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Constantin ME, Fokkens L, de Sain M, Takken FLW, Rep M. Number of Candidate Effector Genes in Accessory Genomes Differentiates Pathogenic From Endophytic Fusarium oxysporum Strains. FRONTIERS IN PLANT SCIENCE 2021; 12:761740. [PMID: 34912358 PMCID: PMC8666634 DOI: 10.3389/fpls.2021.761740] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/08/2021] [Indexed: 05/21/2023]
Abstract
The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investigated at the molecular level, and the genetic basis that underlies endophytic versus pathogenic behavior is unknown. To investigate this, 44 Fo strains from non-cultivated Australian soils, grass roots from Spain, and tomato stems from United States were characterized genotypically by whole genome sequencing, and phenotypically by examining their ability to symptomlessly colonize tomato plants and to confer resistance against Fusarium Wilt. Comparison of the genomes of the validated endophytic Fo strains with those of 102 pathogenic strains revealed that both groups have similar genomes sizes, with similar amount of accessory DNA. However, although endophytic strains can harbor homologs of known effector genes, they have typically fewer effector gene candidates and associated non-autonomous transposons (mimps) than pathogenic strains. A pathogenic 'lifestyle' is associated with extended effector gene catalogs and a set of "host specific" effectors. No candidate effector genes unique to endophytic strains isolated from the same plant species were found, implying little or no host-specific adaptation. As plant-beneficial interactions were observed to be common for the tested Fo isolates, the propensity for endophytism and the ability to confer biocontrol appears to be a predominant feature of this organism. These findings allow prediction of the lifestyle of a Fo strain based on its genome sequence as a potential pathogen or as a harmless or even beneficial endophyte by determining its effectorome and mimp number.
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Adhikari TB, Gao A, Ingram T, Louws FJ. Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems. Front Microbiol 2020; 11:1995. [PMID: 32973719 PMCID: PMC7482420 DOI: 10.3389/fmicb.2020.01995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 01/19/2023] Open
Abstract
In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar 'Happy Root' (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.
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Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Anne Gao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.,Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
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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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Jelinski NA, Broz K, Jonkers W, Ma LJ, Kistler HC. Effector Gene Suites in Some Soil Isolates of Fusarium oxysporum Are Not Sufficient Predictors of Vascular Wilt in Tomato. PHYTOPATHOLOGY 2017; 107:842-851. [PMID: 28323535 DOI: 10.1094/phyto-12-16-0437-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Seventy-four Fusarium oxysporum soil isolates were assayed for known effector genes present in an F. oxysporum f. sp. lycopersici race 3 tomato wilt strain (FOL MN-25) obtained from the same fields in Manatee County, Florida. Based on the presence or absence of these genes, four haplotypes were defined, two of which represented 96% of the surveyed isolates. These two most common effector haplotypes contained either all or none of the assayed race 3 effector genes. We hypothesized that soil isolates with all surveyed effector genes, similar to FOL MN-25, would be pathogenic toward tomato, whereas isolates lacking all effectors would be nonpathogenic. However, inoculation experiments revealed that presence of the effector genes alone was not sufficient to ensure pathogenicity on tomato. Interestingly, a nonpathogenic isolate containing the full suite of unmutated effector genes (FOS 4-4) appears to have undergone a chromosomal rearrangement yet remains vegetatively compatible with FOL MN-25. These observations confirm the highly dynamic nature of the F. oxysporum genome and support the conclusion that pathogenesis among free-living populations of F. oxysporum is a complex process. Therefore, the presence of effector genes alone may not be an accurate predictor of pathogenicity among soil isolates of F. oxysporum.
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Affiliation(s)
- Nicolas A Jelinski
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Karen Broz
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Wilfried Jonkers
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Li-Jun Ma
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - H Corby Kistler
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
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van Dam P, Fokkens L, Schmidt SM, Linmans JHJ, Kistler HC, Ma LJ, Rep M. Effector profiles distinguish formae speciales of Fusarium oxysporum. Environ Microbiol 2016; 18:4087-4102. [PMID: 27387256 DOI: 10.1111/1462-2920.13445] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
Abstract
Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was performed on strains from five different ff.spp. (cucumerinum, niveum, melonis, radicis-cucumerinum and lycopersici). In each genome, genes for putative effectors were identified based on small size, secretion signal, and vicinity to a "miniature impala" transposable element. The candidate effector genes of all genomes were collected and the presence/absence patterns in each individual genome were clustered. Members of the same forma specialis turned out to group together, with cucurbit-infecting strains forming a supercluster separate from other ff.spp. Moreover, strains from different clonal lineages within the same forma specialis harbour identical effector gene sequences, supporting horizontal transfer of genetic material. These data offer new insight into the genetic basis of host specificity in the F. oxysporum species complex and show that (putative) effectors can be used to predict host specificity in F. oxysporum.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Sarah M Schmidt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Jasper H J Linmans
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - H Corby Kistler
- United States Department of Agriculture, ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
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Nirmaladevi D, Venkataramana M, Srivastava RK, Uppalapati SR, Gupta VK, Yli-Mattila T, Clement Tsui KM, Srinivas C, Niranjana SR, Chandra NS. Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici. Sci Rep 2016; 6:21367. [PMID: 26883288 PMCID: PMC4756691 DOI: 10.1038/srep21367] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022] Open
Abstract
The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin.
