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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1779. [PMID: 37749249 PMCID: PMC10562209 DOI: 10.1038/s41588-023-01550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1579-1588. [PMID: 37640880 PMCID: PMC10484786 DOI: 10.1038/s41588-023-01486-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Ahn YJ, Kim H, Choi S, Mazo-Molina C, Prokchorchik M, Zhang N, Kim B, Mang H, Koehler N, Kim J, Lee S, Yoon H, Choi D, Kim MS, Segonzac C, Martin GB, Schultink A, Sohn KH. Ptr1 and ZAR1 immune receptors confer overlapping and distinct bacterial pathogen effector specificities. New Phytol 2023; 239:1935-1953. [PMID: 37334551 DOI: 10.1111/nph.19073] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Some nucleotide-binding and leucine-rich repeat receptors (NLRs) indirectly detect pathogen effectors by monitoring their host targets. In Arabidopsis thaliana, RIN4 is targeted by multiple sequence-unrelated effectors and activates immune responses mediated by RPM1 and RPS2. These effectors trigger cell death in Nicotiana benthamiana, but the corresponding NLRs have yet not been identified. To identify N. benthamiana NLRs (NbNLRs) that recognize Arabidopsis RIN4-targeting effectors, we conducted a rapid reverse genetic screen using an NbNLR VIGS library. We identified that the N. benthamiana homolog of Ptr1 (Pseudomonas tomato race 1) recognizes the Pseudomonas effectors AvrRpt2, AvrRpm1, and AvrB. We demonstrated that recognition of the Xanthomonas effector AvrBsT and the Pseudomonas effector HopZ5 is conferred independently by the N. benthamiana homolog of Ptr1 and ZAR1. Interestingly, the recognition of HopZ5 and AvrBsT is contributed unequally by Ptr1 and ZAR1 in N. benthamiana and Capsicum annuum. In addition, we showed that the RLCK XII family protein JIM2 is required for the NbZAR1-dependent recognition of AvrBsT and HopZ5. The recognition of sequence-unrelated effectors by NbPtr1 and NbZAR1 provides an additional example of convergently evolved effector recognition. Identification of key components involved in Ptr1 and ZAR1-mediated immunity could reveal unique mechanisms of expanded effector recognition.
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Affiliation(s)
- Ye Jin Ahn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Haseong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Carolina Mazo-Molina
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Boyoung Kim
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Hyunggon Mang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Naio Koehler
- Fortiphyte Inc., 3071 Research Drive, Richmond, CA, 94806, USA
| | - Jieun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Soeui Lee
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Hayeon Yoon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Doil Choi
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
| | - Min-Sung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Cécile Segonzac
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Alex Schultink
- Fortiphyte Inc., 3071 Research Drive, Richmond, CA, 94806, USA
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
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Kim H, Prokchorchik M, Sohn KH. Investigation of natural RIN4 variants reveals a motif crucial for function and provides an opportunity to broaden NLR regulation specificity. Plant J 2022; 110:58-70. [PMID: 34978118 DOI: 10.1111/tpj.15653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/29/2021] [Accepted: 12/20/2021] [Indexed: 05/27/2023]
Abstract
Multiple bacterial effectors target RPM1-INTERACTING PROTEIN4 (RIN4), the biochemical modifications of which are recognized by several plant nucleotide-binding and leucine-rich repeat immune receptor (NLR) proteins. Recently, a comparative study of Arabidopsis and apple (Malus domestica) RIN4s revealed that the RIN4 specificity motif (RSM) is critical for NLR regulation. Here, we investigated the extent to which the RSM contributes to the functions of natural RIN4 variants. Functional analysis of 33 natural RIN4 variants from 28 plant species showed that the RSM is generally required yet sometimes dispensable for the RIN4-mediated suppression of NLR auto-activity or effector-triggered NLR activation. Association analysis of the sequences and fire blight resistance gene originating from Malus × robusta 5 (FB_MR5) activation functions of the natural RIN4 variants revealed H167 to be an indispensable residue for RIN4 function in the regulation of NLRs. None of the tested natural RIN4 variants could suppress RESISTANCE TO PSEUDOMONAS SYRINGAE PV. MACULICOLA1 (RPM1) auto-activity and activate FB_MR5. To engineer RIN4 to carry broader NLR compatibility, we generated chimeric RIN4 proteins, several of which could regulate RPM1, RESISTANT TO PSEUDOMONAS SYRINGAE2 (RPS2), and FB_MR5. We propose that the intrinsically disordered nature of RIN4 provides a flexible platform to broaden pathogen recognition specificity by establishing compatibility with otherwise incompatible NLRs.
