B D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - B A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - T A Duong
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
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11
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John E, Jacques S, Phan HTT, Liu L, Pereira D, Croll D, Singh KB, Oliver RP, Tan KC. Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat. PLoS Pathog 2022; 18:e1010149. [PMID: 34990464 PMCID: PMC8735624 DOI: 10.1371/journal.ppat.1010149] [Citation(s) in RCA: 2] [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: 08/11/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022] Open
Abstract
The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in representative P. nodorum isolates from Australia and South Africa. The presence of PE401 removed the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both 'selfish' and 'altruistic' characteristics. This offers an insight into a complex NE-NE interaction that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Huyen T. T. Phan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Lifang Liu
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Karam B. Singh
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
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12
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Hudson O, Fulton JC, Dong AK, Dufault NS, Ali ME. Fusarium oxysporum f. sp. niveum Molecular Diagnostics Past, Present and Future. Int J Mol Sci 2021; 22:ijms22189735. [PMID: 34575897 PMCID: PMC8468614 DOI: 10.3390/ijms22189735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
Watermelon is an important commercial crop in the Southeastern United States and around the world. However, production is significantly limited by biotic factors including fusarium wilt caused by the hemibiotrophic fungus Fusarium oxysporum forma specialis niveum (Fon). Unfortunately, this disease has increased significantly in its presence over the last several decades as races have emerged which can overcome the available commercial resistance. Management strategies include rotation, improved crop resistance, and chemical control, but early and accurate diagnostics are required for appropriate management. Accurate diagnostics require molecular and genomic strategies due to the near identical genomic sequences of the various races. Bioassays exist for evaluating both the pathogenicity and virulence of an isolate but are limited by the time and resources required. Molecular strategies are still imperfect but greatly reduce the time to complete the diagnosis. This article presents the current state of the research surrounding races, both how races have been detected and diagnosed in the past and future prospects for improving the system of differentiation. Additionally, the available Fon genomes were analyzed using a strategy previously described in separate formae speciales avirulence gene association studies in Fusarium oxysporum races.
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Affiliation(s)
- Owen Hudson
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (A.K.D.)
| | - James C. Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA;
- Correspondence: (M.E.A.); (J.C.F.)
| | - Alexi K. Dong
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (A.K.D.)
| | - Nicholas S. Dufault
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA;
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (A.K.D.)
- Correspondence: (M.E.A.); (J.C.F.)
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13
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Peck LD, Nowell RW, Flood J, Ryan MJ, Barraclough TG. Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides. BMC Genomics 2021; 22:404. [PMID: 34082717 PMCID: PMC8176585 DOI: 10.1186/s12864-021-07700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 1920s. After successful management, it later re-emerged and by the 2000s comprised two separate epidemics on arabica coffee in Ethiopia and robusta coffee in east and central Africa. RESULTS Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks. Phylogenomic reconstruction using 13,782 single copy orthologs shows that the robusta population arose from the initial outbreak, whilst the arabica population is a divergent sister clade to the other strains. A screen for putative effector genes involved in pathogenesis shows that the populations have diverged in gene content and sequence mainly by vertical processes within lineages. However, 15 putative effector genes show evidence of horizontal acquisition, with close homology to genes from F. oxysporum. Most occupy small regions of homology within wider scaffolds, whereas a cluster of four genes occupy a 20Kb scaffold with strong homology to a region on a mobile pathogenicity chromosome in F. oxysporum that houses known effector genes. Lacking a match to the whole mobile chromosome, we nonetheless found close associations with DNA transposons, especially the miniature impala type previously proposed to facilitate horizontal transfer of pathogenicity genes in F. oxysporum. These findings support a working hypothesis that the arabica and robusta populations partly acquired distinct effector genes via transposition-mediated horizontal transfer from F. oxysporum, which shares coffee as a host and lives on other plants intercropped with coffee. CONCLUSION Our results show how historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with our efforts to resist them. Our list of putative effector genes identifies possible future targets for fungal control. In turn, knowledge of horizontal transfer mechanisms and putative donor taxa might help to design future intercropping strategies that minimize the risk of transfer of effector genes between closely-related Fusarium taxa.