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Affiliation(s)
- D. Nirmaladevi
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - M. Venkataramana
- DRDO-BU-CLS, Barathiar University Campus, Coimbatore, Tamil Nadu, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. R. Uppalapati
- Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | - Vijai Kumar Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - T. Yli-Mattila
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - K. M. Clement Tsui
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - C. Srinivas
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - S. R. Niranjana
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
| | - Nayaka S. Chandra
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
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Durkin J, Bissett J, Pahlavani M, Mooney B, Buchwaldt L. IGS Minisatellites Useful for Race Differentiation in Colletotrichum lentis and a Likely Site of Small RNA Synthesis Affecting Pathogenicity. PLoS One 2015; 10:e0137398. [PMID: 26340001 PMCID: PMC4560493 DOI: 10.1371/journal.pone.0137398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/17/2015] [Indexed: 11/25/2022] Open
Abstract
Colletotrichum lentis is a fungal pathogen of lentil in Canada but rarely reported elsewhere. Two races, Ct0 and Ct1, have been identified using differential lines. Our objective was to develop a PCR-probe differentiating these races. Sequences of the translation elongation factor 1α (tef1α), RNA polymerase II subunit B2 (rpb2), ATP citrate lyase subunit A (acla), and internal transcribed spacer (ITS) regions were monomorphic, while the intergenic spacer (IGS) region showed length polymorphisms at two minisatellites of 23 and 39 nucleotides (nt). A PCR-probe (39F/R) amplifying the 39 nt minisatellite was developed which subsequently revealed 1-5 minisatellites with 1-12 repeats in C. lentis. The probe differentiated race Ct1 isolates having 7, 9 or 7+9 repeats from race Ct0 having primarily 2 or 4 repeats, occasionally 5, 6, or 8, but never 7 or 9 repeats. These isolates were collected between 1991 and 1999. In a 2012 survey isolates with 2 and 4 repeats increased from 34% to 67%, while isolated with 7 or 9 repeats decreased from 40 to 4%, likely because Ct1 resistant lentil varieties had been grown. The 39 nt repeat was identified in C. gloeosporioides, C. trifolii, Ascochyta lentis, Sclerotinia sclerotiorum and Botrytis cinerea. Thus, the 39F/R PCR probe is not species specific, but can differentiate isolates based on repeat number. The 23 nt minisatellite in C. lentis exists as three length variants with ten sequence variations differentiating race Ct0 having 14 or 19 repeats from race Ct1 having 17 repeats, except for one isolate. RNA-translation of 23 nt repeats forms hairpins and has the appropriate length to suggest that IGS could be a site of small RNA synthesis, a hypothesis that warrants further investigation. Small RNA from fungal plant pathogens able to silence genes either in the host or pathogen thereby aiding infection have been reported.
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Affiliation(s)
- Jonathan Durkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Canada
| | - John Bissett
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Ottawa, Canada
| | - Mohammadhadi Pahlavani
- Department of Agronomy and Plant Breeding, Gorgan University of Agricultural Sciences, Gorgan, Iran
| | - Brent Mooney
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Canada
| | - Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Canada
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Jabeen N, Chaudhary Z, Gulfraz M, Rashid H, Mirza B. Expression of Rice Chitinase Gene in Genetically Engineered Tomato Confers Enhanced Resistance to Fusarium Wilt and Early Blight. THE PLANT PATHOLOGY JOURNAL 2015; 31:252-8. [PMID: 26361473 PMCID: PMC4564150 DOI: 10.5423/ppj.oa.03.2015.0026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/18/2015] [Accepted: 06/01/2015] [Indexed: 05/29/2023]
Abstract
This is the first study reporting the evaluation of transgenic lines of tomato harboring rice chitinase (RCG3) gene for resistance to two important fungal pathogens Fusarium oxysporum f. sp. lycopersici (Fol) causing fusarium wilt and Alternaria solani causing early blight (EB). In this study, three transgenic lines TL1, TL2 and TL3 of tomato Solanum lycopersicum Mill. cv. Riogrande genetically engineered with rice chitinase (RCG 3) gene and their R1 progeny was tested for resistance to Fol by root dip method and A. solani by detached leaf assay. All the R0 transgenic lines were highly resistant to these fungal pathogens compared to non-transgenic control plants. The pattern of segregation of three independent transformant for Fol and A. solani was also studied. Mendelian segregation was observed in transgenic lines 2 and 3 while it was not observed in transgenic line 1. It was concluded that introduction of chitinase gene in susceptible cultivar of tomato not only enhanced the resistance but was stably inherited in transgenic lines 2 and 3.
