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Rubilar-Hernández C, Álvarez-Maldini C, Pizarro L, Figueroa F, Villalobos-González L, Pimentel P, Fiore N, Pinto M. Nitric Oxide Mitigates the Deleterious Effects Caused by Infection of Pseudomonas syringae pv. syringae and Modulates the Carbon Assimilation Process in Sweet Cherry under Water Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1361. [PMID: 38794433 PMCID: PMC11125257 DOI: 10.3390/plants13101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
Bacterial canker is an important disease of sweet cherry plants mainly caused by Pseudomonas syringae pv. syringae (Pss). Water deficit profoundly impairs the yield of this crop. Nitric oxide (NO) is a molecule that plays an important role in the plant defense mechanisms. To evaluate the protection exerted by NO against Pss infection under normal or water-restricted conditions, sodium nitroprusside (SNP), a NO donor, was applied to sweet cherry plants cv. Lapins, before they were exposed to Pss infection under normal or water-restricted conditions throughout two seasons. Well-watered plants treated with exogenous NO presented a lower susceptibility to Pss. A lower susceptibility to Pss was also induced in plants by water stress and this effect was increased when water stress was accompanied by exogenous NO. The lower susceptibility to Pss induced either by exogenous NO or water stress was accompanied by a decrease in the internal bacterial population. In well-watered plants, exogenous NO increased the stomatal conductance and the net CO2 assimilation. In water-stressed plants, NO induced an increase in the leaf membranes stability and proline content, but not an increase in the CO2 assimilation or the stomatal conductance.
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Affiliation(s)
- Carlos Rubilar-Hernández
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile; (C.R.-H.); (L.P.); (F.F.)
| | - Carolina Álvarez-Maldini
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile;
- Departamento de Silvicultura, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción 4070374, Chile
| | - Lorena Pizarro
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile; (C.R.-H.); (L.P.); (F.F.)
- Centro UOH de Biología de Sistemas Para la Sanidad Vegetal, Universidad de O’Higgins, San Fernando 3070000, Chile
| | - Franco Figueroa
- Laboratorio de Inmunidad Vegetal, Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile; (C.R.-H.); (L.P.); (F.F.)
| | | | - Paula Pimentel
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo 2940000, Chile; (L.V.-G.); (P.P.)
| | - Nicola Fiore
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile;
| | - Manuel Pinto
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O’Higgins, San Fernando 3070000, Chile;
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Vadillo‐Dieguez A, Zeng Z, Mansfield JW, Grinberg NF, Lynn SC, Gregg A, Connell J, Harrison RJ, Jackson RW, Hulin MT. Genetic dissection of the tissue-specific roles of type III effectors and phytotoxins in the pathogenicity of Pseudomonas syringae pv. syringae to cherry. MOLECULAR PLANT PATHOLOGY 2024; 25:e13451. [PMID: 38590135 PMCID: PMC11002349 DOI: 10.1111/mpp.13451] [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: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024]
Abstract
When compared with other phylogroups (PGs) of the Pseudomonas syringae species complex, P. syringae pv. syringae (Pss) strains within PG2 have a reduced repertoire of type III effectors (T3Es) but produce several phytotoxins. Effectors within the cherry pathogen Pss 9644 were grouped based on their frequency in strains from Prunus as the conserved effector locus (CEL) common to most P. syringae pathogens; a core of effectors common to PG2; a set of PRUNUS effectors common to cherry pathogens; and a FLEXIBLE set of T3Es. Pss 9644 also contains gene clusters for biosynthesis of toxins syringomycin, syringopeptin and syringolin A. After confirmation of virulence gene expression, mutants with a sequential series of T3E and toxin deletions were pathogenicity tested on wood, leaves and fruits of sweet cherry (Prunus avium) and leaves of ornamental cherry (Prunus incisa). The toxins had a key role in disease development in fruits but were less important in leaves and wood. An effectorless mutant retained some pathogenicity to fruit but not wood or leaves. Striking redundancy was observed amongst effector groups. The CEL effectors have important roles during the early stages of leaf infection and possibly acted synergistically with toxins in all tissues. Deletion of separate groups of T3Es had more effect in P. incisa than in P. avium. Mixed inocula were used to complement the toxin mutations in trans and indicated that strain mixtures may be important in the field. Our results highlight the niche-specific role of toxins in P. avium tissues and the complexity of effector redundancy in the pathogen Pss 9644.
