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Wang Q, Zhang Y, Chen R, Zhang L, Fu M, Zhang L. Comparative genomic analyses provide insight into the pathogenicity of three Pseudomonas syringae pv. actinidiae strains from Anhui Province, China. BMC Genomics 2024; 25:461. [PMID: 38734623 PMCID: PMC11088785 DOI: 10.1186/s12864-024-10384-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Pseudomonas syringae pv. actinidiae (Psa) is an important bacterial plant pathogen that causes severe damage to the kiwifruit industry worldwide. Three Psa strains were recently obtained from different kiwifruit orchards in Anhui Province, China. The present study mainly focused on the variations in virulence and genome characteristics of these strains based on the pathogenicity assays and comparative genomic analyses. RESULTS Three strains were identified as biovar 3 (Psa3), along with strain QSY6 showing higher virulence than JZY2 and YXH1 in pathogenicity assays. The whole genome assembly revealed that each of the three strains had a circular chromosome and a complete plasmid. The chromosome sizes ranged from 6.5 to 6.6 Mb with a GC content of approximately 58.39 to 58.46%, and a predicted number of protein-coding sequences ranging from 5,884 to 6,019. The three strains clustered tightly with 8 Psa3 reference strains in terms of average nucleotide identity (ANI), whole-genome-based phylogenetic analysis, and pangenome analysis, while they were evolutionarily distinct from other biovars (Psa1 and Psa5). Variations were observed in the repertoire of effectors of the type III secretion system among all 15 strains. Moreover, synteny analysis of the three sequenced strains revealed eight genomic regions containing 308 genes exclusively present in the highly virulent strain QSY6. Further investigation of these genes showed that 16 virulence-related genes highlight several key factors, such as effector delivery systems (type III secretion systems) and adherence (type IV pilus), which might be crucial for the virulence of QSY6. CONCLUSION Three Psa strains were identified and showed variant virulence in kiwifruit plant. Complete genome sequences and comparative genomic analyses further provided a theoretical basis for the potential pathogenic factors responsible for kiwifruit bacterial canker.
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Affiliation(s)
- Qian Wang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yiju Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Rui Chen
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lei Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Fu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Lixin Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China.
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Pei Y, Ma L, Zheng X, Yao K, Fu X, Chen H, Chang X, Zhang M, Gong G. Identification and Genetic Characterization of Pseudomonas syringae pv. actinidiae from Kiwifruit in Sichuan, China. PLANT DISEASE 2023; 107:3248-3258. [PMID: 37005505 DOI: 10.1094/pdis-01-23-0005-re] [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: 06/19/2023]
Abstract
Pseudomonas syringae pv. actinidiae causes kiwifruit bacterial canker and poses a major threat to the kiwifruit industry. This study aimed to investigate the genetic characteristics of the P. syringae pv. actinidiae population from kiwifruit in Sichuan, China. Sixty-seven isolates obtained from diseased plants were characterized using morphological features, multiplex-PCR, and multilocus sequence analysis (MLSA). The isolates exhibited the typical colony morphology of P. syringae pv. actinidiae. Multiplex PCR amplification identified every isolate as P. syringae pv. actinidiae biovar 3. MLSA of the three housekeeping genes gapA, gyrB, and pfk, revealed that the reference strains of the five described biovars were clearly distinguished by a combined phylogenetic tree, and all of the tested isolates clustered with the reference strains of P. syringae pv. actinidiae biovar 3. Through a phylogenetic tree constructed from a single gene, it was found that pkf gene alone could distinguish biovar 3 from the other biovars. Furthermore, all P. syringae pv. actinidiae isolates analyzed by BOX-A1R-based repetitive extragenic palindromic (BOX)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR clustered into four groups. The clustering results of BOX- and ERIC-PCR indicated that group III had the largest number of isolates, accounting for 56.72 and 61.19% of all 67 isolates, respectively, and the two characterization methods were similar and complementary. The results of this study revealed that the genomes of P. syringae pv. actinidiae isolates from Sichuan had rich genetic diversity but no obvious correlation was found between clustering and geographical region. This research provides novel methodologies for rapidly detecting kiwifruit bacterial canker pathogen and a molecular differentiation at genetic level of P. syringae pv. actinidiae biovar diversity in China.