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Affiliation(s)
- Nyla Jabeen
- Department of Bioinformatics and Biotechnology, International Islamic University Islamabad,
Pakistan
| | | | - Muhammad Gulfraz
- Department of Chemistry, Comsats Institute of Information Technology Abbotabad,
Pakistan
| | - Hamid Rashid
- Department of Bioinformatics, Mohammad Ali Jinnah University, Islamabad,
Pakistan
| | - Bushra Mirza
- Department of Bioinformatics and Biotechnology, International Islamic University Islamabad,
Pakistan
- Department of Biological Sciences, Quaid-i-Azam University, Islamabad,
Pakistan
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9
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Microbial genome-enabled insights into plant–microorganism interactions. Nat Rev Genet 2014; 15:797-813. [DOI: 10.1038/nrg3748] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Jonkers W, Xayamongkhon H, Haas M, Olivain C, van der Does HC, Broz K, Rep M, Alabouvette C, Steinberg C, Kistler HC. EBR1genomic expansion and its role in virulence ofFusariumspecies. Environ Microbiol 2013; 16:1982-2003. [DOI: 10.1111/1462-2920.12331] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Wilfried Jonkers
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Henry Xayamongkhon
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Matthew Haas
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Chantal Olivain
- UMR 1347 Agroécologie; INRA; BP 86510 F-21065 Dijon cedex France
| | - H. Charlotte van der Does
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Karen Broz
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - Martijn Rep
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | | | - Christian Steinberg
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - H. Corby Kistler
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
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11
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Hirano Y, Arie T. Variation and phylogeny of Fusarium oxysporum isolates based on nucleotide sequences of polygalacturonase genes. Microbes Environ 2011; 24:113-20. [PMID: 21566363 DOI: 10.1264/jsme2.me08554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nucleotide sequences of two endopolygalacturonase genes (pg1 and pg5) and two exopolygalacturonase genes (pgx1 and pgx4), which encode members of a major family of secreted cell-wall-degrading enzymes (CWDEs), were compared to detect the extent of genetic variation among isolates of Fusarium oxysporum. The nucleotide variation rate in exons was 0.23-0.93%, higher than that in introns (0.01-0.64%) and untranslated regions (UTRs) (0.07-0.25%), resulting in 0.05-0.31% variation in amino acids. pgx1 exhibited the most genetic diversity. Phylogenetic analysis of the four genes, which reside on different chromosomes, revealed different evolutionary patterns for each. Our results suggest a biased evolution of the polygalacturonase genes of F. oxysporum, or alternatively, that the genes were acquired at different times during evolution.
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Affiliation(s)
- Yasushi Hirano
- Saitama Prefectural Agriculture and Forestry Research Center, 91 Rokumanbu, Kuki, Saitama 346-0037, Japan.
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12
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Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RAE, Chapman S, Coulson R, Coutinho PM, Danchin EGJ, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010; 464:367-73. [PMID: 20237561 PMCID: PMC3048781 DOI: 10.1038/nature08850] [Citation(s) in RCA: 1001] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 01/20/2010] [Indexed: 11/09/2022]
Abstract
Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
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Affiliation(s)
- Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02141, USA
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Houterman PM, Ma L, van Ooijen G, de Vroomen MJ, Cornelissen BJC, Takken FLW, Rep M. The effector protein Avr2 of the xylem-colonizing fungus Fusarium oxysporum activates the tomato resistance protein I-2 intracellularly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:970-8. [PMID: 19228334 DOI: 10.1111/j.1365-313x.2009.03838.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
To promote host colonization, many plant pathogens secrete effector proteins that either suppress or counteract host defences. However, when these effectors are recognized by the host's innate immune system, they trigger resistance rather than promoting virulence. Effectors are therefore key molecules in determining disease susceptibility or resistance. We show here that Avr2, secreted by the vascular wilt fungus Fusarium oxysporum f. sp. lycopersici (Fol), shows both activities: it is required for full virulence in a susceptible host and also triggers resistance in tomato plants carrying the resistance gene I-2. Point mutations in AVR2, causing single amino acid changes, are associated with I-2-breakingFol strains. These point mutations prevent recognition by I-2, both in tomato and when both genes are co-expressed in leaves of Nicotiana benthamiana. Fol strains carrying the Avr2 variants are equally virulent, showing that virulence and avirulence functions can be uncoupled. Although Avr2 is secreted into the xylem sap when Fol colonizes tomato, the Avr2 protein can be recognized intracellularly by I-2, implying uptake by host cells.
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Affiliation(s)
- Petra M Houterman
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94062, 1090 GB Amsterdam, The Netherlands
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