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Affiliation(s)
- Andrea Vadillo‐Dieguez
- NIABCambridgeUK
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | | | | | | | | | | | | | - Richard J. Harrison
- NIABCambridgeUK
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
- Faculty of Natural Sciences, Plant Science GroupWageningen University and ResearchWageningenNetherlands
- Present address:
Faculty of Natural Sciences, Plant Science GroupWageningen University and ResearchWageningenNetherlands
| | - Robert W. Jackson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Michelle T. Hulin
- NIABCambridgeUK
- Department of Plant Soil & Microbial SciencesMichigan State UniversityEast LansingUSA
- Present address:
Department of Plant Soil & Microbial SciencesMichigan State UniversityEast LansingUSA
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McTavish KJ, Almeida RND, Tersigni J, Raimundi MK, Gong Y, Wang PW, Gontijo GF, de Souza RM, de Resende MLV, Desveaux D, Guttman DS. Pseudomonas syringae coffee blight is associated with the horizontal transfer of plasmid-encoded type III effectors. THE NEW PHYTOLOGIST 2024; 241:409-429. [PMID: 37953378 DOI: 10.1111/nph.19364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/29/2023] [Indexed: 11/14/2023]
Abstract
The emergence of new pathogens is an ongoing threat to human health and agriculture. While zoonotic spillovers received considerable attention, the emergence of crop diseases is less well studied. Here, we identify genomic factors associated with the emergence of Pseudomonas syringae bacterial blight of coffee. Fifty-three P. syringae strains from diseased Brazilian coffee plants were sequenced. Comparative and evolutionary analyses were used to identify loci associated with coffee blight. Growth and symptomology assays were performed to validate the findings. Coffee isolates clustered in three lineages, including primary phylogroups PG3 and PG4, and secondary phylogroup PG11. Genome-wide association study of the primary PG strains identified 37 loci, including five effectors, most of which were encoded on a plasmid unique to the PG3 and PG4 coffee strains. Evolutionary analyses support the emergence of coffee blight in PG4 when the coffee-associated plasmid and associated effectors derived from a divergent plasmid carried by strains associated with other hosts. This plasmid was only recently transferred into PG3. Natural diversity and CRISPR-Cas9 plasmid curing were used to show that strains with the coffee-associated plasmid grow to higher densities and cause more severe disease symptoms in coffee. This work identifies possible evolutionary mechanisms underlying the emergence of a new lineage of coffee pathogens.
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Affiliation(s)
- Kathryn J McTavish
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
| | - Renan N D Almeida
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
| | - Jonathan Tersigni
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
| | - Melina K Raimundi
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, MG, CEP 37200-000, Brazil
| | - Yunchen Gong
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M6S 2Y1, Canada
| | - Pauline W Wang
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M6S 2Y1, Canada
| | - Guilherme F Gontijo
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, MG, CEP 37200-000, Brazil
| | - Ricardo M de Souza
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, MG, CEP 37200-000, Brazil
| | - Mario L V de Resende
- Department of Phytopathology, Universidade Federal de Lavras, Lavras, MG, CEP 37200-000, Brazil
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M6S 2Y1, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M6S 2Y1, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M6S 2Y1, Canada
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4
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Díaz D, Zamorano A, García H, Ramos C, Cui W, Carreras C, Beltrán MF, Sagredo B, Pinto M, Fiore N. Development of a Genome-Informed Protocol for Detection of Pseudomonas amygdali pv. morsprunorum Using LAMP and PCR. PLANTS (BASEL, SWITZERLAND) 2023; 12:4119. [PMID: 38140446 PMCID: PMC10747947 DOI: 10.3390/plants12244119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 12/24/2023]
Abstract
One of the causal agents of bacterial canker is Pseudomonas amygdali pv. morsprunorum-Pam (formerly Pseudomonas syringae pv. morsprunorum). Recently detected in Chile, Pam is known to cause lesions in the aerial parts of the plant, followed by more severe symptoms such as cankers and gummosis in the later stages of the disease. This study presents the design of PCR and LAMP detection methods for the specific and sensitive identification of Pseudomonas amygdali pv. morsprunorum (Pam) from cherry trees. Twelve Pseudomonas isolates were collected, sequenced, and later characterized by Multi-locus Sequence Analysis (MLSA) and Average Nucleotide Identity by blast (ANIb). Three of them (11116B2, S1 Pam, and S2 Pam) were identified as Pseudomonas amygdali pv. morsprunorum and were used to find specific genes through RAST server, by comparing their genome with that of other Pseudomonas, including isolates from other Pam strains. The effector gene HopAU1 was selected for the design of primers to be used for both techniques, evaluating sensitivity and specificity, and the ability to detect Pam directly from plant tissues. While the PCR detection limit was 100 pg of purified bacterial DNA per reaction, the LAMP assays were able to detect up to 1 fg of purified DNA per reaction. Similar results were observed using plant tissues, LAMP being more sensitive than PCR, including when using DNA extracted from infected plant tissues. Both detection methods were tested in the presence of 30 other bacterial genera, with LAMP being more sensitive than PCR.
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Affiliation(s)
- Daniela Díaz
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Alan Zamorano
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Héctor García
- Laboratorio Diagnofruit, Avenida Sucre 1521, Santiago 7770273, Chile; (H.G.); (C.R.)
| | - Cecilia Ramos
- Laboratorio Diagnofruit, Avenida Sucre 1521, Santiago 7770273, Chile; (H.G.); (C.R.)
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Campus Providencia, Manuel Montt 948, Santiago 7500975, Chile
| | - Weier Cui
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - Claudia Carreras
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
| | - María Francisca Beltrán
- Instituto de Investigaciones Agropecuarias, INIA Rayentué, Avda. Salamanca s/n, Rengo 2940000, Chile; (M.F.B.); (B.S.)
