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Hafeez AN, Arora S, Ghosh S, Gilbert D, Bowden RL, Wulff BBH. Creation and judicious application of a wheat resistance gene atlas. MOLECULAR PLANT 2021; 14:1053-1070. [PMID: 33991673 DOI: 10.1016/j.molp.2021.05.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 05/18/2023]
Abstract
Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.
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Affiliation(s)
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - David Gilbert
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert L Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14. G3-GENES GENOMES GENETICS 2020; 10:2131-2140. [PMID: 32345704 PMCID: PMC7341154 DOI: 10.1534/g3.120.401265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.
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Monnier N, Cordier M, Dahi A, Santoni V, Guénin S, Clément C, Sarazin C, Penaud A, Dorey S, Cordelier S, Rippa S. Semipurified Rhamnolipid Mixes Protect Brassica napus Against Leptosphaeria maculans Early Infections. PHYTOPATHOLOGY 2020; 110:834-842. [PMID: 31880985 DOI: 10.1094/phyto-07-19-0275-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The rapeseed crop (Brassica napus) has to cope with fungal diseases that significantly impacts yields. In particular, the fungal pathogen Leptosphaeria maculans, the causal agent of blackleg disease (also named Phoma stem canker), is a worldwide issue to this crop. Considering environmental concerns, it is essential to propose alternative natural compounds for rapeseed crop protection to reduce chemical fungicide use. Here we report data showing the efficacy of semipurified rhamnolipid (RL) mixes from bacterial origin to protect rapeseed against L. maculans at early stages of infection in controlled conditions. In addition, we show that RL solutions have excellent adhesion properties when sprayed onto rapeseed leaves, without adding any adjuvant. We demonstrate that RL mixes display direct antimycelial properties against the pathogen and stimulate plant defense responses in rapeseed. Our results validate, a preventive action of low RL concentrations to protect rapeseed against L. maculans and a curative effect in specific conditions when applied after the inoculation of the pathogen spores. Semipurified RL mixes therefore appear to be real cost-effective compounds that could be used in fields as biocontrol products to fight L. maculans early infections of rapeseed.
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Affiliation(s)
- Noadya Monnier
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Sorbonne Universités, Université de Technologie de Compiègne, SFR Condorcet FR CNRS 3417, Compiègne, France
| | - Marion Cordier
- Unité Résistance Induite et Bioprotection des Plantes, EA 4707, Université de Reims Champagne Ardenne, SFR Condorcet FR CNRS 3417, Reims, France
| | - Abdellatif Dahi
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Sorbonne Universités, Université de Technologie de Compiègne, SFR Condorcet FR CNRS 3417, Compiègne, France
| | - Valérie Santoni
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Sorbonne Universités, Université de Technologie de Compiègne, SFR Condorcet FR CNRS 3417, Compiègne, France
| | - Stéphanie Guénin
- Centre de Ressources Régional en Biologie Moléculaire, Université de Picardie Jules Verne, SFR Condorcet FR CNRS 3417, Amiens, France
| | - Christophe Clément
- Unité Résistance Induite et Bioprotection des Plantes, EA 4707, Université de Reims Champagne Ardenne, SFR Condorcet FR CNRS 3417, Reims, France
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Université de Picardie Jules Verne, SFR Condorcet FR CNRS 3417, Amiens, France
| | - Annette Penaud
- Terres Inovia, Département de Génétique et Protection des Cultures-Phytopathologie, Thivernal-Grignon, France
| | - Stephan Dorey
- Unité Résistance Induite et Bioprotection des Plantes, EA 4707, Université de Reims Champagne Ardenne, SFR Condorcet FR CNRS 3417, Reims, France
| | - Sylvain Cordelier
- Unité Résistance Induite et Bioprotection des Plantes, EA 4707, Université de Reims Champagne Ardenne, SFR Condorcet FR CNRS 3417, Reims, France
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Sorbonne Universités, Université de Technologie de Compiègne, SFR Condorcet FR CNRS 3417, Compiègne, France
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Moolhuijzen PM, See PT, Oliver RP, Moffat CS. Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PLoS One 2018; 13:e0206586. [PMID: 30379913 PMCID: PMC6209302 DOI: 10.1371/journal.pone.0206586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
The ToxA effector is a major virulence gene of Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot disease of wheat. ToxA and co-located genes are believed to be the result of a recent horizontally transferred highly conserved 14kb region a major pathogenic event for Ptr. Since this event, monitoring isolates for pathogenic changes has become important to help understand the underlying mechanisms in play. Here we examined ToxA in 100 Ptr isolates from Australia, Europe, North and South America and the Middle East, and uncovered in isolates from Denmark, Germany and New Zealand a new variation, a novel 166 bp insertion element (PtrHp1) which can form a perfectly matched 59 bp inverted repeat hairpin structure located downstream of the ToxA coding sequence in the 3’ UTR exon. A wider examination revealed PtrHp1 elements to be distributed throughout the genome. Analysis of genomes from Australia and North America had 50–112 perfect copies that often overlap other genes. The hairpin element appears to be unique to Ptr and the lack of ancient origins in other species suggests that PtrHp1 emerged after Ptr speciation. Furthermore, the ToxA UTR insertion site is identical for different isolates, which suggests a single insertion event occurred after the ToxA horizontal transfer. In vitro and in planta-detached leaf assays found that the PtrHp1 element insertion had no effect on ToxA expression. However, variation in the expression of ToxA was detected between the Ptr isolates from different demographic locations, which appears to be unrelated to the presence of the element. We envision that this discovery may contribute towards future understanding of the possible role of hairpin elements in Ptr.