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Affiliation(s)
- Lily D Peck
- Science and Solutions for a Changing Planet Doctoral Training Partnership, Grantham Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK. .,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Julie Flood
- CABI, Bakeham Lane, Egham, Surrey, TW20 9TY, UK
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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14
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Jangir P, Mehra N, Sharma K, Singh N, Rani M, Kapoor R. Secreted in Xylem Genes: Drivers of Host Adaptation in Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:628611. [PMID: 33968096 PMCID: PMC8101498 DOI: 10.3389/fpls.2021.628611] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/01/2021] [Indexed: 05/17/2023]
Abstract
Fusarium oxysporum (Fo) is a notorious pathogen that significantly contributes to yield losses in crops of high economic status. It is responsible for vascular wilt characterized by the browning of conductive tissue, wilting, and plant death. Individual strains of Fo are host specific (formae speciales), and approximately, 150 forms have been documented so far. The pathogen secretes small effector proteins in the xylem, termed as Secreted in Xylem (Six), that contribute to its virulence. Most of these proteins contain cysteine residues in even numbers. These proteins are encoded by SIX genes that reside on mobile pathogenicity chromosomes. So far, 14 proteins have been reported. However, formae speciales vary in SIX protein profile and their respective gene sequence. Thus, SIX genes have been employed as ideal markers for pathogen identification. Acquisition of SIX-encoding mobile pathogenicity chromosomes by non-pathogenic lines, through horizontal transfer, results in the evolution of new virulent lines. Recently, some SIX genes present on these pathogenicity chromosomes have been shown to be involved in defining variation in host specificity among formae speciales. Along these lines, the review entails the variability (formae speciales, races, and vegetative compatibility groups) and evolutionary relationships among members of F. oxysporum species complex (FOSC). It provides updated information on the diversity, structure, regulation, and (a)virulence functions of SIX genes. The improved understanding of roles of SIX in variability and virulence of Fo has significant implication in establishment of molecular framework and techniques for disease management. Finally, the review identifies the gaps in current knowledge and provides insights into potential research landscapes that can be explored to strengthen the understanding of functions of SIX genes.
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Affiliation(s)
| | | | | | | | | | - Rupam Kapoor
- Department of Botany, University of Delhi, New Delhi, India
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15
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Gamboa-Becerra R, López-Lima D, Villain L, Breitler JC, Carrión G, Desgarennes D. Molecular and Environmental Triggering Factors of Pathogenicity of Fusarium oxysporum and F. solani Isolates Involved in the Coffee Corky-Root Disease. J Fungi (Basel) 2021; 7:jof7040253. [PMID: 33801572 PMCID: PMC8067267 DOI: 10.3390/jof7040253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Coffee corky-root disease causes serious damages to coffee crop and is linked to combined infection of Fusarium spp. and root-knot nematodes Meloidogyne spp. In this study, 70 Fusarium isolates were collected from both roots of healthy coffee plants and with corky-root disease symptoms. A phylogenetic analysis, and the detection of pathogenicity SIX genes and toxigenicity Fum genes was performed for 59 F. oxysporum and 11 F. solani isolates. Based on the molecular characterization, seven F. oxysporum and three F. solani isolates were assessed for their pathogenicity on coffee seedlings under optimal watering and water stress miming root-knot nematode effect on plants. Our results revealed that a drastic increment of plant colonization capacity and pathogenicity on coffee plants of some Fusarium isolates was caused by water stress. The pathogenicity on coffee of F. solani linked to coffee corky-root disease and the presence of SIX genes in this species were demonstrated for the first time. Our study provides evidence for understanding the pathogenic basis of F. oxysporum and F. solani isolates on coffee and revealed the presence of SIX and Fum genes as one of their pathogenicity-related mechanisms. We also highlight the relevance of chlorophyll, a fluorescence as an early and high-throughput phenotyping tool in Fusarium pathogenicity studies on coffee.
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Affiliation(s)
- Roberto Gamboa-Becerra
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
| | - Daniel López-Lima
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
| | - Luc Villain
- CIRAD, UMR DIADE, F-34394 Montpellier, France; (L.V.); (J.-C.B.)
| | | | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
- Correspondence: (G.C.); (D.D.); Tel.: +52-228-842-1800 (D.D.)
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
- Correspondence: (G.C.); (D.D.); Tel.: +52-228-842-1800 (D.D.)
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16
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Czislowski E, Zeil-Rolfe I, Aitken EAB. Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana ( Musa sp.) Hosts. Int J Mol Sci 2021; 22:ijms22052508. [PMID: 33801529 PMCID: PMC7975973 DOI: 10.3390/ijms22052508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC.
