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de la Rosa S, Schol CR, Ramos Peregrina Á, Winter DJ, Hilgers AM, Maeda K, Iida Y, Tarallo M, Jia R, Beenen HG, Rocafort M, de Wit PJGM, Bowen JK, Bradshaw RE, Joosten MHAJ, Bai Y, Mesarich CH. Sequential breakdown of the Cf-9 leaf mould resistance locus in tomato by Fulvia fulva. THE NEW PHYTOLOGIST 2024. [PMID: 38922927 DOI: 10.1111/nph.19925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Leaf mould, caused by Fulvia fulva, is a devastating disease of tomato plants. In many commercial tomato cultivars, resistance to this disease is governed by the Cf-9 locus, which encodes five paralogous receptor-like proteins. Two of these proteins confer resistance: Cf-9C recognises the previously identified F. fulva effector Avr9 and provides resistance during all plant growth stages, while Cf-9B recognises the yet-unidentified F. fulva effector Avr9B and provides mature plant resistance only. In recent years, F. fulva strains have emerged that can overcome the Cf-9 locus, with Cf-9C circumvented through Avr9 deletion. To understand how Cf-9B is circumvented, we set out to identify Avr9B. Comparative genomics, transient expression assays and gene complementation experiments were used to identify Avr9B, while gene sequencing was used to assess Avr9B allelic variation across a world-wide strain collection. A strict correlation between Avr9 deletion and resistance-breaking mutations in Avr9B was observed in strains recently collected from Cf-9 cultivars, whereas Avr9 deletion but no mutations in Avr9B were observed in older strains. This research showcases how F. fulva has evolved to sequentially break down the Cf-9 locus and stresses the urgent need for commercial tomato cultivars that carry novel, stacked resistance genes active against this pathogen.
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Affiliation(s)
- Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
| | - Christiaan R Schol
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Ángeles Ramos Peregrina
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - David J Winter
- Bioinformatics Group, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Anne M Hilgers
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Kazuya Maeda
- Laboratory of Plant Pathology, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Yuichiro Iida
- Laboratory of Plant Pathology, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
| | - Ruifang Jia
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Henriek G Beenen
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Mercedes Rocafort
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Ltd, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Rosie E Bradshaw
- Laboratory of Molecular Plant Pathology, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
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Zaccaron AZ, Stergiopoulos I. Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes. BMC Biol 2024; 22:25. [PMID: 38281938 PMCID: PMC10823647 DOI: 10.1186/s12915-024-01818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes. RESULTS Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum. CONCLUSIONS Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA.
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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | | | - Yanan Guo
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Richard C. Hamelin
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | | | - Mengmeng Lu
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Hannah M. McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Christiaan R. Schol
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- Plant BreedingWageningen University & ResearchWageningenNetherlands
| | | | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Alex Z. Zaccaron
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Rosie E. Bradshaw
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
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Sudermann MA, McGilp L, Vogel G, Regnier M, Jaramillo AR, Smart CD. The Diversity of Passalora fulva Isolates Collected from Tomato Plants in U.S. High Tunnels. PHYTOPATHOLOGY 2022; 112:1350-1360. [PMID: 35021861 DOI: 10.1094/phyto-06-21-0244-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High tunnels extend the growing season of high value crops, including tomatoes, but the environmental conditions within high tunnels favor the spread of the tomato leaf mold pathogen, Passalora fulva (syn. Cladosporium fulvum). Tomato leaf mold results in defoliation, and if severe, losses in yield. Despite substantial research, little is known regarding the genetic structure and diversity of populations of P. fulva associated with high tunnel tomato production in the United States. From 2016 to 2019, a total of 50 P. fulva isolates were collected from tomato leaf samples in high tunnels in the Northeast and Minnesota. Other Cladosporium species were also isolated from the leaf surfaces. Koch's postulates were conducted to confirm that P. fulva was the cause of the disease symptoms observed. Race determination experiments revealed that the isolates belonged to either race 0 (six isolates) or race 2 (44 isolates). Polymorphisms were identified within four previously characterized effector genes: Avr2, Avr4, Avr4e, and Avr9. The largest number of polymorphisms were observed for Avr2. Both mating type genes, MAT1-1-1 and MAT1-2-1, were present in the isolate collection. For further insights into the pathogen diversity, the 50 isolates were genotyped at 7,514 single-nucleotide polymorphism loci using genotyping-by-sequencing. Differentiation by region but not by year was observed. Within the collection of 50 isolates, there were 18 distinct genotypes. Information regarding P. fulva population diversity will enable better management recommendations for growers, as high tunnel production of tomatoes expands.
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Affiliation(s)
- Martha A Sudermann
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Lillian McGilp
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gregory Vogel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Melissa Regnier
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
- Laboratory of Mycology and Phytopathology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Alejandra Rodríguez Jaramillo
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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Zaccaron AZ, Chen LH, Samaras A, Stergiopoulos I. A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome. Microb Genom 2022; 8:000819. [PMID: 35471194 PMCID: PMC9453070 DOI: 10.1099/mgen.0.000819] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/29/2022] [Indexed: 01/25/2023] Open
Abstract
Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the 'two-speed genome' model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.