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Affiliation(s)
- Paula M Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Richard P Oliver
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
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Syme RA, Tan KC, Rybak K, Friesen TL, McDonald BA, Oliver RP, Hane JK. Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution. Genome Biol Evol 2018; 10:2443-2457. [PMID: 30184068 PMCID: PMC6152946 DOI: 10.1093/gbe/evy192] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 01/01/2023] Open
Abstract
We report a fungal pan-genome study involving Parastagonospora spp., including 21 isolates of the wheat (Triticum aestivum) pathogen Parastagonospora nodorum, 10 of the grass-infecting Parastagonospora avenae, and 2 of a closely related undefined sister species. We observed substantial variation in the distribution of polymorphisms across the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and losses. We also discovered chromosome-scale inter and intraspecific presence/absence variation of some sequences, suggesting the occurrence of one or more accessory chromosomes or regions that may play a role in host-pathogen interactions. The presence of known pathogenicity effector loci SnToxA, SnTox1, and SnTox3 varied substantially among isolates. Three P. nodorum isolates lacked functional versions for all three loci, whereas three P. avenae isolates carried one or both of the SnTox1 and SnTox3 genes, indicating previously unrecognized potential for discovering additional effectors in the P. nodorum-wheat pathosystem. We utilized the pan-genomic comparative analysis to improve the prediction of pathogenicity effector candidates, recovering the three confirmed effectors among our top-ranked candidates. We propose applying this pan-genomic approach to identify the effector repertoire involved in other host-microbe interactions involving necrotrophic pathogens in the Pezizomycotina.
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Affiliation(s)
- Robert A Syme
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kasia Rybak
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Timothy L Friesen
- Cereal Crops Research Unit, USDA-ARS Red River Valley Agricultural Research Center, Fargo, North Dakota
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Richard P Oliver
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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7
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Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan KC, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:779-788. [PMID: 29664319 DOI: 10.1094/mpmi-06-17-0135-fi] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.
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Affiliation(s)
- Stefania Bertazzoni
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Angela H Williams
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Darcy A Jones
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Robert A Syme
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Kar-Chun Tan
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - James K Hane
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
- 2 Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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Li WC, Chen CL, Wang TF. Repeat-induced point (RIP) mutation in the industrial workhorse fungus Trichoderma reesei. Appl Microbiol Biotechnol 2018; 102:1567-1574. [DOI: 10.1007/s00253-017-8731-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/01/2023]
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Zeng F, Lian X, Zhang G, Yu X, Bradley CA, Ming R. A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts. GENOMICS DATA 2017; 13:54-63. [PMID: 28736701 PMCID: PMC5508496 DOI: 10.1016/j.gdata.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/17/2017] [Accepted: 07/07/2017] [Indexed: 11/08/2022]
Abstract
Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively). Synteny or collinearity was limited between genomes of major Mycosphaerella pathogens. Comparative analysis with these related pathogen genomes indicated distinct genome-wide repeat organization features. It suggests repetitive elements might be responsible for considerable evolutionary genomic changes. These results reveal the background of genomic differences and similarities between Dothideomycete species. Wide diversity as well as conservation on genome features forms the potential genomic basis of the pathogen specialization, such as pathogenicity to woody vs. herbaceous hosts. Through comparative genome analysis among five Dothideomycete species, our results have shed light on the genome features of these related fungi species. It provides insight for understanding the genomic basis of fungal pathogenicity and disease resistance in the crop hosts.