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias, INIA Rayentué, Avda. Salamanca s/n, Rengo 2940000, Chile; (M.F.B.); (B.S.)
| | - Manuel Pinto
- Instituto de Ciencias Agroalimentarias Animales y Ambientales (ICA3), Universidad de O’Higgins, Campus Colchagua, Ruta I-90 S/N, San Fernando 3072590, Chile;
| | - Nicola Fiore
- Laboratorio de Fitovirología, Departamento de Sanidad Vegetal, Facultad de Ciencias Agropecuarias, Universidad de Chile, Avenida Santa Rosa 11315, Santiago 8820808, Chile; (D.D.); (A.Z.); (W.C.); (C.C.)
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5
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Jiu S, Chen B, Dong X, Lv Z, Wang Y, Yin C, Xu Y, Zhang S, Zhu J, Wang J, Liu X, Sun W, Yang G, Li M, Li S, Zhang Z, Liu R, Wang L, Manzoor MA, José QG, Wang S, Lei Y, Yang L, Dirlewanger E, Dong Y, Zhang C. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. HORTICULTURE RESEARCH 2023; 10:uhad062. [PMID: 37220556 PMCID: PMC10200261 DOI: 10.1093/hr/uhad062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled P. pusilliflora genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we de novo assembled a chromosome-scale P. pusilliflora genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that P. pusilliflora is closely related to Prunus serrulata and Prunus yedoensis, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that P. pusilliflora has 643 expanded and 1128 contracted gene families. Furthermore, we found that P. pusilliflora is more resistant to Colletotrichum viniferum, Phytophthora capsici, and Pseudomonas syringae pv. tomato (Pst) DC3000 infections than cultivated Prunus avium. P. pusilliflora also has considerably more nucleotide-binding site-type resistance gene analogs than P. avium, which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in P. pusilliflora. Furthermore, 81 MADS-box genes were identified in P. pusilliflora, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality P. pusilliflora genome will be valuable for further research on cherries and molecular breeding.
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Affiliation(s)
| | | | - Xiao Dong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Zhengxin Lv
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yuxuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunjin Yin
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Sen Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Jijun Zhu
- Shanghai Botanical Garden, Shanghai, 200231, P. R. China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Guoqian Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Meng Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu Province, 200037, P. R. China
| | - Shufeng Li
- Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension, Dali, Yunnan Province, 671600, P. R. China
| | - Zhuo Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Quero-García José
- INRAe, UMR 1332 de Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yahui Lei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
| | - Ling Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, P. R. China
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Hulin MT, Rabiey M, Zeng Z, Vadillo Dieguez A, Bellamy S, Swift P, Mansfield JW, Jackson RW, Harrison RJ. Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface. THE NEW PHYTOLOGIST 2023; 237:959-973. [PMID: 36285389 PMCID: PMC10107160 DOI: 10.1111/nph.18573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.
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Affiliation(s)
- Michelle T. Hulin
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
- The Sainsbury LaboratoryNorwichNR4 7UHUK
| | - Mojgan Rabiey
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | - Ziyue Zeng
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
| | | | | | - Phoebe Swift
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | | | - Robert W. Jackson
- School of Biosciences and the Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamB15 2TTUK
| | - Richard J. Harrison
- NIABLawrence Weaver RoadCambridgeCB3 0LEUK
- Present address:
Plant Science GroupWageningen University and ResearchWageningen6708WBthe Netherlands
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7
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Ricardo-Rodrigues S, Laranjo M, Agulheiro-Santos AC. Methods for quality evaluation of sweet cherry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:463-478. [PMID: 35870155 DOI: 10.1002/jsfa.12144] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/27/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Sweet cherry (Prunus avium L.) is a highly valued fruit, whose quality can be evaluated using several objective methodologies, such as calibre, colour, texture, soluble solids content (SSC), titratable acidity (TA), as well as maturity indexes. Functional and nutritional compounds are also frequently determined, in response to consumer demand. The aim of the present review is to clarify and establish quality evaluation parameters and methodologies for the whole cherry supply chain, in order to promote easy and faithful communication among all stakeholders. The use of near-infrared spectroscopy (NIRS) as a non-destructive and expeditious method for assessing some quality parameters is discussed. In this review, the results of a wide survey to assess the most common methodologies for cherry quality evaluation, carried out among cherry researchers and producers within the framework of the COST Action FA1104 'Sustainable production of high-quality cherries for the European market', are also reported. The standardisation of quality evaluation parameters is expected to contribute to the preservation and shelf-life extension of sweet cherries, and the valorisation of the whole supply chain. For future studies on sweet cherry, we put forward a proposal regarding both sample size and the tests chosen to evaluate each parameter. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Sara Ricardo-Rodrigues
- MED-Mediterranean Institute for Agriculture, Environment and Development, IIFA - Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, IIFA - Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Ana Cristina Agulheiro-Santos
- MED-Mediterranean Institute for Agriculture, Environment and Development, IIFA - Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
- Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Évora, Portugal
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8