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Affiliation(s)
- Alex Z. Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, USA
| | - Li-Hung Chen
- Department of Plant Pathology, University of California Davis, Davis, USA
- Present address: Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Anastasios Samaras
- Department of Plant Pathology, University of California Davis, Davis, USA
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Aylward J, Havenga M, Wingfield BD, Wingfield MJ, Dreyer LL, Roets F, Steenkamp ET. Novel mating-type-associated genes and gene fragments in the genomes of Mycosphaerellaceae and Teratosphaeriaceae fungi. Mol Phylogenet Evol 2022; 171:107456. [DOI: 10.1016/j.ympev.2022.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022]
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Adhikari TB, Muzhinji N, Halterman D, Louws FJ. Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin. Sci Rep 2021; 11:17024. [PMID: 34426589 PMCID: PMC8382843 DOI: 10.1038/s41598-021-95486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
Early blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association \documentclass[12pt]{minimal}
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\begin{document}$$\left( {\overline{r}_{d} } \right)$$\end{document}r¯d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.
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Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Norman Muzhinji
- Department of Applied and Natural Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Dennis Halterman
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Vegetable Crops Research Unit, Madison, WI, 53706, USA
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA.
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Pearce TL, Scott JB, Pilkington SJ, Pethybridge SJ, Hay FS. Evidence for Sexual Recombination in Didymella tanaceti Populations, and Their Evolution Over Spring Production in Australian Pyrethrum Fields. PHYTOPATHOLOGY 2019; 109:155-168. [PMID: 29989847 DOI: 10.1094/phyto-08-17-0280-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tan spot, caused by Didymella tanaceti, is one of the most important foliar diseases affecting pyrethrum in Tasmania, Australia. Population dynamics, including mating-type ratios and genetic diversity of D. tanaceti, was characterized within four geographically separated fields in both late winter and spring 2012. A set of 10 microsatellite markers was developed and used to genotype 774 D. tanaceti isolates. Isolates were genotypically diverse, with 123 multilocus genotypes (MLG) identified across the four fields. Fifty-eight MLG contained single isolates and Psex analysis estimated that, within many of the recurrent MLG, there were multiple clonal lineages derived from recombination. Isolates of both mating types were at a 1:1 ratio following clone correction in each field at each sampling period, which was suggestive of sexual recombination. No evidence of genetic divergence of isolates of each mating type was identified, indicating admixture within the population. Linkage equilibrium in two of the four field populations sampled in late winter could not be discounted following clone correction. Evaluation of temporal changes in gene and genotypic diversity identified that they were both similar for the two sampling periods despite an increased D. tanaceti isolation frequency in spring. Genetic differentiation was similar in populations sampled between the two sampling periods within fields or between fields. These results indicated that sexual reproduction may have contributed to tan spot epidemics within Australian pyrethrum fields and has contributed to a genetically diverse D. tanaceti population.
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Affiliation(s)
- Tamieka L Pearce
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Jason B Scott
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Stacey J Pilkington
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Frank S Hay
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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Romero Luna MP, Aime MC, Chilvers MI, Wise KA. Genetic Diversity of Stenocarpella maydis in the Major Corn Production Areas of the United States. PLANT DISEASE 2017; 101:2020-2026. [PMID: 30677369 DOI: 10.1094/pdis-02-17-0292-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The fungus Stenocarpella maydis (Berk.) B. Sutton, causal agent of Diplodia ear rot, is a prevalent corn (Zea mays L.) pathogen in the United States. Although S. maydis reduces grain quality, causes yield loss, and can produce mycotoxins in some countries, few studies have examined its biology and genetic diversity. We analyzed the genetic diversity of 174 S. maydis isolates sampled across the major corn production areas in the United States using nine different microsatellites. In all, 55 unique multilocus genotypes (MLG) were observed out of the 174 S. maydis isolates tested. After conducting a Bayesian clustering analysis by STRUCTURE, it was observed that the most probable number of genetic groups was two; however, no separation by their geographical location was identified. According to the minimum spanning network, the S. maydis population is linked across geographic regions of the United States but also contains private genotypes. Temporal diversity in the inoculum source was also observed at one location across 4 years. The haploid stage of S. maydis was confirmed and both mating type genes were amplified among selected isolates with unique MLG. We theorize that, although S. maydis is primarily an asexual fungus, sporadic cryptic recombination may occur, which could contribute to the genetic diversity observed in this study.
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Affiliation(s)
- Martha P Romero Luna
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
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10
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Pearce TL, Scott JB, Hay FS, Pethybridge SJ. Mating-Type Gene Structure and Spatial Distribution of Didymella tanaceti in Pyrethrum Fields. PHYTOPATHOLOGY 2016; 106:1521-1529. [PMID: 27398744 DOI: 10.1094/phyto-01-16-0038-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tan spot of pyrethrum (Tanacetum cinerariifolium) is caused by the ascomycete Didymella tanaceti. To assess the evolutionary role of ascospores in the assumed asexual species, the structure and arrangement of mating-type (MAT) genes were examined. A single MAT1-1 or MAT1-2 idiomorph was identified in all isolates examined, indicating that the species is heterothallic. The idiomorphs were flanked upstream and downstream by regions encoding pyridoxamine phosphate oxidase-like and DNA lyase-like proteins, respectively. A multiplex MAT-specific polymerase chain reaction assay was developed and used to genotype 325 isolates collected within two transects in each of four fields in Tasmania, Australia. The ratio of isolates of each mating-type in each transect was consistent with a 1:1 ratio. The spatial distribution of the isolates of the two mating-types within each transect was random for all except one transect for MAT1-1 isolates, indicating that clonal patterns of each mating-type were absent. However, evidence of a reduced selection pressure on MAT1-1 isolates was observed, with a second haplotype of the MAT1-1-1 gene identified in 4.4% of MAT1-1 isolates. In vitro crosses between isolates with opposite mating-types failed to produce ascospores. Although the sexual morph could not be induced, the occurrence of both mating-types in equal frequencies suggested that a cryptic sexual mode of reproduction may occur within field populations.