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Affiliation(s)
- Fanchang Zeng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China.,Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Xin Lian
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Guirong Zhang
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
| | - Xiaoman Yu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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Deng CH, Plummer KM, Jones DAB, Mesarich CH, Shiller J, Taranto AP, Robinson AJ, Kastner P, Hall NE, Templeton MD, Bowen JK. Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics 2017; 18:339. [PMID: 28464870 PMCID: PMC5412055 DOI: 10.1186/s12864-017-3699-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. RESULTS Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. CONCLUSIONS Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Affiliation(s)
- Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Kim M. Plummer
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT Australia
| | - Darcy A. B. Jones
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: The Centre for Crop and Disease Management, Curtin University, Bentley, Australia
| | - Carl H. Mesarich
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Present Address: Institute of Agriculture & Environment, Massey University, Palmerston North, New Zealand
| | - Jason Shiller
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: INRA-Angers, Beaucouzé, Cedex, France
| | - Adam P. Taranto
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew J. Robinson
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Patrick Kastner
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
| | - Nathan E. Hall
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K. Bowen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
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11
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Testa AC, Oliver RP, Hane JK. OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes. Genome Biol Evol 2016; 8:2044-64. [PMID: 27289099 PMCID: PMC4943192 DOI: 10.1093/gbe/evw121] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/03/2022] Open
Abstract
We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as "OcculterCut" (https://sourceforge.net/projects/occultercut, last accessed April 30, 2016), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighboring repeat-rich regions. Over time RIP perpetuates "two speeds" of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions.
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Affiliation(s)
- Alison C Testa
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - Richard P Oliver
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - James K Hane
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia Curtin Institute for Computation, Curtin University, Perth, Australia
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Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SAG, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics 2016; 17:191. [PMID: 26945779 PMCID: PMC4779268 DOI: 10.1186/s12864-016-2486-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. RESULTS Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. CONCLUSIONS We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.
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Affiliation(s)
- Angela H Williams
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Louise F Thatcher
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - James K Hane
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
- Department of Environment and Agriculture, Curtin Institute for Computation, and CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Perth, WA, 6102, Australia.
| | - Jana Sperschneider
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Brendan N Kidd
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Jonathan P Anderson
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Gagan Garg
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Judith Lichtenzveig
- Department of Environment and Agriculture, Pulse Pathology and Genetics, Centre for Crop and Disease Management and Curtin Institute for Computation, Curtin University, Perth, WA, 6102, Australia.
| | - H Corby Kistler
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA.
| | | | - Sarah Young
- The Broad Institute, Cambridge, MA, 02141, USA.
| | - Sally-Anne G Buck
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Lars G Kamphuis
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Rachit Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Rajeev K Varshney
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Karam B Singh
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
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Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, Ortega-Abboud E, Lebrun MH, Henrissat B, Gendrault A, Rodolphe F, Tharreau D, Fournier E. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol 2015; 7:2896-912. [PMID: 26454013 PMCID: PMC4684704 DOI: 10.1093/gbe/evv187] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
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Affiliation(s)
- Hélène Chiapello
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Ludovic Mallet
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Cyprien Guérin
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Gabriela Aguileta
- CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain
| | - Joëlle Amselem
- INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Thomas Kroj
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Enrique Ortega-Abboud
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Marc-Henri Lebrun
- INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annie Gendrault
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - François Rodolphe
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Didier Tharreau
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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Shoji JY, Charlton ND, Yi M, Young CA, Craven KD. Vegetative hyphal fusion and subsequent nuclear behavior in Epichloë grass endophytes. PLoS One 2015; 10:e0121875. [PMID: 25837972 PMCID: PMC4383479 DOI: 10.1371/journal.pone.0121875] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/18/2015] [Indexed: 01/18/2023] Open
Abstract
Epichloë species (including the former genus Neotyphodium) are fungal symbionts of many agronomically important forage grasses, and provide their grass hosts with protection from a wide range of biotic and abiotic stresses. Epichloë species include many interspecific hybrids with allodiploid-like genomes, which may provide the potential for combined traits or recombination to generate new traits. Though circumstantial evidence suggests that such interspecific hybrids might have arisen from nuclear fusion events following vegetative hyphal fusion between different Epichloë strains, this hypothesis has not been addressed empirically. Here, we investigated vegetative hyphal fusion and subsequent nuclear behavior in Epichloë species. A majority of Epichloë strains, especially those having a sexual stage, underwent self vegetative hyphal fusion. Vegetative fusion also occurred between two hyphae from different Epichloë strains. Though Epichloë spp. are uninucleate fungi, hyphal fusion resulted in two nuclei stably sharing the same cytoplasm, which might ultimately lead to nuclear fusion. In addition, protoplast fusion experiments gave rise to uninucleate putative hybrids, which apparently had two markers, one from each parent within the same nucleus. These results are consistent with the notion that interspecific hybrids arise from vegetative hyphal fusion. However, we also discuss additional factors, such as post-hybridization selection, that may be important to explain the recognized prevalence of hybrids in Epichloë species.