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Almeida RND, Greenberg M, Bundalovic-Torma C, Martel A, Wang PW, Middleton MA, Chatterton S, Desveaux D, Guttman DS. Predictive modeling of Pseudomonas syringae virulence on bean using gradient boosted decision trees. PLoS Pathog 2022; 18:e1010716. [PMID: 35877772 PMCID: PMC9352200 DOI: 10.1371/journal.ppat.1010716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/04/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae is a genetically diverse bacterial species complex responsible for numerous agronomically important crop diseases. Individual P. syringae isolates are assigned pathovar designations based on their host of isolation and the associated disease symptoms, and these pathovar designations are often assumed to reflect host specificity although this assumption has rarely been rigorously tested. Here we developed a rapid seed infection assay to measure the virulence of 121 diverse P. syringae isolates on common bean (Phaseolus vulgaris). This collection includes P. syringae phylogroup 2 (PG2) bean isolates (pathovar syringae) that cause bacterial spot disease and P. syringae phylogroup 3 (PG3) bean isolates (pathovar phaseolicola) that cause the more serious halo blight disease. We found that bean isolates in general were significantly more virulent on bean than non-bean isolates and observed no significant virulence difference between the PG2 and PG3 bean isolates. However, when we compared virulence within PGs we found that PG3 bean isolates were significantly more virulent than PG3 non-bean isolates, while there was no significant difference in virulence between PG2 bean and non-bean isolates. These results indicate that PG3 strains have a higher level of host specificity than PG2 strains. We then used gradient boosting machine learning to predict each strain’s virulence on bean based on whole genome k-mers, type III secreted effector k-mers, and the presence/absence of type III effectors and phytotoxins. Our model performed best using whole genome data and was able to predict virulence with high accuracy (mean absolute error = 0.05). Finally, we functionally validated the model by predicting virulence for 16 strains and found that 15 (94%) had virulence levels within the bounds of estimated predictions. This study strengthens the hypothesis that P. syringae PG2 strains have evolved a different lifestyle than other P. syringae strains as reflected in their lower level of host specificity. It also acts as a proof-of-principle to demonstrate the power of machine learning for predicting host specific adaptation. Pseudomonas syringae is a genetically diverse Gammaproteobacterial species complex responsible for numerous agronomically important crop diseases. Strains in the P. syringae species complex are frequently categorized into pathovars depending on pathogenic characteristics such as host of isolation and disease symptoms. Common bean pathogens from P. syringae are known to cause two major diseases: (1) pathovar phaseolicola strains from phylogroup 3 cause halo blight disease, characterized by large necrotic lesions surrounded by a chlorotic zone or halo of yellow tissue; and (2) pathovar syringae strains from phylogroup 2 causes bacterial spot disease, characterized by brown leaf spots. While halo blight can cause serious crop losses, bacterial spot disease is generally of minor agronomic concern. Recently, statistical genetic and machine learning approaches have been applied to genomic data to identify genes underlying traits of interest or predict the outcome of host-microbe interactions. Here, we apply machine learning to P. syringae genomic data to predict virulence on bean. We first characterized the virulence of P. syringae isolates on common bean using a seed infection assay and then applied machine learning to the genomic data from the same strains to generate a predictive model for virulence on bean. We found that machine learning models built with k-mers from either full genome data or virulence factors could predict bean virulence with high accuracy. We also confirmed prior work showing that phylogroup 3 halo blight pathogens display a stronger degree of phylogenetic clustering and host specificity compared to phylogroup 2 brown spot pathogens. This works serves as a proof-of-principle for the power of machine learning for predicting host specificity and may find utility in agricultural diagnostic microbiology.
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Affiliation(s)
- Renan N. D. Almeida
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Michael Greenberg
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | | | - Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - Pauline W. Wang
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Maggie A. Middleton
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - Syama Chatterton
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - David S. Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
- * E-mail:
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9
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Hulin MT, Vadillo Dieguez A, Cossu F, Lynn S, Russell K, Neale HC, Jackson RW, Arnold DL, Mansfield JW, Harrison RJ. Identifying resistance in wild and ornamental cherry towards bacterial canker caused by Pseudomonas syringae. PLANT PATHOLOGY 2022; 71:949-965. [PMID: 35909801 PMCID: PMC9305585 DOI: 10.1111/ppa.13513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 05/31/2023]
Abstract
Bacterial canker is a major disease of stone fruits and is a critical limiting factor to sweet cherry (Prunus avium) production worldwide. One important strategy for disease control is the development of resistant varieties. Partial varietal resistance in sweet cherry is discernible using shoot or whole tree inoculations; however, these quantitative differences in resistance are not evident in detached leaf assays. To identify novel sources of resistance to canker, we used a rapid leaf pathogenicity test to screen a range of wild cherry, ornamental Prunus species and sweet cherry × ornamental cherry hybrids with the canker pathogens, Pseudomonas syringae pvs syringae, morsprunorum races 1 and 2, and avii. Several Prunus accessions exhibited limited symptom development following inoculation with each of the pathogens, and this resistance extended to 16 P. syringae strains pathogenic on sweet cherry and plum. Resistance was associated with reduced bacterial multiplication after inoculation, a phenotype similar to that of commercial sweet cherry towards nonhost strains of P. syringae. Progeny resulting from a cross of a resistant ornamental species Prunus incisa with susceptible sweet cherry (P. avium) exhibited resistance indicating it is an inherited trait. Identification of accessions with resistance to the major bacterial canker pathogens is the first step towards characterizing the underlying genetic mechanisms of resistance and introducing these traits into commercial germplasm.