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Affiliation(s)
- Tamieka L Pearce
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Jason B Scott
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Frank S Hay
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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Muller MF, Barnes I, Kunene NT, Crampton BG, Bluhm BH, Phillips SM, Olivier NA, Berger DK. Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation. PHYTOPATHOLOGY 2016; 106:1194-1205. [PMID: 27392176 DOI: 10.1094/phyto-02-16-0084-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The outcomes of this genome-enabled study are important for disease management since the high diversity has implications for dispersal of fungicide resistance should it emerge and the need for diversified resistance breeding.
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Affiliation(s)
- Mischa F Muller
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Irene Barnes
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Ncobile T Kunene
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Bridget G Crampton
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Burton H Bluhm
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Sonia M Phillips
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Nicholas A Olivier
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Dave K Berger
- First, third, fourth, sixth, seventh, and eighth authors: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa; second author: Department of Genetics, FABI, University of Pretoria, Pretoria 0028, South Africa; fifth author: Department of Plant Pathology, University of Arkansas; and seventh author: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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12
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Mating type genes in the genus Neofusicoccum: Mating strategies and usefulness in species delimitation. Fungal Biol 2016; 121:394-404. [PMID: 28317541 DOI: 10.1016/j.funbio.2016.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/25/2016] [Indexed: 12/16/2022]
Abstract
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed. Homothallism was the predominant mating strategy among the species tested. Furthermore, the potential of mating type gene sequences for species delimitation was evaluated. Phylogenetic analyses were performed on both MAT genes and compared with multigene genealogies using sequences of the ribosomal internal transcribed spacer region, translation elongation factor 1-alpha and beta-tubulin. Phylogenies based on mating type genes could discriminate between the species analysed and are in concordance with the results obtained with the more conventional multilocus phylogenetic analysis approach. Thus, MAT genes represent a powerful tool to delimit cryptic species in the genus Neofusicoccum.
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Iida Y, van ‘t Hof P, Beenen H, Mesarich C, Kubota M, Stergiopoulos I, Mehrabi R, Notsu A, Fujiwara K, Bahkali A, Abd-Elsalam K, Collemare J, de Wit PJGM. Novel Mutations Detected in Avirulence Genes Overcoming Tomato Cf Resistance Genes in Isolates of a Japanese Population of Cladosporium fulvum. PLoS One 2015; 10:e0123271. [PMID: 25902074 PMCID: PMC4406682 DOI: 10.1371/journal.pone.0123271] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/19/2015] [Indexed: 12/15/2022] Open
Abstract
Leaf mold of tomato is caused by the biotrophic fungus Cladosporium fulvum which complies with the gene-for-gene system. The disease was first reported in Japan in the 1920s and has since been frequently observed. Initially only race 0 isolates were reported, but since the consecutive introduction of resistance genes Cf-2, Cf-4, Cf-5 and Cf-9 new races have evolved. Here we first determined the virulence spectrum of 133 C. fulvum isolates collected from 22 prefectures in Japan, and subsequently sequenced the avirulence (Avr) genes Avr2, Avr4, Avr4E, Avr5 and Avr9 to determine the molecular basis of overcoming Cf genes. Twelve races of C. fulvum with a different virulence spectrum were identified, of which races 9, 2.9, 4.9, 4.5.9 and 4.9.11 occur only in Japan. The Avr genes in many of these races contain unique mutations not observed in races identified elsewhere in the world including (i) frameshift mutations and (ii) transposon insertions in Avr2, (iii) point mutations in Avr4 and Avr4E, and (iv) deletions of Avr4E, Avr5 and Avr9. New races have developed by selection pressure imposed by consecutive introductions of Cf-2, Cf-4, Cf-5 and Cf-9 genes in commercially grown tomato cultivars. Our study shows that molecular variations to adapt to different Cf genes in an isolated C. fulvum population in Japan are novel but overall follow similar patterns as those observed in populations from other parts of the world. Implications for breeding of more durable C. fulvum resistant varieties are discussed.
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Affiliation(s)
- Yuichiro Iida
- National Agriculture and Food Research Organization, Tsu, Mie, Japan
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Pieter van ‘t Hof
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Henriek Beenen
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Carl Mesarich
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Masaharu Kubota
- National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | | | - Rahim Mehrabi
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
- Seed and Plant Improvement Institute, Karaj, Iran
| | - Ayumi Notsu
- Hokkaido Research Organization, Ornamental Plants and Vegetables Research Center, Hokkaido, Japan
| | - Kazuki Fujiwara
- National Agriculture and Food Research Organization, Tsu, Mie, Japan
| | - Ali Bahkali
- King Saud University, College of Science, Botany and Microbiology Department, Riyadh, Saudi Arabia
| | - Kamel Abd-Elsalam
- King Saud University, College of Science, Botany and Microbiology Department, Riyadh, Saudi Arabia
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Jérôme Collemare
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Pierre J. G. M. de Wit
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
- Centre for Biosystems Genomics, Wageningen, The Netherlands
- * E-mail:
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14
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Stotz HU, Mitrousia GK, de Wit PJGM, Fitt BDL. Effector-triggered defence against apoplastic fungal pathogens. TRENDS IN PLANT SCIENCE 2014; 19:491-500. [PMID: 24856287 PMCID: PMC4123193 DOI: 10.1016/j.tplants.2014.04.009] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 04/07/2014] [Accepted: 04/23/2014] [Indexed: 05/18/2023]
Abstract
R gene-mediated host resistance against apoplastic fungal pathogens is not adequately explained by the terms pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) or effector-triggered immunity (ETI). Therefore, it is proposed that this type of resistance is termed 'effector-triggered defence' (ETD). Unlike PTI and ETI, ETD is mediated by R genes encoding cell surface-localised receptor-like proteins (RLPs) that engage the receptor-like kinase SOBIR1. In contrast to this extracellular recognition, ETI is initiated by intracellular detection of pathogen effectors. ETI is usually associated with fast, hypersensitive host cell death, whereas ETD often triggers host cell death only after an elapsed period of endophytic pathogen growth. In this opinion, we focus on ETD responses against foliar fungal pathogens of crops.