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Affiliation(s)
- Jun-ya Shoji
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Nikki D. Charlton
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Mihwa Yi
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Carolyn A. Young
- The Samuel Roberts Noble Foundation, Forage Improvement Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
| | - Kelly D. Craven
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, United States of America
- * E-mail:
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:40-50. [PMID: 27839074 DOI: 10.1094/mpmi-10-13-0313-ta.testissue] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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16
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Hane JK, Williams AH, Taranto AP, Solomon PS, Oliver RP. Repeat-Induced Point Mutation: A Fungal-Specific, Endogenous Mutagenesis Process. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10503-1_4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:17-27. [PMID: 27839075 DOI: 10.1094/mpmi-10-13-0313-cr.testissue] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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18
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Golicz AA, Martinez PA, Zander M, Patel DA, Van De Wouw AP, Visendi P, Fitzgerald TL, Edwards D, Batley J. Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct Integr Genomics 2014; 15:189-96. [PMID: 25421464 DOI: 10.1007/s10142-014-0412-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/29/2014] [Accepted: 11/04/2014] [Indexed: 12/31/2022]
Abstract
Recent comparisons of the increasing number of genome sequences have revealed that variation in gene content is considerably more prevalent than previously thought. This variation is likely to have a pronounced effect on phenotypic diversity and represents a crucial target for the assessment of genomic diversity. Leptosphaeria maculans, a causative agent of phoma stem canker, is the most devastating fungal pathogen of Brassica napus (oilseed rape/canola). A number of L. maculans genes are known to be present in some isolates but lost in the others. We analyse gene content variation within three L. maculans isolates using a hybrid mapping and genome assembly approach and identify genes which are present in one of the isolates but missing in the others. In total, 57 genes are shown to be missing in at least one isolate. The genes encode proteins involved in a range of processes including oxidative processes, DNA maintenance, cell signalling and sexual reproduction. The results demonstrate the effectiveness of the method and provide new insight into genomic diversity in L. maculans.
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Affiliation(s)
- Agnieszka A Golicz
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
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20
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Vleeshouwers VGAA, Oliver RP. Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:196-206. [PMID: 24405032 DOI: 10.1094/mpmi-10-13-0313-ia] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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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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22
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Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 2014; 23:753-73. [DOI: 10.1111/mec.12631] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Pierre Gladieux
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Hélène Badouin
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Antoine Branca
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Gabriela Aguileta
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
| | - Damien M. Vienne
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
- Laboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558 Villeurbanne 69622 France
| | - Ricardo C. Rodríguez de la Vega
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Sara Branco
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
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van der Burgt A, Severing E, Collemare J, de Wit PJGM. Automated alignment-based curation of gene models in filamentous fungi. BMC Bioinformatics 2014; 15:19. [PMID: 24433567 PMCID: PMC3898260 DOI: 10.1186/1471-2105-15-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 01/11/2014] [Indexed: 11/16/2022] Open
Abstract
Background Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The wealth of available fungal genomes has not yet been exploited by an automated method that applies quality control of gene models in order to obtain more accurate genome annotations. Results We provide a novel method named alignment-based fungal gene prediction (ABFGP) that is particularly suitable for plastic genomes like those of fungi. It can assess gene models on a gene-by-gene basis making use of informant gene loci. Its performance was benchmarked on 6,965 gene models confirmed by full-length unigenes from ten different fungi. 79.4% of all gene models were correctly predicted by ABFGP. It improves the output of ab initio gene prediction software due to a higher sensitivity and precision for all gene model components. Applicability of the method was shown by revisiting the annotations of six different fungi, using gene loci from up to 29 fungal genomes as informants. Between 7,231 and 8,337 genes were assessed by ABFGP and for each genome between 1,724 and 3,505 gene model revisions were proposed. The reliability of the proposed gene models is assessed by an a posteriori introspection procedure of each intron and exon in the multiple gene model alignment. The total number and type of proposed gene model revisions in the six fungal genomes is correlated to the quality of the genome assembly, and to sequencing strategies used in the sequencing centre, highlighting different types of errors in different annotation pipelines. The ABFGP method is particularly successful in discovering sequence errors and/or disruptive mutations causing truncated and erroneous gene models. Conclusions The ABFGP method is an accurate and fully automated quality control method for fungal gene catalogues that can be easily implemented into existing annotation pipelines. With the exponential release of new genomes, the ABFGP method will help decreasing the number of gene models that require additional manual curation.