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Affiliation(s)
- Michelle T. Hulin
- NIAB EMREast MallingUK
- Present address:
The Sainsbury LaboratoryNorwichUK
| | | | | | | | | | - Helen C. Neale
- Centre for Research in BioscienceFaculty of Health and Applied SciencesThe University of the West of EnglandFrenchay CampusBristolUK
| | - Robert W. Jackson
- Birmingham Institute of Forest Research (BIFoR)University of BirminghamBirminghamUK
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Dawn L. Arnold
- Centre for Research in BioscienceFaculty of Health and Applied SciencesThe University of the West of EnglandFrenchay CampusBristolUK
- Harper Adams UniversityNewportShropshireUK
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10
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Han VC, Yu NH, Yoon H, Ahn NH, Son YK, Lee BH, Kim JC. Identification, Characterization, and Efficacy Evaluation of Bacillus velezensis for Shot-Hole Disease Biocontrol in Flowering Cherry. THE PLANT PATHOLOGY JOURNAL 2022; 38:115-130. [PMID: 35385917 PMCID: PMC9343898 DOI: 10.5423/ppj.oa.01.2022.0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Though information exists regarding the pathogenesis of the shot-hole disease (SH) in flowering cherry (FC), there has been a lack of research focusing on SH management. Therefore, here, we investigated the inhibitory activities of antagonistic bacteria against SH pathogens both in vitro and in vivo as well as their biochemical characteristics and bioactive compounds. Two biosurfactant-producing bacterial antagonists, identified as Bacillus velezensis strains JCK-1618 and JCK-1696, exhibited the best effects against the growth of both bacterial and fungal SH pathogens in vitro through their cell-free culture filtrates (CFCFs). These two strains also strongly inhibited the growth of the pathogens via the action of their antimicrobial diffusible compounds and antimicrobial volatile organic compounds (VOCs). Crude enzymes, solvent extracts, and biosurfactants of the two strains exhibited antimicrobial activities. Liquid chromatography/electrospray ionization time-of-flight mass spectrometric analysis of the partially purified active fractions revealed that the two antagonists produced three cyclic lipopeptides, including iturin A, fengycin A, and surfactin, and a polyketide, oxydifficidin. In a detached leaf assay, pre-treatment and co-treatment of FC leaves with the CFCFs led to a large reduction in the severity of the leaf spots caused by Epicoccum tobaicum and Bukholderia contaminans, respectively. In addition, the two antagonists produced indole-3-acetic acid, siderophore, and a series of hydrolytic enzymes, along with the formation of a substantial biofilm. To our knowledge, this is the first report of the antimicrobial activities of the diffusible compounds and VOCs of B. velezensis against the SH pathogens and their efficiency in the biocontrol of SH.
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Affiliation(s)
- Viet-Cuong Han
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Neung-Ho Ahn
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Youn Kyoung Son
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea
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11
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Jung H, Kim HS, Han G, Park J, Seo YS. Comparative Analyses of Four Complete Genomes in Pseudomonas amygdali Revealed Differential Adaptation to Hostile Environments and Secretion Systems. THE PLANT PATHOLOGY JOURNAL 2022; 38:167-174. [PMID: 35385921 PMCID: PMC9343901 DOI: 10.5423/ppj.nt.11.2021.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.
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Affiliation(s)
- Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Hong-Seop Kim
- Korea Seed & Variety Service, Pyeongchang 25343, Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
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12
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Oksel C, Avin FA, Mirik M, Baysal-Gurel F. Identification and Genetic Characterization of Pseudomonas syringae pv. syringae from Sweet Cherry in Turkey. PLANT DISEASE 2022; 106:1253-1261. [PMID: 34818912 DOI: 10.1094/pdis-10-21-2241-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pseudomonas syringae pv. syringae, which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex because of its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry (Prunus avium L.) trees in different locations of the Marmara region in Turkey between 2016 and 2018. Sixty-three isolates were identified as P. syringae pv. syringae by pathogenicity, LOPAT, GATTa, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for repetitive element sequence-based PCR and multilocus sequence typing analyses to gain insight into the relationships of those isolates. The cluster analysis of enterobacterial repetitive intergenic consensus-, repetitive extragenic palindromic-, and BOX-A1R-based repetitive extragenic-palindromic-PCR techniques could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location. The multilocus sequencing typing analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationships among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of P. syringae pv. syringae from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, this study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the evolutionary progress of P. syringae pv. syringae and the genetic diversity of sweet cherry isolates.