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Affiliation(s)
- Haseong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Incheon, 21983, Republic of Korea
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5
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Choi S, Prokchorchik M, Lee H, Gupta R, Lee Y, Chung EH, Cho B, Kim MS, Kim ST, Sohn KH. Direct acetylation of a conserved threonine of RIN4 by the bacterial effector HopZ5 or AvrBsT activates RPM1-dependent immunity in Arabidopsis. Mol Plant 2021; 14:1951-1960. [PMID: 34329778 DOI: 10.1016/j.molp.2021.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/28/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Plant pathogenic bacteria deliver effectors into plant cells to suppress immunity and promote pathogen survival; however, these effectors can be recognized by plant disease resistance proteins to activate innate immunity. The bacterial acetyltransferase effectors HopZ5 and AvrBsT trigger immunity in Arabidopsis thaliana genotypes lacking SUPPRESSOR OF AVRBST-ELICITED RESISTANCE 1 (SOBER1). Using an Arabidopsis accession, Tscha-1, that naturally lacks functional SOBER1 but is unable to recognize HopZ5, we demonstrated that RESISTANCE TO P. SYRINGAE PV MACULICOLA 1 (RPM1) and RPM1-INTERACTING PROTEIN 4 (RIN4) are indispensable for HopZ5- or AvrBsT-triggered immunity. Remarkably, T166 of RIN4, the phosphorylation of which is induced by AvrB and AvrRpm1, is directly acetylated by HopZ5 and AvrBsT. Furthermore, we demonstrated that the acetylation of RIN4 T166 is required and sufficient for HopZ5- or AvrBsT-triggered RPM1-dependent defense activation. Finally, we showed that SOBER1 interferes with HopZ5- or AvrBsT-triggered immunity by deacetylating RIN4 T166. Collectively, our study elucidates detailed molecular mechanisms underlying the activation and suppression of plant innate immunity triggered by two bacterial acetyltransferases, HopZ5 and AvrBsT, from different bacterial pathogens.
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Affiliation(s)
- Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hyeonjung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea; Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Eui-Hwan Chung
- Division of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Buhyeon Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Min-Sung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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6
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Pandey A, Moon H, Choi S, Yoon H, Prokchorchik M, Jayaraman J, Sujeevan R, Kang YM, McCann HC, Segonzac C, Kim CM, Park SJ, Sohn KH. Ralstonia solanacearum Type III Effector RipJ Triggers Bacterial Wilt Resistance in Solanum pimpinellifolium. Mol Plant Microbe Interact 2021; 34:962-972. [PMID: 33881922 DOI: 10.1094/mpmi-09-20-0256-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt disease in solanaceous crops. Identification of avirulence type III-secreted effectors recognized by specific disease resistance proteins in host plant species is an important step toward developing durable resistance in crops. In the present study, we show that R. solanacearum effector RipJ functions as an avirulence determinant in Solanum pimpinellifolium LA2093. In all, 10 candidate avirulence effectors were shortlisted based on the effector repertoire comparison between avirulent Pe_9 and virulent Pe_1 strains. Infection assays with transgenic strain Pe_1 individually carrying a candidate avirulence effector from Pe_9 revealed that only RipJ elicits strong bacterial wilt resistance in S. pimpinellifolium LA2093. Furthermore, we identified that several RipJ natural variants do not induce bacterial wilt resistance in S. pimpinellifolium LA2093. RipJ belongs to the YopJ family of acetyltransferases. Our sequence analysis indicated the presence of partially conserved putative catalytic residues. Interestingly, the conserved amino acid residues in the acetyltransferase catalytic triad are not required for effector-triggered immunity. In addition, we show that RipJ does not autoacetylate its lysine residues. Our study reports the identification of the first R. solanacearum avirulence protein that triggers bacterial wilt resistance in tomato. We expect that our discovery of RipJ as an avirulence protein will accelerate the development of bacterial wilt-resistant tomato varieties in the future.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Ankita Pandey
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hayoung Moon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hayeon Yoon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Germany
| | - Jay Jayaraman
- New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Auckland 1025, New Zealand
| | - Rajendran Sujeevan
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Yu Mi Kang
- Division of Horticulture Industry, Wonkwang University, Iksan 554438, Republic of Korea
| | - Honour C McCann
- Institute of Advanced Studies, Massey University, Auckland 0745, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cécile Segonzac
- Department of Plant Science, Plant Genome and Breeding Institute, Agricultural Life Science Research Institute, Seoul National University, 08826, Seoul, Republic of Korea
- Plant Immunity Research Center, Seoul National University, 08826, Seoul, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, 08826, Seoul, Republic of Korea
| | - Chul Min Kim
- Division of Horticulture Industry, Wonkwang University, Iksan 554438, Republic of Korea
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Biosciences and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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7
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Moon H, Pandey A, Yoon H, Choi S, Jeon H, Prokchorchik M, Jung G, Witek K, Valls M, McCann HC, Kim M, Jones JDG, Segonzac C, Sohn KH. Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum. Mol Plant Pathol 2021; 22:317-333. [PMID: 33389783 PMCID: PMC7865085 DOI: 10.1111/mpp.13030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease.