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Affiliation(s)
| | | | | | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University & Research Centre, P,O, Box 16, 6700 AA Wageningen, The Netherlands.
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Abstract
Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.
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Affiliation(s)
- Darren Soanes
- Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom;
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Sánchez-Vallet A, Saleem-Batcha R, Kombrink A, Hansen G, Valkenburg DJ, Thomma BPHJ, Mesters JR. Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. eLife 2013; 2:e00790. [PMID: 23840930 PMCID: PMC3700227 DOI: 10.7554/elife.00790] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 05/30/2013] [Indexed: 12/28/2022] Open
Abstract
While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear. Structural analysis of the LysM effector Ecp6 of the fungal tomato pathogen Cladosporium fulvum reveals a novel mechanism for chitin binding, mediated by intrachain LysM dimerization, leading to a chitin-binding groove that is deeply buried in the effector protein. This composite binding site involves two of the three LysMs of Ecp6 and mediates chitin binding with ultra-high (pM) affinity. Intriguingly, the remaining singular LysM domain of Ecp6 binds chitin with low micromolar affinity but can nevertheless still perturb chitin-triggered immunity. Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex. DOI:http://dx.doi.org/10.7554/eLife.00790.001.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Centro de Biotecnología y Genómica de Plantas , Universidad Politécnica de Madrid , Madrid , Spain ; Laboratory of Phytopathology , Wageningen University , Wageningen , Netherlands
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Sánchez-Vallet A, Saleem-Batcha R, Kombrink A, Hansen G, Valkenburg DJ, Thomma BPHJ, Mesters JR. Fungal effector Ecp6 outcompetes host immune receptor for chitin binding through intrachain LysM dimerization. eLife 2013; 2:e00790. [PMID: 23840930 DOI: 10.7554/elife.00790.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 05/30/2013] [Indexed: 05/23/2023] Open
Abstract
While host immune receptors detect pathogen-associated molecular patterns to activate immunity, pathogens attempt to deregulate host immunity through secreted effectors. Fungi employ LysM effectors to prevent recognition of cell wall-derived chitin by host immune receptors, although the mechanism to compete for chitin binding remained unclear. Structural analysis of the LysM effector Ecp6 of the fungal tomato pathogen Cladosporium fulvum reveals a novel mechanism for chitin binding, mediated by intrachain LysM dimerization, leading to a chitin-binding groove that is deeply buried in the effector protein. This composite binding site involves two of the three LysMs of Ecp6 and mediates chitin binding with ultra-high (pM) affinity. Intriguingly, the remaining singular LysM domain of Ecp6 binds chitin with low micromolar affinity but can nevertheless still perturb chitin-triggered immunity. Conceivably, the perturbation by this LysM domain is not established through chitin sequestration but possibly through interference with the host immune receptor complex. DOI:http://dx.doi.org/10.7554/eLife.00790.001.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Centro de Biotecnología y Genómica de Plantas , Universidad Politécnica de Madrid , Madrid , Spain ; Laboratory of Phytopathology , Wageningen University , Wageningen , Netherlands
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Rouxel T, Balesdent MH. From model to crop plant-pathogen interactions: cloning of the first resistance gene to Leptosphaeria maculans in Brassica napus. THE NEW PHYTOLOGIST 2013; 197:356-358. [PMID: 23253328 DOI: 10.1111/nph.12099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Thierry Rouxel
- INRA-Bioger, Av. Lucien Brétignières, 78850, Thiverval-Grignon, France
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