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Affiliation(s)
- Cansu Oksel
- Department of Plant Protection, Tekirdag Namık Kemal University, Tekirdag 59100, Turkey
| | - Farhat A Avin
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110, U.S.A
| | - Mustafa Mirik
- Department of Plant Protection, Tekirdag Namık Kemal University, Tekirdag 59100, Turkey
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110, U.S.A
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13
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Han VC, Yu NH, Park AR, Yoon H, Son YK, Lee BH, Kim JC. First Report of Shot-Hole on Flowering Cherry Caused by Burkholderia contaminans and Pseudomonas syringae pv. syringae. PLANT DISEASE 2021; 105:3795-3802. [PMID: 34142849 DOI: 10.1094/pdis-03-21-0547-sc] [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: 06/12/2023]
Abstract
Shot-hole disease (SH) is one of the most common and important diseases affecting flowering cherry (FC; Prunus × yedoensis Matsumura; Somei-yoshino) trees in South Korea every year, resulting in premature defoliation and reduced flowering in the following year. However, pathogens associated with the disease remain unknown, which has rendered disease management challenging. Here, the pathogens associated with SH, their biochemical characteristics, and their host range were elucidated. Detached-leaf and in planta assays revealed that two biofilm-forming bacteria-namely, Burkholderia contaminans and Pseudomonas syringae pv. syringae-caused SH of FC trees. These pathogens were recorded for the first time as the causes of SH of FC trees in South Korea. Additionally, the two pathogens induced similar disease symptoms in several stone fruit belonging to the genus Prunus, including peach (Prunus persica), plum (P. salicina), and apricot (P. mume), with peach being the most susceptible. These results indicate that B. contaminans and P. syringae pv. syringae caused SH on FC trees and presented a broad spectrum of hosts. Furthermore, Xanthomonas arboricola pv. pruni, the causative agent of leaf spot on stone fruit, incited brown spots and shot holes on FC leaves. Therefore, FC trees are susceptible to infections by various pathogenic bacteria, including B. contaminans, P. syringae pv. syringae, and X. arboricola pv. pruni. These findings will be of great importance as a reference for effective management of SH in the face of possible cross-infection between Prunus spp. in the future.
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Affiliation(s)
- Viet-Cuong Han
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, 77 Yong-bong-ro, Buk-gu, Gwangju 61186, South Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, 77 Yong-bong-ro, Buk-gu, Gwangju 61186, South Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, 77 Yong-bong-ro, Buk-gu, Gwangju 61186, South Korea
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, South Korea
| | - Youn Kyoung Son
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, South Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon 22689, South Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, 77 Yong-bong-ro, Buk-gu, Gwangju 61186, South Korea
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14
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Dillon MM, Ruiz-Bedoya T, Bundalovic-Torma C, Guttman KM, Kwak H, Middleton MA, Wang PW, Horuz S, Aysan Y, Guttman DS. Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey. Microb Genom 2021; 7. [PMID: 34227931 PMCID: PMC8477409 DOI: 10.1099/mgen.0.000585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas is a highly diverse genus that includes species that cause disease in both plants and animals. Recently, pathogenic pseudomonads from the Pseudomonas syringae and Pseudomonas fluorescens species complexes have caused significant outbreaks in several agronomically important crops in Turkey, including tomato, citrus, artichoke and melon. We characterized 169 pathogenic Pseudomonas strains associated with recent outbreaks in Turkey via multilocus sequence analysis and whole-genome sequencing, then used comparative and evolutionary genomics to characterize putative virulence mechanisms. Most of the isolates are closely related to other plant pathogens distributed among the primary phylogroups of P. syringae, although there are significant numbers of P. fluorescens isolates, which is a species better known as a rhizosphere-inhabiting plant-growth promoter. We found that all 39 citrus blast pathogens cluster in P. syringae phylogroup 2, although strains isolated from the same host do not cluster monophyletically, with lemon, mandarin orange and sweet orange isolates all being intermixed throughout the phylogroup. In contrast, 20 tomato pith pathogens are found in two independent lineages: one in the P. syringae secondary phylogroups, and the other from the P. fluorescens species complex. These divergent pith necrosis strains lack characteristic virulence factors like the canonical tripartite type III secretion system, large effector repertoires and the ability to synthesize multiple bacterial phytotoxins, suggesting they have alternative molecular mechanisms to cause disease. These findings highlight the complex nature of host specificity among plant pathogenic pseudomonads.
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Affiliation(s)
- Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Present address: Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Kevin M Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Haejin Kwak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Maggie A Middleton
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sumer Horuz
- Department of Plant Protection, Erciyes University, Kayseri, Turkey
| | - Yesim Aysan
- Department of Plant Protection, University of Çukurova, Adana, Turkey
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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15
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Transposon Mutagenesis of Pseudomonas syringae Pathovars syringae and morsprunorum to Identify Genes Involved in Bacterial Canker Disease of Cherry. Microorganisms 2021; 9:microorganisms9061328. [PMID: 34207283 PMCID: PMC8234094 DOI: 10.3390/microorganisms9061328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
Bacterial canker of Prunus, affecting economically important stone fruit crops including cherry, peach, apricot and plum, is caused by the plant pathogen Pseudomonas syringae (P.s.). Strains from two pathovars—P.s. pv. syringae (Pss) and P.s. pv. morsprunorum race 1 (PsmR1) and 2 (PsmR2)—in three phylogenetically distant clades have convergently evolved to infect Prunus. The bacteria enter woody tissues through wounds and leaf scars, causing black necrotic cankers. Symptoms are also produced on blossom, fruit and leaves. Little is known about the mechanisms P.s. uses to colonise tree hosts such as Prunus. Here, we created transposon (Tn) mutant libraries in one strain of P.s. from each of the three clades and screened the mutants on immature cherry fruit to look for changes in virulence. Mutants (242) with either reduced or enhanced virulence were detected and further characterised by in vitro screens for biofilm formation, swarming ability, and pathogenicity on leaves and cut shoots. In total, 18 genes affecting virulence were selected, and these were involved in diverse functions including motility, type III secretion, membrane transport, amino acid synthesis, DNA repair and primary metabolism. Interestingly, mutation of the effector gene, hopAU1, led to an increase in virulence of Psm R2.