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Affiliation(s)
- Henrik U Stotz
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Georgia K Mitrousia
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Pierre J G M de Wit
- Wageningen University and Research Centre, Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bruce D L Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK.
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15
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Mesarich CH, Griffiths SA, van der Burgt A, Okmen B, Beenen HG, Etalo DW, Joosten MHAJ, de Wit PJGM. Transcriptome sequencing uncovers the Avr5 avirulence gene of the tomato leaf mold pathogen Cladosporium fulvum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:846-57. [PMID: 24678832 DOI: 10.1094/mpmi-02-14-0050-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Cf-5 gene of tomato confers resistance to strains of the fungal pathogen Cladosporium fulvum carrying the avirulence gene Avr5. Although Cf-5 has been cloned, Avr5 has remained elusive. We report the cloning of Avr5 using a combined bioinformatic and transcriptome sequencing approach. RNA-Seq was performed on the sequenced race 0 strain (0WU; carrying Avr5), as well as a race 5 strain (IPO 1979; lacking a functional Avr5 gene) during infection of susceptible tomato. Forty-four in planta-induced C. fulvum candidate effector (CfCE) genes of 0WU were identified that putatively encode a secreted, small cysteine-rich protein. An expressed transcript sequence comparison between strains revealed two polymorphic CfCE genes in IPO 1979. One of these conferred avirulence to IPO 1979 on Cf-5 tomato following complementation with the corresponding 0WU allele, confirming identification of Avr5. Complementation also led to increased fungal biomass during infection of susceptible tomato, signifying a role for Avr5 in virulence. Seven of eight race 5 strains investigated escape Cf-5-mediated resistance through deletion of the Avr5 gene. Avr5 is heavily flanked by repetitive elements, suggesting that repeat instability, in combination with Cf-5-mediated selection pressure, has led to the emergence of race 5 strains deleted for the Avr5 gene.
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16
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van der Burgt A, Karimi Jashni M, Bahkali AH, de Wit PJGM. Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past. MOLECULAR PLANT PATHOLOGY 2014; 15:133-44. [PMID: 24393451 PMCID: PMC6638865 DOI: 10.1111/mpp.12072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non- or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment-based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi-gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).
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Affiliation(s)
- Ate van der Burgt
- Laboratory of Phytopathology, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, the Netherlands; Applied Bioinformatics, Plant Research International, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, the Netherlands
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17
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Stewart JE, Thomas KA, Lawrence CB, Dang H, Pryor BM, Timmer LMP, Peever TL. Signatures of recombination in clonal lineages of the citrus brown spot pathogen, Alternaria alternata sensu lato. PHYTOPATHOLOGY 2013; 103:741-749. [PMID: 23441968 DOI: 10.1094/phyto-08-12-0211-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Most Alternaria spp. are considered asexual but recent molecular evolution analyses of Alternaria mating-type genes show that the mating locus is under strong purifying selection, indicating a possible role in sexual reproduction. The objective of this study was to determine the mode of reproduction of an Alternaria alternata sensu lato population causing citrus brown spot in central Florida. Mating type of each isolate was determined, and isolates were sequenced at six putatively unlinked loci. Three genetically distinct subpopulations (SH1, SH4A, and SH4B) were identified using network and Bayesian population structure analyses. Results demonstrate that most subpopulations of A. alternata associated with citrus are clonal but some have the ability to extensively recombine through a cryptic sexual cycle or parasexual cycle. Although isolates were sampled in close physical proximity (≈2,500-m² area), we were able to reject a random mating model using multilocus gametic disequilibrium tests for two subpopulations, SH1 and SH4B, suggesting that these subpopulations were predominantly asexual. However, three recombination events were identified in SH1 and SH4B and localized to individuals of opposite mating type, possibly indicating meiotic recombination. In contrast, in the third subpopulation (SH4A), where only one mating type was present, extensive reticulation was evident in network analyses, and multilocus gametic disequilibrium tests were consistent with recombination. Recombination among isolates of the same mating type suggests that a nonmeiotic mechanism of recombination such as the parasexual cycle may be operating in this subpopulation. The level of gene flow detected among subpopulations does not appear to be sufficient to prevent differentiation, and perhaps future speciation, of these A. alternata subpopulations.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, USA.
