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Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R, Kvitko BH, Smits THM, Venter SN, Coutinho TA, Heath LS, Palmer M, Vinatzer BA. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999. [PMID: 38029109 PMCID: PMC10665919 DOI: 10.3389/fmicb.2023.1254999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
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Affiliation(s)
- Katherine C. Crosby
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mariah Rojas
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Theo H. M. Smits
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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2
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White RT, Taylor W, Klukowski N, Vaughan-Higgins R, Williams E, Petrovski S, Rose JJA, Sarker S. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring ( Pezoporus flaviventris). Microb Genom 2023; 9:001101. [PMID: 37665208 PMCID: PMC10569725 DOI: 10.1099/mgen.0.001101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023] Open
Abstract
Pantoea stewartii, a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle (Chaetocnema pulicaria) being the primary carrier. P. stewartii is a bacterium belonging to the order Enterobacterales and can lead to crop diseases that have a significant economic impact worldwide. Due to its high potential for spread, P. stewartii is classified as a quarantine organism in numerous countries. Despite its impact on agriculture, the limited genome sequences of P. stewartii hamper understanding of its pathogenicity and host specificity, and the development of effective control strategies. In this study, a P. stewartii strain (C10109_Jinnung) was discovered in the faecal matter of the Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris) in Australia, which to our knowledge is the first reported P. stewartii genome from a bird source. Whole-genome sequencing and phylogenomic analysis of strain C10109_Jinnung, obtained from a captive psittacine, provides new insights into the genetic diversity and potential transmission route for the spread of P. stewartii beyond insects and plants, where P. stewartii is typically studied. Our findings provide new insights into the potential transmission route for spread of P. stewartii and expand the known transmission agents beyond insects and plants. Expanding the catalogue of P. stewartii genomes is fundamental to improving understanding of the pathogenicity, evolution and dissemination, and to develop effective control strategies to reduce the substantial economic losses associated with P. stewartii in various crops and the potential impact of endangered animal species.
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Affiliation(s)
- Rhys T. White
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - William Taylor
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Natalie Klukowski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | | | - Ernest Williams
- Institute of Environmental Science and Research, Wallaceville, New Zealand
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J. A. Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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Zhao M, Shin GY, Stice S, Bown JL, Coutinho T, Metcalf WW, Gitaitis R, Kvitko B, Dutta B. A Novel Biosynthetic Gene Cluster Across the Pantoea Species Complex Is Important for Pathogenicity in Onion. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:176-188. [PMID: 36534063 PMCID: PMC10433531 DOI: 10.1094/mpmi-08-22-0165-r] [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] [Indexed: 06/01/2023]
Abstract
Onion center rot is caused by at least four species of genus Pantoea (P. ananatis, P. agglomerans, P. allii, and P. stewartii subsp. indologenes). Critical onion pathogenicity determinants for P. ananatis were recently described, but whether those determinants are common among other onion-pathogenic Pantoea species remains unknown. In this work, we report onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. We identified two distinct secondary metabolite biosynthetic gene clusters present separately in different strains of onion-pathogenic P. stewartii subsp. indologenes. One cluster is similar to the previously described HiVir phosphonate biosynthetic cluster identified in P. ananatis and another is a novel putative phosphonate biosynthetic gene cluster, which we named Halophos. The Halophos gene cluster was also identified in P. allii strains. Both clusters are predicted to be phosphonate biosynthetic clusters based on the presence of a characteristic phosphoenolpyruvate phosphomutase (pepM) gene. The deletion of the pepM gene from either HiVir or Halophos clusters in P. stewartii subsp. indologenes caused loss of necrosis on onion leaves and red onion scales and resulted in significantly lower bacterial populations compared with the corresponding wild-type and complemented strains. Seven (halB to halH) of 11 genes (halA to halK) in the Halophos gene cluster are required for onion necrosis phenotypes. The onion nonpathogenic strain PNA15-2 (P. stewartii subsp. indologenes) gained the capacity to cause foliar necrosis on onion via exogenous expression of a minimal seven-gene Halophos cluster (genes halB to halH). Furthermore, cell-free culture filtrates of PNA14-12 expressing the intact Halophos gene cluster caused necrosis on onion leaves consistent with the presence of a secreted toxin. Based on the similarity of proteins to those with experimentally determined functions, we are able to predict most of the steps in Halophos biosynthesis. Together, these observations indicate that production of the toxin phosphonate seems sufficient to account for virulence of a variety of different Pantoea strains, although strains differ in possessing a single but distinct phosphonate biosynthetic cluster. Overall, this is the first report of onion pathogenicity determinants in P. stewartii subsp. indologenes and P. allii. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mei Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Shaun Stice
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Jonathon Luke Bown
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Teresa Coutinho
- The Genomics Research Institute, University of Pretoria, Hatfield, South Africa
| | - William W. Metcalf
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL
| | - Ron Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton GA USA
| | - Brian Kvitko
- Department of Plant Pathology, University of Georgia, Athens GA USA
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton GA USA
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Zhao M, Tyson C, Gitaitis R, Kvitko B, Dutta B. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front Microbiol 2022; 13:1054813. [DOI: 10.3389/fmicb.2022.1054813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch’s postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.