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16
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Gossner MM, Beenken L, Arend K, Begerow D, Peršoh D. Insect herbivory facilitates the establishment of an invasive plant pathogen. ISME COMMUNICATIONS 2021; 1:6. [PMID: 37938649 PMCID: PMC9723786 DOI: 10.1038/s43705-021-00004-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 05/17/2023]
Abstract
Plants can be severely affected by insect herbivores and phytopathogenic fungi, but interactions between these plant antagonists are poorly understood. We analysed the impact of feeding damage by the abundant herbivore Orchestes fagi on infection rates of beech (Fagus sylvatica) leaves with Petrakia liobae, an invasive plant pathogenic fungus. The fungus was not detected in hibernating beetles, indicating that O. fagi does not serve as vector for P. liobae, at least not between growing seasons. Abundance of the fungus in beech leaves increased with feeding damage of the beetle and this relationship was stronger for sun-exposed than for shaded leaves. A laboratory experiment revealed sun-exposed leaves to have thicker cell walls and to be more resistant to pathogen infection than shaded leaves. Mechanical damage significantly increased frequency and size of necroses in the sun, but not in shade leaves. Our findings indicate that feeding damage of adult beetles provides entry ports for fungal colonization by removal of physical barriers and thus promotes infection success by pathogenic fungi. Feeding activity by larvae probably provides additional nutrient sources or eases access to substrates for the necrotrophic fungus. Our study exemplifies that invasive pathogens may benefit from herbivore activity, which may challenge forest health in light of climate change.
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Affiliation(s)
- Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Center for Food and Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
- ETH Zurich, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Zurich, Switzerland.
| | - Ludwig Beenken
- Forest Protection, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kirstin Arend
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany
| | - Dominik Begerow
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany
| | - Derek Peršoh
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany.
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17
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Rabiey M, Roy SR, Holtappels D, Franceschetti L, Quilty BJ, Creeth R, Sundin GW, Wagemans J, Lavigne R, Jackson RW. Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry. Microb Biotechnol 2020; 13:1428-1445. [PMID: 32383813 PMCID: PMC7415359 DOI: 10.1111/1751-7915.13585] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/14/2022] Open
Abstract
Bacterial canker is a major disease of Prunus species, such as cherry (Prunus avium). It is caused by Pseudomonas syringae pathovars, including P. syringae pv. syringae (Pss) and P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2). Concerns over the environmental impact of, and the development of bacterial resistance to, traditional copper controls calls for new approaches to disease management. Bacteriophage-based biocontrol could provide a sustainable and natural alternative approach to combat bacterial pathogens. Therefore, seventy phages were isolated from soil, leaf and bark of cherry trees in six locations in the south east of England. Subsequently, their host range was assessed against strains of Pss, Psm1 and Psm2. While these phages lysed different Pss, Psm and some other P. syringae pathovar isolates, they did not infect beneficial bacteria such as Pseudomonas fluorescens. A subset of thirteen phages were further characterized by genome sequencing, revealing five distinct clades in which the phages could be clustered. No known toxins or lysogeny-associated genes could be identified. Using bioassays, selected phages could effectively reduce disease progression in vivo, both individually and in cocktails, reinforcing their potential as biocontrol agents in agriculture.
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Affiliation(s)
- Mojgan Rabiey
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
| | - Shyamali R. Roy
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
| | | | - Linda Franceschetti
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
| | - Billy J. Quilty
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
| | - Ryan Creeth
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
| | | | - Jeroen Wagemans
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenLeuvenBelgium
| | - Rob Lavigne
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenLeuvenBelgium
| | - Robert W. Jackson
- School of Biological SciencesUniversity of ReadingKnight BuildingReadingRG6 6AJUK
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
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18
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Hulin MT, Jackson RW, Harrison RJ, Mansfield JW. Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits. PLANT PATHOLOGY 2020; 69:962-978. [PMID: 32742023 PMCID: PMC7386918 DOI: 10.1111/ppa.13189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 05/10/2023]
Abstract
Bacterial canker disease is a major limiting factor in the growing of cherry and other Prunus species worldwide. At least five distinct clades within the bacterial species complex Pseudomonas syringae are known to be causal agents of the disease. The different pathogens commonly coexist in the field. Reducing canker is a challenging prospect as the efficacy of chemical controls and host resistance may vary against each of the diverse clades involved. Genomic analysis has revealed that the pathogens use a variable repertoire of virulence factors to cause the disease. Significantly, strains of P. syringae pv. syringae possess more genes for toxin biosynthesis and fewer encoding type III effector proteins. There is also a shared pool of key effector genes present on mobile elements such as plasmids and prophages that may have roles in virulence. By contrast, there is evidence that absence or truncation of certain effector genes, such as hopAB, is characteristic of cherry pathogens. Here we highlight how recent research, underpinned by the earlier epidemiological studies, is allowing significant progress in our understanding of the canker pathogens. This fundamental knowledge, combined with emerging insights into host genetics, provides the groundwork for development of precise control measures and informed approaches to breed for disease resistance.