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18
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Duong TA, de Beer ZW, Wingfield BD, Wingfield MJ. Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum. Fungal Biol 2013; 117:411-21. [PMID: 23809651 DOI: 10.1016/j.funbio.2013.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 11/20/2022]
Abstract
Leptographium procerum and the closely related species Leptographium profanum, are ascomycetes associated with root-infesting beetles on pines and hardwood trees, respectively. Both species occur in North America where they are apparently native. L. procerum has also been found in Europe, China New Zealand, and South Africa where it has most probably been introduced. As is true for many other Leptographium species, sexual states have never been observed in L. procerum or L. profanum. The objectives of this study were to clone and characterize the mating type loci of these fungi, and to develop markers to determine the mating types of individual isolates. To achieve this, a partial sequence of MAT1-2-1 was amplified using degenerate primers targeting the high mobility group (HMG) sequence. A complete MAT1-2 idiomorph of L. profanum was subsequently obtained by screening a genomic library using the HMG sequence as a probe. Long range PCR was used to amplify the complete MAT1-1 idiomorph of L. profanum and both the MAT1-1 and MAT1-2 idiomorphs of L. procerum. Characterization of the MAT idiomorphs suggests that the MAT genes are fully functional and that individuals of both these species are self-sterile in nature with a heterothallic mating system. Mating type markers were developed and tested on a population of L. procerum isolates from the USA, the assumed center of origin for this species. The results suggest that cryptic sexual reproduction is occurring or has recently taken place within this population.
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Affiliation(s)
- Tuan A Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute-FABI, University of Pretoria, Pretoria 0002, South Africa.
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19
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The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet 2012; 8:e1003088. [PMID: 23209441 PMCID: PMC3510045 DOI: 10.1371/journal.pgen.1003088] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/19/2012] [Indexed: 01/07/2023] Open
Abstract
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.
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20
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Woudenberg JHC, De Gruyter J, Crous PW, Zwiers LH. Analysis of the mating-type loci of co-occurring and phylogenetically related species of Ascochyta and Phoma. MOLECULAR PLANT PATHOLOGY 2012; 13:350-62. [PMID: 22014305 PMCID: PMC6638728 DOI: 10.1111/j.1364-3703.2011.00751.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ascochyta and Phoma are fungal genera containing several important plant pathogenic species. These genera are morphologically similar, and recent molecular studies performed to unravel their phylogeny have resulted in the establishment of several new genera within the newly erected Didymellaceae family. An analysis of the structure of fungal mating-type genes can contribute to a better understanding of the taxonomic relationships of these plant pathogens, and may shed some light on their evolution and on differences in sexual strategy and pathogenicity. We analysed the mating-type loci of phylogenetically closely related Ascochyta and Phoma species (Phoma clematidina, Didymella vitalbina, Didymella clematidis, Peyronellaea pinodes and Peyronellaea pinodella) that co-occur on the same hosts, either on Clematis or Pisum. The results confirm that the mating-type genes provide the information to distinguish between the homothallic Pey. pinodes (formerly Ascochyta pinodes) and the heterothallic Pey. pinodella (formerly Phoma pinodella), and indicate the close phylogenetic relationship between these two species that are part of the disease complex responsible for Ascochyta blight on pea. Furthermore, our analysis of the mating-type genes of the fungal species responsible for causing wilt of Clematis sp. revealed that the heterothallic D. vitalbina (Phoma anamorph) is more closely related to the homothallic D. clematidis (Ascochyta anamorph) than to the heterothallic P. clematidina. Finally, our results indicate that homothallism in D. clematidis resulted from a single crossover between MAT1-1 and MAT1-2 sequences of heterothallic ancestors, whereas a single crossover event followed by an inversion of a fused MAT1/2 locus resulted in homothallism in Pey. pinodes.
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Affiliation(s)
- Joyce H C Woudenberg
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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21
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Bolton MD, Secor GA, Rivera V, Weiland JJ, Rudolph K, Birla K, Rengifo J, Campbell LG. Evaluation of the potential for sexual reproduction in field populations of Cercospora beticola from USA. Fungal Biol 2012; 116:511-21. [PMID: 22483049 DOI: 10.1016/j.funbio.2012.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 02/04/2023]
Abstract
Cercospora leaf spot, caused by the hemibiotrophic fungal pathogen Cercospora beticola, is the most economically damaging foliar disease of sugarbeet worldwide. Although most C. beticola populations display characteristics reminiscent of sexual recombination, no teleomorph has been described. To assess whether populations in northern United States have characteristics consistent with sexual reproduction, 1024 isolates collected over a 3-y period were analyzed for frequency and distribution of mating type genes. After clone correction, an approximately equal distribution of mating types was found for each sampling year. Mating type frequency was also assessed in individual lesions. Lesions always consisted of isolates with a single mating type and microsatellite haplotype, but both mating types and up to five microsatellite haplotypes could be found on an individual leaf. The MAT1-1-1 and MAT1-2-1 genes were sequenced from 28 MAT1-1 and 28 MAT1-2 isolates, respectively. Three MAT1-1-1 nucleotide haplotypes were identified that encoded a single amino acid sequence. For MAT1-2-1, five nucleotide haplotypes were identified that encoded four protein variants. MAT1-1-1 and MAT1-2-1 gene expression analyses were conducted on plants inoculated with either or both mating types. MAT1-1-1 expression remained low, but MAT1-2-1 spiked during late stages of colonization. A segment of the MAT1-2-1 coding sequence was also found in MAT1-1 isolates. Taken together, these results suggest that C. beticola has the potential for sexual reproduction.
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Affiliation(s)
- Melvin D Bolton
- United States Department of Agriculture - Agricultural Research Service, Northern Crops Science Laboratory, Fargo, ND 58102-2765, USA.