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17
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Simbaqueba J, Rodríguez EA, Burbano-David D, González C, Caro-Quintero A. Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali ( Foph) That Infects Cape Gooseberry Plants. Front Microbiol 2021; 11:593915. [PMID: 33537009 PMCID: PMC7847934 DOI: 10.3389/fmicb.2020.593915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/28/2020] [Indexed: 02/02/2023] Open
Abstract
The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A transcriptomic analysis of a highly virulent strain of F. oxysporum in cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other formae speciales (ff. spp.) of F. oxysporum. This pathogenic strain was classified as a new f. sp. named Foph, due to its specificity for cape gooseberry hosts. Here, we sequenced and assembled the genome of five strains of F. oxysporum from a fungal collection associated to the cape gooseberry crop (including Foph), focusing on the validation of the presence of SIX homologous and on the identification of putative effectors unique to Foph. By comparative and phylogenomic analyses based on single-copy orthologous, we found that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol that contain effector genes and identified six new putative effector genes, specific to Foph pathogenic strains. We also conducted a molecular characterization using this set of putative novel effectors in a panel of 36 additional stains of F. oxysporum including two of the four sequenced strains, from the fungal collection mentioned above. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified in this genomic analysis, represent new sources involved in the interaction between Foph and cape gooseberry, that could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.
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Affiliation(s)
- Jaime Simbaqueba
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Edwin A Rodríguez
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Diana Burbano-David
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Carolina González
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
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18
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Cui Y, Wu B, Peng A, Song X, Chen X. The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:629859. [PMID: 33613610 PMCID: PMC7889605 DOI: 10.3389/fpls.2021.629859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Fusarium species have been identified as pathogens causing many different plant diseases, and here we report an emerging banana leaf blight (BLB) caused by F. sacchari (Fs) discovered in Guangdong, China. From the symptomatic tissues collected in the field, a fungal isolate was obtained, which induced similar symptoms on healthy banana seedlings after inoculation. Koch's postulates were fulfilled after the re-isolation of the pathogen. Phylogenetic analysis on two gene segments and the whole genome sequence identified the pathogen belonging to Fs and named as Fs str. FS66. A 45.74 Mb genome of FS66 was acquired through de novo assembly using long-read sequencing data, and its contig N50 (1.97 Mb) is more than 10-fold larger than the previously available genome in the species. Based on transcriptome sequencing and ab initio gene annotation, a total of 14,486 protein-encoding genes and 418 non-coding RNAs were predicted. A total of 48 metabolite biosynthetic gene clusters including the fusaric acid biosynthesis gene cluster were predicted in silico in the FS66 genome. Comparison between FS66 and other 11 Fusarium genomes identified tens to hundreds of genes specifically gained and lost in FS66, including some previously correlated with Fusarium pathogenicity. The FS66 genome also harbors widespread gene transfer on the core chromosomes putatively from F. oxysporum species complex (FOSC), including 30 involved in Fusarium pathogenicity/virulence. This study not only reports the BLB caused by Fs, but also provides important information and clues for further understanding of the genome evolution among pathogenic Fusarium species.
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Affiliation(s)
- Yiping Cui
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Bo Wu
- School of Computing, Clemson University, Clemson, SC, United States
| | - Aitian Peng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaobing Song
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xia Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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19
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Henry P, Kaur S, Pham QAT, Barakat R, Brinker S, Haensel H, Daugovish O, Epstein L. Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii. BMC Genomics 2020; 21:730. [PMID: 33081696 PMCID: PMC7576743 DOI: 10.1186/s12864-020-07141-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3. RESULTS A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other. CONCLUSIONS There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.
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Affiliation(s)
- Peter Henry
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Quyen Anh Tran Pham
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080, USA
| | - Radwan Barakat
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Department of Plant Production & Protection, College of Agriculture, Hebron University, Hebron, Palestine
| | - Samuel Brinker
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Hannah Haensel
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Oleg Daugovish
- University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.
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20
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Abstract
Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.