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Affiliation(s)
| | - Robert W. Jackson
- Birmingham Institute of Forest Research (BIFoR), University of BirminghamBirminghamUK
- School of Biosciences, University of BirminghamBirminghamUK
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19
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Bophela KN, Petersen Y, Bull CT, Coutinho TA. Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa. PLANT DISEASE 2020; 104:882-892. [PMID: 31935341 DOI: 10.1094/pdis-05-19-1102-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.
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Affiliation(s)
- Khumbuzile N Bophela
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Yolanda Petersen
- Crop Development Division, Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA 16801, U.S.A
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield 0028, Pretoria, South Africa
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20
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Li CX, Fan YF, Luan W, Dai Y, Wang MX, Wei CM, Wang Y, Tao X, Mao P, Ma XR. Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity. MICROBIAL ECOLOGY 2019; 77:967-979. [PMID: 30357425 DOI: 10.1007/s00248-018-1273-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.
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Affiliation(s)
- Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yan-Fen Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Xiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Mei Wei
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
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21
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Ruinelli M, Blom J, Smits THM, Pothier JF. Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp. BMC Genomics 2019; 20:172. [PMID: 30836956 PMCID: PMC6402114 DOI: 10.1186/s12864-019-5555-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 02/22/2019] [Indexed: 11/22/2022] Open
Abstract
Background Diseases on Prunus spp. have been associated with a large number of phylogenetically different pathovars and species within the P. syringae species complex. Despite their economic significance, there is a severe lack of genomic information of these pathogens. The high phylogenetic diversity observed within strains causing disease on Prunus spp. in nature, raised the question whether other strains or species within the P. syringae species complex were potentially pathogenic on Prunus spp. Results To gain insight into the genomic potential of adaptation and virulence in Prunus spp., a total of twelve de novo whole genome sequences of P. syringae pathovars and species found in association with diseases on cherry (sweet, sour and ornamental-cherry) and peach were sequenced. Strains sequenced in this study covered three phylogroups and four clades. These strains were screened in vitro for pathogenicity on Prunus spp. together with additional genome sequenced strains thus covering nine out of thirteen of the currently defined P. syringae phylogroups. Pathogenicity tests revealed that most of the strains caused symptoms in vitro and no obvious link was found between presence of known virulence factors and the observed pathogenicity pattern based on comparative genomics. Non-pathogenic strains were displaying a two to three times higher generation time when grown in rich medium. Conclusion In this study, the first set of complete genomes of cherry associated P. syringae strains as well as the draft genome of the quarantine peach pathogen P. syringae pv. persicae were generated. The obtained genomic data were matched with phenotypic data in order to determine factors related to pathogenicity to Prunus spp. Results of this study suggest that the inability to cause disease on Prunus spp. in vitro is not the result of host specialization but rather linked to metabolic impairments of individual strains. Electronic supplementary material The online version of this article (10.1186/s12864-019-5555-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michela Ruinelli
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland.
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences, CH-8820, Wädenswil, Switzerland
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22
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Hulin MT, Armitage AD, Vicente JG, Holub EB, Baxter L, Bates HJ, Mansfield JW, Jackson RW, Harrison RJ. Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium). THE NEW PHYTOLOGIST 2018; 219:672-696. [PMID: 29726587 DOI: 10.1111/nph.15182] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/22/2018] [Indexed: 05/12/2023]
Abstract
Genome-wide analyses of the effector- and toxin-encoding genes were used to examine the phylogenetics and evolution of pathogenicity amongst diverse strains of Pseudomonas syringae causing bacterial canker of cherry (Prunus avium), including pathovars P. syringae pv morsprunorum (Psm) races 1 and 2, P. syringae pv syringae (Pss) and P. syringae pv avii. Phylogenetic analyses revealed Psm races and P. syringae pv avii clades were distinct and were each monophyletic, whereas cherry-pathogenic strains of Pss were interspersed amongst strains from other host species. A maximum likelihood approach was used to predict effectors associated with pathogenicity on cherry. Pss possesses a smaller repertoire of type III effectors but has more toxin biosynthesis clusters than Psm and P. syringae pv avii. Evolution of cherry pathogenicity was correlated with gain of genes such as hopAR1 and hopBB1 through putative phage transfer and horizontal transfer respectively. By contrast, loss of the avrPto/hopAB redundant effector group was observed in cherry-pathogenic clades. Ectopic expression of hopAB and hopC1 triggered the hypersensitive reaction in cherry leaves, confirming computational predictions. Cherry canker provides a fascinating example of convergent evolution of pathogenicity that is explained by the mix of effector and toxin repertoires acting on a common host.
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Affiliation(s)
- Michelle T Hulin
- NIAB EMR, New Road, East Malling, ME19 6BJ, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK
| | | | - Joana G Vicente
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Laura Baxter
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | | | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK
| | - Richard J Harrison
- NIAB EMR, New Road, East Malling, ME19 6BJ, UK
- School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK
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23
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Baltrus DA, Orth KN. Understanding genomic diversity in Pseudomonas syringae throughout the forest and on the trees. THE NEW PHYTOLOGIST 2018; 219:482-484. [PMID: 29927494 DOI: 10.1111/nph.15269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Kelly N Orth
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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