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Lorenzi AS, Bonatelli ML, Chia MA, Peressim L, Quecine MC. Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook. Microorganisms 2022; 10:microorganisms10102072. [PMID: 36296348 PMCID: PMC9610544 DOI: 10.3390/microorganisms10102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2022] Open
Abstract
Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.
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Affiliation(s)
- Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Maria Letícia Bonatelli
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany
| | - Mathias Ahii Chia
- Department of Botany, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Leonardo Peressim
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
- Correspondence:
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Shin GY, Smith A, Coutinho TA, Dutta B, Kvitko BH. Validation of Species-Specific PCR Assays for the Detection of Pantoea ananatis, P. agglomerans, P. allii, and P. stewartii. PLANT DISEASE 2022; 106:2563-2570. [PMID: 35171633 DOI: 10.1094/pdis-08-21-1810-sc] [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: 06/14/2023]
Abstract
Species of Pantoea represent a group of plant pathogenic bacteria that infect a variety of agro-economically important plant species. Among these, a complex of P. ananatis, P. allii, P. agglomerans, and P. stewartii subsp. indologenes cause center rot in onion, resulting in significant economic losses. As species of Pantoea are phenotypically closely related, identification of Pantoea species relies on the sequencing and phylogenetic analysis of housekeeping genes. To aid in rapid identification of Pantoea species, efforts have been made in developing species-specific primers to be used in PCR assays. In the current study, two P. ananatis, one P. allii, one P. agglomerans, and three P. stewartii published primers as well as newly developed P. agglomerans PagR primers were evaluated for their specificity against 79 Pantoea strains, belonging to 15 different species. To ensure that selected primers were evaluated against accurately identified species, sequencing and phylogenetic analysis of housekeeping gene infB were conducted. Thereafter, PCR assays using selected species-specific primers were performed. The results showed that previously described P. ananatis-specific PANA_1008; P. allii-specific allii-leuS; P. stewartii-specific PANST_rpoB, 3614galE, and DC283galE primers; and one newly designed P. agglomerans-specific PagR primer pair were highly specific for their target Pantoea species. They accurately identified these strains into their species and, in some cases, their subspecies level. The findings of the current study will facilitate rapid and reliable identification of P. ananatis, P. agglomerans, P. allii, and P. stewartii.
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Affiliation(s)
- Gi Yoon Shin
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
| | - Amy Smith
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
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Khanal M, Timilsina S, Bhatta BP, Bophela K, Coutinho T, Cochran K, Malla S. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int J Syst Evol Microbiol 2022; 72. [PMID: 35442877 DOI: 10.1099/ijsem.0.005311] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20T (99.3 %), Pseudomonas corrugata CFBP 2431T (99.2 %), and Pseudomonas viciae 11K1T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172T represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172T (=NCIMB 15426T=CIP 112022T).
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA.,Present address: Charles River Laboratories, Newark, DE, USA
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
| | - Khumbuzile Bophela
- Department of Plant and Soil Sciences, University of Pretoria, 0002 Pretoria, South Africa
| | - Teresa Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa
| | - Kimberly Cochran
- Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas 77843, USA.,Texas A&M AgriLife Research and Extension Center, Uvalde, Texas 78801, USA
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Agarwal G, Gitaitis RD, Dutta B. Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer. Microorganisms 2021; 9:1761. [PMID: 34442840 PMCID: PMC8399035 DOI: 10.3390/microorganisms9081761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.
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Affiliation(s)
- Gaurav Agarwal
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
| | | | - Bhabesh Dutta
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA;
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