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Balotf S, Wilson R, Wilson C. Transcriptomics is essential but not sufficient to unravel complex plant-pathogen interactions. PLANT CELL REPORTS 2024; 43:175. [PMID: 38884679 DOI: 10.1007/s00299-024-03248-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024]
Abstract
KEY MESSAGE A group of genes that were upregulated in a resistant cultivar while downregulated in a susceptible cultivar in a transcriptomics analysis of potato challenged by Spongospora subterranea infection, did not show the same expression pattern at the protein level.
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Affiliation(s)
- Sadegh Balotf
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia.
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia.
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, Australia
| | - Calum Wilson
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
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Ianiri G, Barone G, Palmieri D, Quiquero M, Gaeta I, De Curtis F, Castoria R. Transcriptomic investigation of the interaction between a biocontrol yeast, Papiliotrema terrestris strain PT22AV, and the postharvest fungal pathogen Penicillium expansum on apple. Commun Biol 2024; 7:359. [PMID: 38519651 PMCID: PMC10960036 DOI: 10.1038/s42003-024-06031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) Papiliotrema terrestris, the pathogen Penicillium expansum, and the host Malus domestica. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissue, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to P. expansum analysis, 1017 DEGs are upregulated when grown in apple tissue, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host M. domestica finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with P. expansum. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.
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Affiliation(s)
- Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy.
| | - Giuseppe Barone
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Davide Palmieri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Michela Quiquero
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Ilenia Gaeta
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Filippo De Curtis
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy
| | - Raffaello Castoria
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100, Campobasso, Italy.
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Borhan MH, Van de Wouw AP, Larkan NJ. Molecular Interactions Between Leptosphaeria maculans and Brassica Species. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:237-257. [PMID: 35576591 DOI: 10.1146/annurev-phyto-021621-120602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Canola is an important oilseed crop, providing food, feed, and fuel around the world. However, blackleg disease, caused by the ascomycete Leptosphaeria maculans, causes significant yield losses annually. With the recent advances in genomic technologies, the understanding of the Brassica napus-L. maculans interaction has rapidly increased, with numerous Avr and R genes cloned, setting this system up as a model organism for studying plant-pathogen associations. Although the B. napus-L. maculans interaction follows Flor's gene-for-gene hypothesis for qualitative resistance, it also puts some unique spins on the interaction. This review discusses the current status of the host-pathogen interaction and highlights some of the future gaps that need addressing moving forward.
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Affiliation(s)
- M Hossein Borhan
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada;
| | | | - Nicholas J Larkan
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada;
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Urquhart AS, Elliott CE, Zeng W, Idnurm A. Constitutive expression of transcription factor SirZ blocks pathogenicity in Leptosphaeria maculans independently of sirodesmin production. PLoS One 2021; 16:e0252333. [PMID: 34111151 PMCID: PMC8191991 DOI: 10.1371/journal.pone.0252333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/14/2021] [Indexed: 11/28/2022] Open
Abstract
Sirodesmin, the major secondary metabolite produced by the plant pathogenic fungus Leptosphaeria maculans in vitro, has been linked to disease on Brassica species since the 1970s, and yet its role has remained ambiguous. Re-examination of gene expression data revealed that all previously described genes and two newly identified genes within the sir gene cluster in the genome are down-regulated during the crucial early establishment stages of blackleg disease on Brassica napus. To test if this is a strategy employed by the fungus to avoid damage to and then detection by the host plant during the L. maculans asymptomatic biotrophic phase, sirodesmin was produced constitutively by overexpressing the sirZ gene encoding the transcription factor that coordinates the regulation of the other genes in the sir cluster. The sirZ over-expression strains had a major reduction in pathogenicity. Mutation of the over-expression construct restored pathogenicity. However, mutation of two genes, sirP and sirG, required for specific steps in the sirodesmin biosynthesis pathway, in the sirZ over-expression background resulted in strains that were unable to synthesize sirodesmin, yet were still non-pathogenic. Elucidating the basis for this pathogenicity defect or finding ways to overexpress sirZ during disease may provide new strategies for the control of blackleg disease.
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Affiliation(s)
- Andrew S. Urquhart
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Applied BioSciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Candace E. Elliott
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Biosecurity Operations Division, Department of Agriculture, Water and the Environment, Post Entry Quarantine, Mickleham, Victoria, Australia
| | - Wei Zeng
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T, Balesdent MH. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol 2021; 19:55. [PMID: 33757516 PMCID: PMC7986464 DOI: 10.1186/s12915-021-00989-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. RESULTS We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. CONCLUSION This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Juliette Linglin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Levrel
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Jocelyne Lemoine
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Regine Delourme
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
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Henry P, Kaur S, Pham QAT, Barakat R, Brinker S, Haensel H, Daugovish O, Epstein L. Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii. BMC Genomics 2020; 21:730. [PMID: 33081696 PMCID: PMC7576743 DOI: 10.1186/s12864-020-07141-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3. RESULTS A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other. CONCLUSIONS There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.
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Affiliation(s)
- Peter Henry
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Quyen Anh Tran Pham
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080, USA
| | - Radwan Barakat
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Department of Plant Production & Protection, College of Agriculture, Hebron University, Hebron, Palestine
| | - Samuel Brinker
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Hannah Haensel
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Oleg Daugovish
- University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.
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