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Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024; 16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Moon YJ, Lee SY, Kim U, Oh SW. Naked-eye detection with loop-mediated isothermal amplification for P. carotovorum subsp. carotovorum in agricultural products. Food Sci Biotechnol 2024; 33:203-209. [PMID: 38186613 PMCID: PMC10766909 DOI: 10.1007/s10068-023-01315-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 01/09/2024] Open
Abstract
Pectobacterium carotovorum causing soft-rot disease requires on-site detection before the distribution of agricultural products. Loop-mediated isothermal amplification (LAMP), which is resistant to food inhibitors, is known for its high detection sensitivity for pathogens and when coupled with lateral flow immunoassay (LFA) enables visualizations. For detection of soft-rot disease, we developed a LAMP-LFA system targeting 16S ribosomal RNA, a partial sequence gene of P. carotovorum subsp. carotovorum. The LAMP-LFA was performed at 60 °C for 50 min followed by hybridization of digoxygenin-labeled LAMP amplicon and biotinylated probe. Detection sensitivity was 3.22 × 101 CFU/mL in pure culture, which specifically detected the target. In Chinese cabbage and potato, the target was detected up to low levels of 1.57 × 102 CFU/g and 1.29 × 102 CFU/g, respectively. This study showed potential applicability as a sensitive point-of-care system for soft-rot disease bacteria detection in agricultural products. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01315-z.
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Affiliation(s)
- Ye-Ji Moon
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - So-Young Lee
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Unji Kim
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
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Hong SM, Ten LN, Park KT, Back CG, Waleron M, Kang IK, Lee SY, Jung HY. Pectobacterium jejuense sp. nov. Isolated from Cucumber Stem Tissue. Curr Microbiol 2023; 80:308. [PMID: 37528256 DOI: 10.1007/s00284-023-03419-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/16/2023] [Indexed: 08/03/2023]
Abstract
A single Pectobacterium-like strain named 13-115T was isolated from a specimen of diseased cucumber stem tissue collected on Jeju Island, South Korea. The strain presented a rod-like shape and was negative for Gram staining. When grown on R2A medium at 25 °C, strain 13-115T formed round, convex and white colonies. This strain showed growth at temperatures ranging from 10 to 30 °C and tolerated a pH range of 6-9. The strain could also tolerate NaCl concentrations up to 5%. Analysis of the 16S rRNA gene sequence revealed that strain 13-115T exhibited similarity of over 99% with Pectobacterium brasiliense, P. carotovorum, P. polaris, and P. parvum. By conducting multilocus sequence analyses using dnaX, leuS, and recA genes, a separate phylogenetic lineage was discovered between strain 13-115T and other members of the genus Pectobacterium. Moreover, the strain showed relatively low in silico DNA-DNA hybridization (<60.6%) and average nucleotide identity (ANI) (<94.9%) values with recognized Pectobacterium species. The isolate has a genome size of 5,069,478 bp and a genomic G + C content of 52.04 mol%. Major fatty acids identified in the strain included C16:0 (28.99%), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c; 28.85%), and C18:1 ω7c (19.01%). Pathogenicity assay confirmed that the novel strain induced soft rot symptoms in cucumber plants and Koch's postulates were fulfilled. Molecular analysis and phenotypic data indicated that strain 13-115T could be classified as a new species within the Pectobacterium genus, which has been named Pectobacterium jejuense. The type strain is 13-115T (= KCTC 92800T = JCM 35940T).
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Affiliation(s)
- Soo-Min Hong
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Leonid N Ten
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyoung-Taek Park
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Chang-Gi Back
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Malgorzata Waleron
- Intercollegiate Faculty of Biotechnology UG and MUG, 58 Abrahama Street, 80-307, Gdansk, Poland
| | - In-Kyu Kang
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Czajkowski R, Arif M, Chapman T. Editorial: Genome-wide analyses of Pectobacterium and Dickeya species, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1224293. [PMID: 37332713 PMCID: PMC10275604 DOI: 10.3389/fpls.2023.1224293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Affiliation(s)
- Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology Univesity of Gdansk (UG) and Medical University of Gdansk (MUG), University of Gdansk, Gdansk, Poland
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Toni Chapman
- Biosecurity and Food Safety, New South Wales (NSW) Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, NSW, Australia
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DeLude A, Wells R, Boomla S, Chuang SC, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona F, Ali ME, Odani J, Bingham JP, Jenkins DM, Fletcher J, Stack JP, Alvarez AM, Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Sci Rep 2022; 12:19193. [PMID: 36357509 PMCID: PMC9649655 DOI: 10.1038/s41598-022-22023-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18-20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.
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Affiliation(s)
- Anuhea DeLude
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Riley Wells
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Sherine Boomla
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shu-Cheng Chuang
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Frank Urena
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Aaron Shipman
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Noelle Rubas
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Donna Lee Kuehu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Buster Bickerton
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Taylor Peterson
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shefali Dobhal
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Dario Arizala
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Diksha Klair
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Francisco Ochoa-Corona
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - Md Emran Ali
- grid.213876.90000 0004 1936 738XDepartment of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Jenee Odani
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jon-Paul Bingham
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Daniel M. Jenkins
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jacqueline Fletcher
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - James P. Stack
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Anne M. Alvarez
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Mohammad Arif
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
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