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Affiliation(s)
- Hayoung Moon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Ankita Pandey
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hayeon Yoon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Sera Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hyelim Jeon
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
| | - Maxim Prokchorchik
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Gayoung Jung
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Marc Valls
- Department of GeneticsUniversity of BarcelonaBarcelonaSpain
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)BellaterraSpain
| | - Honour C. McCann
- New Zealand Institute of Advanced StudiesMassey UniversityAucklandNew Zealand
- Max Planck Institute for Developmental BiologyTübingenGermany
| | - Min‐Sung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- Division of Integrative Biosciences and BiotechnologyPohang University of Science and TechnologyRepublic of Korea
| | | | - Cécile Segonzac
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
- Department of Plant Science, Plant Genomics and Breeding InstituteAgricultural Life Science Research InstituteSeoul National UniversitySeoulRepublic of Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangRepublic of Korea
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Prokchorchik M, Pandey A, Moon H, Kim W, Jeon H, Jung G, Jayaraman J, Poole S, Segonzac C, Sohn KH, McCann HC. Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea. Microb Genom 2020; 6:mgen000461. [PMID: 33151139 PMCID: PMC7725338 DOI: 10.1099/mgen.0.000461] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) threatens the cultivation of important crops worldwide. We sequenced 30 RSSC phylotype I (R. pseudosolanacearum) strains isolated from pepper (Capsicum annuum) and tomato (Solanum lycopersicum) across the Republic of Korea. These isolates span the diversity of phylotype I, have extensive effector repertoires and are subject to frequent recombination. Recombination hotspots among South Korean phylotype I isolates include multiple predicted contact-dependent inhibition loci, suggesting that microbial competition plays a significant role in Ralstonia evolution. Rapid diversification of secreted effectors presents challenges for the development of disease-resistant plant varieties. We identified potential targets for disease resistance breeding by testing for allele-specific host recognition of T3Es present among South Korean phyloype I isolates. The integration of pathogen population genomics and molecular plant pathology contributes to the development of location-specific disease control and development of plant cultivars with durable resistance to relevant threats.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ankita Pandey
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hayoung Moon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Wanhui Kim
- Department of Plant Science, Plant Genome and Breeding Institute, Agricultural Life Science Research Institute, Seoul National University, Seoul 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyelim Jeon
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea
| | - Gayoung Jung
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Stephen Poole
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, USA
| | - Cécile Segonzac
- Department of Plant Science, Plant Genome and Breeding Institute, Agricultural Life Science Research Institute, Seoul National University, Seoul 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul 08826, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University Albany, New Zealand
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Kim W, Prokchorchik M, Tian Y, Kim S, Jeon H, Segonzac C. Perception of unrelated microbe-associated molecular patterns triggers conserved yet variable physiological and transcriptional changes in Brassica rapa ssp. pekinensis. Hortic Res 2020; 7:186. [PMID: 33328480 PMCID: PMC7603518 DOI: 10.1038/s41438-020-00410-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 05/12/2023]
Abstract
Pattern-triggered immunity (PTI) includes the different transcriptional and physiological responses that enable plants to ward off microbial invasion. Surface-localized pattern-recognition receptors (PRRs) recognize conserved microbe-associated molecular patterns (MAMPs) and initiate a branched signaling cascade that culminate in an effective restriction of pathogen growth. In the model species Arabidopsis thaliana, early PTI events triggered by different PRRs are broadly conserved although their nature or intensity is dependent on the origin and features of the detected MAMP. In order to provide a functional basis for disease resistance in leafy vegetable crops, we surveyed the conservation of PTI events in Brassica rapa ssp. pekinensis. We identified the PRR homologs present in B. rapa genome and found that only one of the two copies of the bacterial Elongation factor-Tu receptor (EFR) might function. We also characterized the extent and unexpected specificity of the transcriptional changes occurring when B. rapa seedlings are treated with two unrelated MAMPs, the bacterial flagellin flg22 peptide and the fungal cell wall component chitin. Finally, using a MAMP-induced protection assay, we could show that bacterial and fungal MAMPs elicit a robust immunity in B. rapa, despite significant differences in the kinetic and amplitude of the early signaling events. Our data support the relevance of PTI for crop protection and highlight specific functional target for disease resistance breeding in Brassica crops.
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Affiliation(s)
- Wanhui Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Maxim Prokchorchik
- Life Sciences Department, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Yonghua Tian
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seulgi Kim
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyelim Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea.