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21
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The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Commun Biol 2020; 3:50. [PMID: 32005944 PMCID: PMC6994591 DOI: 10.1038/s42003-020-0770-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. Here we report four unique LS chromosomes in a human pathogenic strain NRRL 32931, isolated from a leukemia patient. These LS chromosomes were devoid of housekeeping genes, but were significantly enriched in genes encoding metal ion transporters and cation transporters. Homologs of NRRL 32931 LS genes, including a homolog of ceruloplasmin and the genes that contribute to the expansion of the alkaline pH-responsive transcription factor PacC/Rim1p, were also present in the genome of NRRL 47514, a strain associated with Fusarium keratitis outbreak. This study provides the first evidence, to our knowledge, for genomic compartmentalization in two human pathogenic fungal genomes and suggests an important role of LS chromosomes in niche adaptation. Zhang, Yang et al. compare a Fusarium oxysporum isolate obtained clinically to a phytopathogenic strain to examine transfer of lineage-specific chromosomes in determining host specificity. They find four unique lineage-specific chromosomes that seem to contribute to fungal adaptation to human hosts.
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Taylor A, Armitage AD, Handy C, Jackson AC, Hulin MT, Harrison RJ, Clarkson JP. Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi. Front Microbiol 2019; 10:2905. [PMID: 31921077 PMCID: PMC6930931 DOI: 10.3389/fmicb.2019.02905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | - Claire Handy
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | | | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
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Chang W, Li H, Chen H, Qiao F, Zeng H. Identification of mimp-associated effector genes in Fusarium oxysporum f. sp. cubense race 1 and race 4 and virulence confirmation of a candidate effector gene. Microbiol Res 2019; 232:126375. [PMID: 31783262 DOI: 10.1016/j.micres.2019.126375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022]
Abstract
Effectors secreted by microbes contribute to pathogen virulence and/or avirulence on host plants in the interaction of plants and microbes. Also, the effector repertoire determines the host specificity of a pathogen. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of banana wilt; however, knowledge about Foc effector genes is very limited. In this study, genome-wide effector gene identification was performed in Foc race 1 (Foc 1) and Foc race 4 (Foc 4) based on the context association between the effector genes and the transposable element mimp. A total of 20 candidate effector genes were identified, of which 3 were Foc 1-specific, 6 were Foc 4-specific, and 11 were present in both Foc 1 and Foc 4. Most genes (14 out of 20) showed a significant transcriptional burst in planta compared with in-culture conditions, from more than 10-fold to 1,617-fold, and at the highest 32,725-fold. In addition to Foc 1- and Foc 4-specific genes, the genes Foc 283, Foc 495, and Foc 594 also exhibited transcriptional race specificity. Sixteen of the twenty genes were predicted to have a signal peptide, nine genes might encode real effectors predicted by EffectorP 2.0, and eight genes had predicted motifs. To validate the pathogenicity of the candidate effector genes, we generated knockout mutant and complementants of the gene Foc 1324 and tested their virulence on banana plants. The results showed that Foc 1324 was a virulent factor and required for the pathogenicity of Foc 4.
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Affiliation(s)
- Wenjun Chang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China.
| | - Heng Li
- College of Tropical Agriculture and Forestry, Hainan University, Renmin Avenue 58, Haikou 570208, China
| | - Hanqing Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China
| | - Fan Qiao
- College of Tropical Agriculture and Forestry, Hainan University, Renmin Avenue 58, Haikou 570208, China
| | - Huicai Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China
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Lombard L, Sandoval-Denis M, Lamprecht S, Crous P. Epitypification of Fusarium oxysporum - clearing the taxonomic chaos. PERSOONIA 2018; 43:1-47. [PMID: 32214496 PMCID: PMC7085860 DOI: 10.3767/persoonia.2019.43.01] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/19/2018] [Indexed: 01/06/2023]
Abstract
Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.
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Affiliation(s)
- L. Lombard
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Simbaqueba J, Catanzariti A, González C, Jones DA. Evidence for horizontal gene transfer and separation of effector recognition from effector function revealed by analysis of effector genes shared between cape gooseberry- and tomato-infecting formae speciales of Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2018; 19:2302-2318. [PMID: 29786161 PMCID: PMC6638030 DOI: 10.1111/mpp.12700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA sequencing (RNAseq) reads from cape gooseberry plants (Physalis peruviana) infected with Fusarium oxysporumf. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporumf. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1(designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer. Foph SIX1a and SIX1bwere tested for their ability to complement a SIX1 knockout mutant of Fol. This mutant shows reduced pathogenicity on susceptible tomato plants, but is able to infect otherwise resistant tomato plants carrying the I-3 gene for Fusarium wilt resistance (SIX1 corresponds to Avr3). Neither SIX1a nor SIX1b could restore full pathogenicity on susceptible tomato plants, suggesting that any role they may play in pathogenicity is likely to be specific to cape gooseberry. SIX1b, but not SIX1a, was able to restore avirulence on tomato plants carrying I-3.These findings separate the recognition of SIX1 from its role as an effector and suggest direct recognition by I-3. A hypervariable region of SIX1undergoing diversifying selection within the F. oxysporum species complex is likely to play an important role in SIX1 recognition. These findings also indicate that I-3could potentially be deployed as a transgene in cape gooseberry to protect this emerging crop from Foph.Alternatively, cape gooseberry germplasm could be explored for I-3homologues capable of providing resistance to Foph.