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Affiliation(s)
- Yangang Pei
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Li Ma
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
- Plant Protection Station, Sichuan Provincial Department of Agriculture and Rural Affairs, Chengdu 610041, P.R. China
| | - Xiaojuan Zheng
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Kaikai Yao
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiangru Fu
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Huabao Chen
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xiaoli Chang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Ming Zhang
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Guoshu Gong
- Department of Plant Pathology, Sichuan Agricultural University, Chengdu 611130, P.R. China
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Li Y, Zhu Q, Zhi T, Fan R, Xie T, Zhao Z, Long Y, Li Z. Genetic Causes of Non-pathogenic Pseudomonas syringae pv. actinidiae Isolates in Kiwifruit Orchards. Front Microbiol 2021; 12:650099. [PMID: 33841374 PMCID: PMC8027508 DOI: 10.3389/fmicb.2021.650099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial canker disease has become the largest threat to kiwifruit cultivation and production. A monomorphic subpopulation of Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) is responsible for the pandemic worldwide. Diversity in pathogenicity has been found in the pandemic subpopulation and in other Psa3 subpopulations causing epidemics in China. However, the genetic bases have not yet been elucidated. In this study, 117 Psa3 isolates were identified by Psa- and Psa3-specific primers, and evaluated for pathogenicity. Three isolates G4, G40, and S2 are not pathogenic to kiwifruit and do not elicit hypersensitivity responses (HRs) in non-host Nicotiana benthamiana leaves. Two isolates, G25 and G35, exhibited attenuated HR-eliciting activity in non-host N. benthamiana, but they exhibited greatly and slightly reduced pathogenicity in host plants, respectively. The genomes of the five isolates were sequenced and compared with closely related isolates revealed by MLVA and whole-genome typing methods. The candidate genetic loci responsible for the changes in pathogenicity and HR elicitation, were further evaluated by allele replacement experiments. We found that the three non-pathogenic isolates were formed due to the independent, identical insertion events of ISPsy36 transposon in the hrpR gene, encoding a key regulator of type III secretion system (T3SS) and type III effectors (T3Es). In the symptomatic sample from which G4 was isolated, 27% HR negative isolates were detected. In isolate G25, transposon insertion of ISPsy32 at the non-coding sequence upstream of the hrpR gene was detected, similar to a previously reported low-virulent Psa3 strain M227. In isolate G35, we detected disruptions of T3Es hopBB1-1 and hopBB1-2, which induce HR in N. benthamiana leaves revealed by Agrobacterium tumefaciens infiltration. These phenotype-changed isolates were formed at low frequencies during the course of pathogen infection in host plants, supported by the binding assay of ISPsy32 and the non-coding DNA sequences upstream of the hrpR gene, the co-isolation of the virulent isolates belonging to the same MLVA clade, and the low levels of transcription of the transposon genes. Taken together, in terms of short-term field evolution, transposon insertions in the T3SS-related genes resulted in the formation of non-pathogenic and low-virulent Psa3 isolates.
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Affiliation(s)
- Yue Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Qiaomei Zhu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Taihui Zhi
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Rong Fan
- Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Ting Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.,Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Youhua Long
- Kiwifruit Engineering and Technology Research Center, Guizhou University, Guiyang, China
| | - Zhong Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
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Kim GH, Lee YS, Jung JS, Koh YJ, Poulter RTM, Butler M. Genomic analyses of Pseudomonas syringae pv. actinidiae isolated in Korea suggest the transfer of the bacterial pathogen via kiwifruit pollen. J Med Microbiol 2020; 69:132-138. [DOI: 10.1099/jmm.0.001115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Gyoung Hee Kim
- Department of Plant Medicine, Sunchon National University, Sunchon 57922, Republic of Korea
| | - Young-Sun Lee
- Department of Plant Medicine, Sunchon National University, Sunchon 57922, Republic of Korea
| | - Jae Sung Jung
- Department of Plant Medicine, Sunchon National University, Sunchon 57922, Republic of Korea
| | - Young-Jin Koh
- Department of Plant Medicine, Sunchon National University, Sunchon 57922, Republic of Korea
| | | | - Margi Butler
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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Flores O, Prince C, Nuñez M, Vallejos A, Mardones C, Yañez C, Besoain X, Bastías R. Genetic and Phenotypic Characterization of Indole-Producing Isolates of Pseudomonas syringae pv. actinidiae Obtained From Chilean Kiwifruit Orchards. Front Microbiol 2018; 9:1907. [PMID: 30186252 PMCID: PMC6113925 DOI: 10.3389/fmicb.2018.01907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/30/2018] [Indexed: 12/29/2022] Open
Abstract
In recent years, Chilean kiwifruit production has been affected by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), which has caused losses to the industry. In this study, we report the genotypic and phenotypic characterization of 18 Psa isolates obtained from Chilean kiwifruits orchards between 2012 and 2016 from different geographic origins. Genetic analysis by multilocus sequence analysis (MLSA) using four housekeeping genes (gyrB, rpoD, gltA, and gapA) and the identification of type III effector genes suggest that the Chilean Psa isolates belong to the Psa Biovar 3 cluster. All of the isolates were highly homogenous in regard to their phenotypic characteristics. None of the isolates were able to form biofilms over solid plastic surfaces. However, all of the isolates formed cellular aggregates in the air-liquid interface. All of the isolates, except for Psa 889, demonstrated swimming motility, while only isolate Psa 510 demonstrated swarming motility. The biochemical profiles of the isolates revealed differences in 22% of the tests in at least one Psa isolate when analyzed with the BIOLOG system. Interestingly, all of the isolates were able to produce indole using a tryptophan-dependent pathway. PCR analysis revealed the presence of the genes aldA/aldB and iaaL/matE, which are associated with the production of indole-3-acetic acid (IAA) and indole-3-acetyl-3-L-lysine (IAA-Lys), respectively, in P. syringae. In addition, IAA was detected in the cell free supernatant of a representative Chilean Psa strain. This work represents the most extensive analysis in terms of the time and geographic origin of Chilean Psa isolates. To our knowledge, this is the first report of Psa being able to produce IAA. Further studies are needed to determine the potential role of IAA in the virulence of Psa during kiwifruit infections and whether this feature is observed in other Psa biovars.
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Affiliation(s)
- Oriana Flores
- Laboratorio de Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Camila Prince
- Laboratorio de Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Mauricio Nuñez
- Laboratorio de Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alejandro Vallejos
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Claudia Mardones
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Carolina Yañez
- Laboratorio de Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Ximena Besoain
- Laboratorio de Fitopatología, Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Roberto Bastías
- Laboratorio de Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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