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Lee Y, Cho KS, Seo JH, Sohn KH, Prokchorchik M. Improved Genome Sequence and Gene Annotation Resource for the Potato Late Blight Pathogen Phytophthora infestans. Mol Plant Microbe Interact 2020; 33:1025-1028. [PMID: 32310703 DOI: 10.1094/mpmi-02-20-0023-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phytophthora infestans is a devastating pathogen causing potato late blight (Solanum tuberosum). Here we report the sequencing, assembly and genome annotation for two Phytophthora infestans isolates sampled in Republic of Korea. Genome sequencing was carried out using long read (Oxford Nanopore) and short read (Illumina Nextseq) sequencing technologies that significantly improved the contiguity and quality of P. infestans genome assembly. Our resources would help researchers better understand the molecular mechanisms by which P. infestans causes late blight disease in the future.
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Affiliation(s)
- Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kwang-Soo Cho
- Potato Research Team, Highland Agriculture Research Institute, Rural Development Administration, Gangwon 25342, Republic of Korea
| | - Jin-Hee Seo
- Potato Research Team, Highland Agriculture Research Institute, Rural Development Administration, Gangwon 25342, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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11
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Prokchorchik M, Choi S, Chung EH, Won K, Dangl JL, Sohn KH. A host target of a bacterial cysteine protease virulence effector plays a key role in convergent evolution of plant innate immune system receptors. New Phytol 2020; 225:1327-1342. [PMID: 31550400 DOI: 10.1111/nph.16218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Some virulence effectors secreted from pathogens target host proteins and induce biochemical modifications that are monitored by nucleotide-binding and leucine-rich repeat (NLR) immune receptors. Arabidopsis RIN4 protein (AtRIN4: RPM1-interacting protein 4) homologs are present in diverse plant species and targeted by several bacterial type III effector proteins including the cysteine protease AvrRpt2. RIN4 is 'guarded' by several independently evolved NLRs from various plant species, including Arabidopsis RPS2. Recently, it was shown that the MR5 NLR from a wild apple relative can recognize the AvrRpt2 effector from Erwinia amylovora, but the details of this recognition remained unclear. The present contribution reports the mechanism of AvrRpt2 recognition by independently evolved NLRs, MR5 from apple and RPS2, both of which require proteolytically processed RIN4 for activation. It shows that the C-terminal cleaved product of apple RIN4 (MdRIN4) but not AtRIN4 is necessary and sufficient for MR5 activation. Additionally, two polymorphic residues in AtRIN4 and MdRIN4 are identified that are crucial in the regulation of and physical association with NLRs. It is proposed that polymorphisms in RIN4 from distantly related plant species allow it to remain an effector target while maintaining compatibility with multiple NLRs.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- Bioprotection Research Centre, Institute of Agriculture and Environment, Massey University, Palmerston North, 4474, New Zealand
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, 54875, Korea
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Korea
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Prokchorchik M, Won K, Lee Y, Segonzac C, Sohn KH. Whole Genome Enabled Phylogenetic and Secretome Analyses of Two Venturia nashicola Isolates. Plant Pathol J 2020; 36:98-105. [PMID: 32089665 PMCID: PMC7012575 DOI: 10.5423/ppj.nt.10.2019.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 05/19/2023]
Abstract
Venturia nashicola is a fungal pathogen causing scab disease in Asian pears. It is particularly important in the Northeast Asia region where Asian pears are intensively grown. Venturia nashicola causes disease in Asian pear but not in European pear. Due to the highly restricted host range of Venturia nashicola, it is hypothesized that the small secreted proteins deployed by the pathogen are responsible for the host determination. Here we report the whole genome based phylogenetic analysis and predicted secretomes for V. nashicola isolates. We believe that our data will provide a valuable information for further validation and functional characterization of host determinants in V. nashicola.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju 58216,
Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673,
Korea
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13
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Prokchorchik M, Won K, Lee Y, Choi ED, Segonzac C, Sohn KH. High Contiguity Whole Genome Sequence and Gene Annotation Resource for Two Venturia nashicola Isolates. Mol Plant Microbe Interact 2019; 32:1091-1094. [PMID: 31008683 DOI: 10.1094/mpmi-03-19-0072-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Venturia nashicola is a fungal pathogen that causes Asian pear scab disease. This pathogen is of particular importance in Northeast Asian countries, where Asian pears are grown industrially. Scab disease in Asian pear is currently controlled by fungicide spraying and this situation calls for developing scab resistant cultivars. High-quality genome data are therefore required for in-depth comparative genome analysis of different isolates of V. nashicola and V. pyrina, a closely related species, which only infects European pear plants. Here, we report the high-contiguity whole genome assembly of two V. nashicola isolates, which is expected to enable genome comparisons for identification of the genes involved in host range determination of V. nashicola.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Eu Ddeum Choi
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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