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Abdelsalam SSH, Kouzai Y, Watanabe M, Inoue K, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Tsuge S, Mochida K, Noutoshi Y. Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon. Sci Rep 2020; 10:14889. [PMID: 32913311 PMCID: PMC7483729 DOI: 10.1038/s41598-020-71968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
Rhizoctonia solani is a necrotrophic phytopathogen belonging to basidiomycetes. It causes rice sheath blight which inflicts serious damage in rice production. The infection strategy of this pathogen remains unclear. We previously demonstrated that salicylic acid-induced immunity could block R. solani AG-1 IA infection in both rice and Brachypodium distachyon. R. solani may undergo biotrophic process using effector proteins to suppress host immunity before necrotrophic stage. To identify pathogen genes expressed at the early infection process, here we developed an inoculation method using B. distachyon which enables to sample an increased amount of semi-synchronous infection hyphae. Sixty-one R. solani secretory effector-like protein genes (RsSEPGs) were identified using in silico approach with the publicly available gene annotation of R. solani AG-1 IA genome and our RNA-sequencing results obtained from hyphae grown on agar medium. Expression of RsSEPGs was analyzed at 6, 10, 16, 24, and 32 h after inoculation by a quantitative reverse transcription-polymerase chain reaction and 52 genes could be detected at least on a single time point tested. Their expressions showed phase-specific patterns which were classified into 6 clusters. The 23 RsSEPGs in the cluster 1–3 and 29 RsSEPGs in the cluster 4–6 are expected to be involved in biotrophic and necrotrophic interactions, respectively.
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Affiliation(s)
- Sobhy S H Abdelsalam
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Plant Pathology Department, Faculty of Agriculture, Alexandria University, El-Shatby, Egypt
| | - Yusuke Kouzai
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Seiji Tsuge
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.,Institute for Plant Science and Resources (IPSR), Okayama University, Okayama, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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Leal I, Bergeron MJ, Feau N, Tsui CKM, Foord B, Pellow K, Hamelin RC, Sturrock RN. Cryptic Speciation in Western North America and Eastern Eurasia of the Pathogens Responsible for Laminated Root Rot. PHYTOPATHOLOGY 2019; 109:456-468. [PMID: 30145938 DOI: 10.1094/phyto-12-17-0399-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coniferiporia sulphurascens is a facultative fungal pathogen that causes laminated root rot (LRR) in commercially important coniferous species worldwide. This fungus spreads primarily by way of vegetative mycelium transferring at points of contact between infected and healthy roots. Successful intervention to control LRR requires a better understanding of the population structure and genetic variability of C. sulphurascens. In this study, we investigated the population genetic structure and origin of C. sulphurascens populations in western North America and eastern Eurasia collected from multiple coniferous hosts. By analyzing the small and large mitochondrial ribosomal RNA subunit genes combined with six nuclear loci (internal transcribed spacer region, actin, RNA polymerase II largest subunit, RNA polymerase II second-largest subunit, laccase-like multicopper oxidase, and translation elongation factor 1-α), we observed that none of the alleles among the loci were shared between North American (NA) and Eurasian C. sulphurascens populations. In total, 55 multilocus genotypes (MLGs) were retrieved in C. sulphurascens isolates occurring in these two continental regions. Of these, 41 MLGs were observed among 58 isolates collected from widespread locations in British Columbia (Canada) and the northwestern United States, while 14 MLGs were observed among 16 isolates sampled in Siberia and Japan. Our data showed that the levels of genetic differentiation between the NA and Eurasian populations are much greater than the populations from within each continental region; the two continental populations formed clearly divergent phylogenetic clades or lineages since they were separated approximately 7.5 million years ago. Moreover, the Eurasian population could be the source of the NA population. Our study indicates the existence of cryptic diversity in this pathogen species, and strongly suggests that the NA and Eurasian populations represent two lineages, which have progressively diverged from each other in allopatry.
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Affiliation(s)
- I Leal
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - M-J Bergeron
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - N Feau
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - C K M Tsui
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - B Foord
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - K Pellow
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R C Hamelin
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R N Sturrock
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
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Bradshaw RE, Guo Y, Sim AD, Kabir MS, Chettri P, Ozturk IK, Hunziker L, Ganley RJ, Cox MP. Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata. MOLECULAR PLANT PATHOLOGY 2016; 17:210-24. [PMID: 25919703 PMCID: PMC4746707 DOI: 10.1111/mpp.12273] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We present genome-wide gene expression patterns as a time series through the infection cycle of the fungal pine needle blight pathogen, Dothistroma septosporum, as it invades its gymnosperm host, Pinus radiata. We determined the molecular changes at three stages of the disease cycle: epiphytic/biotrophic (early), initial necrosis (mid) and mature sporulating lesion (late). Over 1.7 billion combined plant and fungal reads were sequenced to obtain 3.2 million fungal-specific reads, which comprised as little as 0.1% of the sample reads early in infection. This enriched dataset shows that the initial biotrophic stage is characterized by the up-regulation of genes encoding fungal cell wall-modifying enzymes and signalling proteins. Later necrotrophic stages show the up-regulation of genes for secondary metabolism, putative effectors, oxidoreductases, transporters and starch degradation. This in-depth through-time transcriptomic study provides our first snapshot of the gene expression dynamics that characterize infection by this fungal pathogen in its gymnosperm host.
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Affiliation(s)
- Rosie E Bradshaw
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Yanan Guo
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Andre D Sim
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - M Shahjahan Kabir
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Pranav Chettri
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Ibrahim K Ozturk
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Lukas Hunziker
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
| | - Rebecca J Ganley
- Scion, NZ Forest Research Institute Ltd, Rotorua, 3010, New Zealand
| | - Murray P Cox
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand
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