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Rubini A, Belfiori B, Riccioni C, Tisserant E, Arcioni S, Martin F, Paolocci F. Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum. THE NEW PHYTOLOGIST 2011; 189:710-722. [PMID: 20961294 DOI: 10.1111/j.1469-8137.2010.03492.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
• The genome of Tuber melanosporum has recently been sequenced. Here, we used this information to identify genes involved in the reproductive processes of this edible fungus. The sequenced strain (Mel28) possesses only one of the two master genes required for mating, that is, the gene that codes for the high mobility group (HMG) transcription factor (MAT1-2-1), whereas it lacks the gene that codes for the protein containing the α-box- domain (MAT1-1-1), suggesting that this fungus is heterothallic. • A PCR-based approach was initially employed to screen truffles for the presence of the MAT1-2-1 gene and amplify the conserved regions flanking the mating type (MAT) locus. The MAT1-1-1 gene was finally identified using primers designed from the conserved regions of strains that lack the MAT1-2-1 gene. • Mating type-specific primer pairs were developed to screen asci and gleba from truffles of different origins and to genotype single ascospores within the asci. These analyses provided definitive evidence that T. melanosporum is a heterothallic species with a MAT locus that is organized similarly to those of ancient fungal lineages. • A greater understanding of the reproductive mechanisms that exist in Tuber spp. allows for optimization of truffle plantation management strategies.
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Affiliation(s)
- Andrea Rubini
- National Research Council, Plant Genetics Institute - Perugia Division, Via della Madonna Alta 130, I-06128 Perugia, Italy
| | - Beatrice Belfiori
- National Research Council, Plant Genetics Institute - Perugia Division, Via della Madonna Alta 130, I-06128 Perugia, Italy
| | - Claudia Riccioni
- National Research Council, Plant Genetics Institute - Perugia Division, Via della Madonna Alta 130, I-06128 Perugia, Italy
| | - Emilie Tisserant
- UMR 1136, Interactions Arbres/Microorganismes, INRA-Nancy, F-54280 Champenoux, France
| | - Sergio Arcioni
- National Research Council, Plant Genetics Institute - Perugia Division, Via della Madonna Alta 130, I-06128 Perugia, Italy
| | - Francis Martin
- UMR 1136, Interactions Arbres/Microorganismes, INRA-Nancy, F-54280 Champenoux, France
| | - Francesco Paolocci
- National Research Council, Plant Genetics Institute - Perugia Division, Via della Madonna Alta 130, I-06128 Perugia, Italy
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Stergiopoulos I, van den Burg HA, Ökmen B, Beenen HG, van Liere S, Kema GHJ, de Wit PJGM. Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots. Proc Natl Acad Sci U S A 2010; 107:7610-5. [PMID: 20368413 PMCID: PMC2867746 DOI: 10.1073/pnas.1002910107] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most fungal effectors characterized so far are species-specific and facilitate virulence on a particular host plant. During infection of its host tomato, Cladosporium fulvum secretes effectors that function as virulence factors in the absence of cognate Cf resistance proteins and induce effector-triggered immunity in their presence. Here we show that homologs of the C. fulvum Avr4 and Ecp2 effectors are present in other pathogenic fungi of the Dothideomycete class, including Mycosphaerella fijiensis, the causal agent of black Sigatoka disease of banana. We demonstrate that the Avr4 homolog of M. fijiensis is a functional ortholog of C. fulvum Avr4 that protects fungal cell walls against hydrolysis by plant chitinases through binding to chitin and, despite the low overall sequence homology, triggers a Cf-4-mediated hypersensitive response (HR) in tomato. Furthermore, three homologs of C. fulvum Ecp2 are found in M. fijiensis, one of which induces different levels of necrosis or HR in tomato lines that lack or contain a putative cognate Cf-Ecp2 protein, respectively. In contrast to Avr4, which acts as a defensive virulence factor, M. fijiensis Ecp2 likely promotes virulence by interacting with a putative host target causing host cell necrosis, whereas Cf-Ecp2 could possibly guard the virulence target of Ecp2 and trigger a Cf-Ecp2-mediated HR. Overall our data suggest that Avr4 and Ecp2 represent core effectors that are collectively recognized by single cognate Cf-proteins. Transfer of these Cf genes to plant species that are attacked by fungi containing these cognate core effectors provides unique ways for breeding disease-resistant crops.