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Affiliation(s)
- Jaime Simbaqueba
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| | - Ann‐Maree Catanzariti
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
| | | | - David A. Jones
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityActonACT2601Australia
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van Dam P, de Sain M, Ter Horst A, van der Gragt M, Rep M. Use of Comparative Genomics-Based Markers for Discrimination of Host Specificity in Fusarium oxysporum. Appl Environ Microbiol 2018; 84:e01868-17. [PMID: 29030446 PMCID: PMC5734036 DOI: 10.1128/aem.01868-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/10/2017] [Indexed: 12/29/2022] Open
Abstract
The polyphyletic nature of many formae speciales of Fusarium oxysporum prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicity. We therefore compared candidate effector genes extracted from 60 existing and 22 newly generated genome assemblies, specifically targeting strains affecting cucurbit plant species. Based on these candidate effector genes, a total of 18 PCR primer pairs were designed to discriminate between each of the seven Cucurbitaceae-affecting formae speciales When tested on a collection of strains encompassing different clonal lineages of these formae speciales, nonpathogenic strains, and strains of other formae speciales, they allowed clear recognition of the host range of each evaluated strain. Within Fusarium oxysporum f. sp. melonis more genetic variability exists than anticipated, resulting in three F. oxysporum f. sp. melonis marker patterns that partially overlapped with the cucurbit-infecting Fusarium oxysporum f. sp. cucumerinum, Fusarium oxysporum f. sp. niveum, Fusarium oxysporum f. sp. momordicae, and/or Fusarium oxysporum f. sp. lagenariae For F. oxysporum f. sp. niveum, a multiplex TaqMan assay was evaluated and was shown to allow quantitative and specific detection of template DNA quantities as low as 2.5 pg. These results provide ready-to-use marker sequences for the mentioned F. oxysporum pathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms of F. oxysporumIMPORTANCE Pathogenic strains of Fusarium oxysporum are differentiated into formae speciales based on their host range, which is normally restricted to only one or a few plant species. However, horizontal gene transfer between strains in the species complex has resulted in a polyphyletic origin of host specificity in many of these formae speciales This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains of F. oxysporum with each other, specifically targeting virulence-related genes that are typically highly similar within each forma specialis Using this approach, we identified marker sequences that allow the discrimination of F. oxysporum strains affecting various cucurbit plant species through different PCR-based methods.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Mara de Sain
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Anneliek Ter Horst
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Michelle van der Gragt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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van Dam P, Fokkens L, Ayukawa Y, van der Gragt M, Ter Horst A, Brankovics B, Houterman PM, Arie T, Rep M. A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. Sci Rep 2017; 7:9042. [PMID: 28831051 PMCID: PMC5567276 DOI: 10.1038/s41598-017-07995-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
The genome of Fusarium oxysporum (Fo) consists of a set of eleven 'core' chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, and a chromosome that shows all the hallmarks of a pathogenicity chromosome comprised two contigs. A central part of this chromosome contains all identified candidate effector genes, including homologs of SIX6, SIX9, SIX11 and SIX 13. We show that SIX6 contributes to virulence of Forc. Through horizontal chromosome transfer (HCT) to a non-pathogenic strain, we also show that the accessory chromosome containing the SIX gene homologs is indeed a pathogenicity chromosome for cucurbit infection. Conversely, complete loss of virulence was observed in Forc016 strains that lost this chromosome. We conclude that also a non-wilt-inducing Fo pathogen relies on effector proteins for successful infection and that the Forc pathogenicity chromosome contains all the information necessary for causing root rot of cucurbits. Three out of nine HCT strains investigated have undergone large-scale chromosome alterations, reflecting the remarkable plasticity of Fo genomes.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Yu Ayukawa
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Michelle van der Gragt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anneliek Ter Horst
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Petra M Houterman
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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