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Affiliation(s)
- Ioannis Stergiopoulos
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
| | - Harrold A. van den Burg
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB, Wageningen, The Netherlands; and
| | - Bilal Ökmen
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
| | - Henriek G. Beenen
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
| | - Sabine van Liere
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
| | - Gert H. J. Kema
- Plant Research International BV, 6700 AA, Wageningen, The Netherlands
| | - Pierre J. G. M. de Wit
- Laboratory of Phytopathology, Wageningen University and Research Centre, 6708 PB, Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB, Wageningen, The Netherlands; and
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Arzanlou M, Crous PW, Zwiers LH. Evolutionary dynamics of mating-type loci of Mycosphaerella spp. occurring on banana. EUKARYOTIC CELL 2010; 9:164-72. [PMID: 19915079 PMCID: PMC2805284 DOI: 10.1128/ec.00194-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 11/02/2009] [Indexed: 11/20/2022]
Abstract
The devastating Sigatoka disease complex of banana is primarily caused by three closely related heterothallic fungi belonging to the genus Mycosphaerella: M. fijiensis, M. musicola, and M. eumusae. Previous phylogenetic work showing common ancestry led us to analyze the mating-type loci of these Mycosphaerella species occurring on banana. We reasoned that this might provide better insight into the evolutionary history of these species. PCR and chromosome-walking approaches were used to clone the mating-type loci of M. musicola and M. eumusae. Sequences were compared to the published mating-type loci of M. fijiensis and other Mycosphaerella spp., and a novel organization of the MAT loci was found. The mating-type loci of the examined Mycosphaerella species are expanded, containing two additional Mycosphaerella-specific genes in a unique genomic organization. The proteins encoded by these novel genes show a higher interspecies than intraspecies homology. Moreover, M. fijiensis, M. musicola, and M. eumusae contain two additional mating-type-like loci, containing parts of both MAT1-1-1 and MAT1-2-1. The data indicate that M. fijiensis, M. musicola, and M. eumusae share an ancestor in which a fusion event occurred between MAT1-1-1 and MAT1-2-1 sequences and in which additional genes became incorporated into the idiomorph. The new genes incorporated have since then evolved independently in the MAT1-1 and MAT1-2 loci. Thus, these data are an example of the evolutionary dynamics of fungal MAT loci in general and show the great flexibility of the MAT loci of Mycosphaerella species in particular.
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Affiliation(s)
- Mahdi Arzanlou
- Evolutionary Phytopathology, CBS-KNAW Fungal Biodiversity Center, Utrecht 3508 AD, The Netherlands, Wageningen University and Research Center (WUR), Laboratory of Phytopathology, Wageningen 6708 PB, The Netherlands, Plant Protection Department, Agriculture Faculty, University of Tabriz, Tabriz, P.O. Box 5166614766, Iran
| | - Pedro W. Crous
- Evolutionary Phytopathology, CBS-KNAW Fungal Biodiversity Center, Utrecht 3508 AD, The Netherlands, Wageningen University and Research Center (WUR), Laboratory of Phytopathology, Wageningen 6708 PB, The Netherlands, Plant Protection Department, Agriculture Faculty, University of Tabriz, Tabriz, P.O. Box 5166614766, Iran
| | - Lute-Harm Zwiers
- Evolutionary Phytopathology, CBS-KNAW Fungal Biodiversity Center, Utrecht 3508 AD, The Netherlands, Wageningen University and Research Center (WUR), Laboratory of Phytopathology, Wageningen 6708 PB, The Netherlands, Plant Protection Department, Agriculture Faculty, University of Tabriz, Tabriz, P.O. Box 5166614766, Iran
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25
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Torres I, García AM, Hernández O, González A, McEwen JG, Restrepo A, Arango M. Presence and expression of the mating type locus in Paracoccidioides brasiliensis isolates. Fungal Genet Biol 2009; 47:373-80. [PMID: 19932183 DOI: 10.1016/j.fgb.2009.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 11/12/2009] [Accepted: 11/13/2009] [Indexed: 10/20/2022]
Abstract
Paracoccidioides brasiliensis has been classified in the phylum Ascomycota, order Onygenales, family Ajellomycetaceae, even in the absence of a known sexual cycle or mating system. The objective of this work was to determine the presence of the mating type locus in 71 P. brasiliensis isolates from various sources. A PCR assay using specific primers for the MAT 1 gene was developed and applied for the detection of such genes. Two heterothallic groups (MAT1-1 or MAT1-2) were recognized and, in some isolates, gene expression was confirmed indicating the existence of a basal gene expression. The distribution of two mating type loci in the studied population suggested that sexual reproduction might occur in P. brasiliensis. This finding points towards the possibility of applying a more precise definition of the concept of biological species to P. brasiliensis. Further studies should be conducted to confirm the sexual capacity of this fungus and its implications among phylogenetic species and geographical distribution.
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Affiliation(s)
- I Torres
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia
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26
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Wulff BBH, Chakrabarti A, Jones DA. Recognitional specificity and evolution in the tomato-Cladosporium fulvum pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1191-202. [PMID: 19737093 DOI: 10.1094/mpmi-22-10-1191] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The interactions between plants and many biotrophic or hemibiotrophic pathogens are controlled by receptor proteins in the host and effector proteins delivered by the pathogen. Pathogen effectors facilitate pathogen growth through the suppression of host defenses and the manipulation of host metabolism, but recognition of a pathogen-effector protein by a host receptor enables the host to activate a suite of defense mechanisms that limit pathogen growth. In the tomato (Lycopersicon esculentum syn. Solanum lycopersicum)-Cladosporium fulvum (leaf mold fungus syn. Passalora fulva) pathosystem, the host receptors are plasma membrane-anchored, leucine-rich repeat, receptor-like proteins encoded by an array of Cf genes conferring resistance to C. fulvum. The pathogen effectors are mostly small, secreted, cysteine-rich, but otherwise largely dissimilar, extracellular proteins encoded by an array of avirulence (Avr) genes, so called because of their ability to trigger resistance and limit pathogen growth when the corresponding Cf gene is present in tomato. A number of Cf and Avr genes have been isolated, and details of the complex molecular interplay between tomato Cf proteins and C. fulvum effector proteins are beginning to emerge. Each effector appears to have a different role; probably most bind or modify different host proteins, but at least one has a passive role masking the pathogen. It is, therefore, not surprising that each effector is probably detected in a distinct and specific manner, some by direct binding, others as complexes with host proteins, and others via their modification of host proteins. The two papers accompanying this review contribute further to our understanding of the molecular specificity underlying effector perception by Cf proteins. This review, therefore, focuses on our current understanding of recognitional specificity in the tomato-C. fulvum pathosystem and highlights some of the critical questions that remain to be addressed. It also addresses the evolutionary causes and consequences of this specificity.
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Affiliation(s)
- B B H Wulff
- Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), 12 rue du Général Zimmer, 67084 Strasbourg, France.
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27
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28
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Bolton MD, van Esse HP, Vossen JH, de Jonge R, Stergiopoulos I, Stulemeijer IJE, van den Berg GCM, Borrás-Hidalgo O, Dekker HL, de Koster CG, de Wit PJGM, Joosten MHAJ, Thomma BPHJ. The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species. Mol Microbiol 2008; 69:119-36. [PMID: 18452583 DOI: 10.1111/j.1365-2958.2008.06270.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During tomato leaf colonization, the biotrophic fungus Cladosporium fulvum secretes several effector proteins into the apoplast. Eight effectors have previously been characterized and show no significant homology to each other or to other fungal genes. To discover novel C. fulvum effectors that might play a role in virulence, we utilized two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) to visualize proteins secreted during C. fulvum-tomato interactions. Three novel C. fulvum proteins were identified: CfPhiA, Ecp6 and Ecp7. CfPhiA shows homology to proteins found on fungal sporogenous cells called phialides. Ecp6 contains lysin motifs (LysM domains) that are recognized as carbohydrate-binding modules. Ecp7 encodes a small, cysteine-rich protein with no homology to known proteins. Heterologous expression of Ecp6 significantly increased the virulence of the vascular pathogen Fusarium oxysporum on tomato. Furthermore, by RNA interference (RNAi)-mediated gene silencing we demonstrate that Ecp6 is instrumental for C. fulvum virulence on tomato. Hardly any allelic variation was observed in the Ecp6 coding region of a worldwide collection of C. fulvum strains. Although none of the C. fulvum effectors identified so far have obvious orthologues in other organisms, conserved Ecp6 orthologues were identified in various fungal species. Homology-based modelling suggests that the LysM domains of C. fulvum Ecp6 may be involved in chitin binding.
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Affiliation(s)
- Melvin D Bolton
- Laboratory of Phytopathology, Wageningen University, Binnenhaven 5, Wageningen, The Netherlands
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Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum. Curr Genet 2008; 53:287-97. [PMID: 18347798 DOI: 10.1007/s00294-008-0185-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/25/2008] [Accepted: 03/02/2008] [Indexed: 01/28/2023]
Abstract
Repeat induced point mutation (RIP) is a gene silencing mechanism present in fungal genomes. During RIP, duplicated sequences are efficiently and irreversibly mutated by transitions from C:G to T:A. For the first time, we have identified traces of RIP in transposable elements of Aspergillus niger and Penicillium chrysogenum, two biotechnologically relevant fungi. We found that RIP in P. chrysogenum has affected a large set of sequences, which also contain other mutations. On the other hand, RIP in A. niger is limited to only few sequences, but literally all mutations are RIP-like. Surprisingly, RIP occurred only in transposon sequences that have disrupted open reading frames in A. niger, a phenomenon not yet reported for other fungi. In both fungal species, we identified two sequences with strong sequence similarity to Neurospora crassa RID. RID is a putative DNA methyltransferase and the only known enzyme involved in the RIP process. Our findings suggest that both A. niger and P. chrysogenum either had a sexual past or have a sexual potential. These findings have important implications for future strain development of these fungi.
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30
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van der Does HC, Rep M. Virulence genes and the evolution of host specificity in plant-pathogenic fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1175-82. [PMID: 17918619 DOI: 10.1094/mpmi-20-10-1175] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.
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Affiliation(s)
- H Charlotte van der Does
- Swammerdam Institute for Life Sciences, University of Amsterdam, P.O. Box 94062, 1090 GB Amsterdam, The Netherlands
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31
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Stergiopoulos I, De Kock MJD, Lindhout P, De Wit PJGM. Allelic variation in the effector genes of the tomato pathogen Cladosporium fulvum reveals different modes of adaptive evolution. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1271-83. [PMID: 17918629 DOI: 10.1094/mpmi-20-10-1271] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The allelic variation in four avirulence (Avr) and four extracellular protein (Ecp)-encoding genes of the tomato pathogen Cladosporium fulvum was analyzed for a worldwide collection of strains. The majority of polymorphisms observed in the Avr genes are deletions, point mutations, or insertions of transposon-like elements that are associated with transitions from avirulence to virulence, indicating adaptive evolution of the Avr genes to the cognate C. fulvum resistance genes that are deployed in commercial tomato lines. Large differences in types of polymorphisms between the Avr genes were observed, especially between Avr2 (indels) and Avr4 (amino-acid substitutions), indicating that selection pressure favors different types of adaptation. In contrast, only a limited number of polymorphisms were observed in the Ecp genes, which mostly involved synonymous modifications. A haplotype network based on the polymorphisms observed in the effector genes revealed a complex pattern of evolution marked by reticulations that suggests the occurrence of genetic recombination in this presumed asexual fungus. This, as well as the identification of strains with identical polymorphisms in Avr and Ecp genes but with opposite mating-type genes, suggests that development of complex races can be the combined result of positive selection and genetic recombination.
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Affiliation(s)
- Ioannis Stergiopoulos
- Laboratory of Phytopathology, Wageningen University & Research Centre, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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