Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia
Abstract Background A zucchini disease outbreak with unusual symptoms associated with Pseudomonas syringae clade 2b was identified in Bundaberg, Australia during autumn 2016. To investigate the genetic diversity of the 11 Australian isolates obtained from the outbreak, the genomes were compared to t...
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| Format: | Article |
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BMC
2022-11-01
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| Series: | BMC Microbiology |
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| Online Access: | https://doi.org/10.1186/s12866-022-02678-9 |
| _version_ | 1811186920388034560 |
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| author | Noel Djitro Rebecca Roach Rachel Mann Paul R. Campbell Brendan Rodoni Cherie Gambley |
| author_facet | Noel Djitro Rebecca Roach Rachel Mann Paul R. Campbell Brendan Rodoni Cherie Gambley |
| author_sort | Noel Djitro |
| collection | DOAJ |
| description | Abstract Background A zucchini disease outbreak with unusual symptoms associated with Pseudomonas syringae clade 2b was identified in Bundaberg, Australia during autumn 2016. To investigate the genetic diversity of the 11 Australian isolates obtained from the outbreak, the genomes were compared to the publicly available P. syringae strains in phylogroup 2. Results Average nucleotide identity refined the P. syringae clade 2b-a into four clusters (Cluster A, B, C1 and C2), an expansion from the previously identified A, B and C. Australian isolates were in Cluster A, C1 and C2. Genomic analyses highlighted several key factors that may contribute to the virulence of these isolates. Six orthologous groups, including three virulence factors, were associated with P. syringae phylogroup 2 cucurbit-infecting strains. A region of genome plasticity analysis identified a type VI secretion system pathway in clade 2b-a strains which could also contribute to virulence. Pathogenicity assays on isolates KL004-k1, KFR003-1 and 77-4C, as representative isolates of Cluster A, C1 and C2, respectively, determined that all three isolates can infect pumpkin, squash, watermelon and zucchini var. Eva with different levels of disease severity. Subsequently, type III effectors were investigated and four type III effectors (avrRpt2, hopZ5, hopC1 and hopH1) were associated with host range. The hopZ effector family was also predicted to be associated with disease severity. Conclusions This study refined the taxonomy of the P. syringae clade 2b-a, supported the association between effector profile and pathogenicity in cucurbits established in a previous study and provides new insight into important genomic features of these strains. This study also provided a detailed and comprehensive resource for future genomic and functional studies of these strains. |
| first_indexed | 2024-04-11T13:54:22Z |
| format | Article |
| id | doaj.art-e6689bc5a81f4928b0ea81adf6e70b93 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-11T13:54:22Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-e6689bc5a81f4928b0ea81adf6e70b932022-12-22T04:20:26ZengBMCBMC Microbiology1471-21802022-11-0122111410.1186/s12866-022-02678-9Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in AustraliaNoel Djitro0Rebecca Roach1Rachel Mann2Paul R. Campbell3Brendan Rodoni4Cherie Gambley5School of Applied Systems Biology, La Trobe UniversityDepartment of Agriculture and Fisheries, Ecosciences PrecinctAgriculture Victoria Research, Department of Jobs, Precincts and RegionsDepartment of Agriculture and Fisheries, Ecosciences PrecinctAgriculture Victoria Research, Department of Jobs, Precincts and RegionsDepartment of Agriculture and Fisheries, Maroochy Research FacilityAbstract Background A zucchini disease outbreak with unusual symptoms associated with Pseudomonas syringae clade 2b was identified in Bundaberg, Australia during autumn 2016. To investigate the genetic diversity of the 11 Australian isolates obtained from the outbreak, the genomes were compared to the publicly available P. syringae strains in phylogroup 2. Results Average nucleotide identity refined the P. syringae clade 2b-a into four clusters (Cluster A, B, C1 and C2), an expansion from the previously identified A, B and C. Australian isolates were in Cluster A, C1 and C2. Genomic analyses highlighted several key factors that may contribute to the virulence of these isolates. Six orthologous groups, including three virulence factors, were associated with P. syringae phylogroup 2 cucurbit-infecting strains. A region of genome plasticity analysis identified a type VI secretion system pathway in clade 2b-a strains which could also contribute to virulence. Pathogenicity assays on isolates KL004-k1, KFR003-1 and 77-4C, as representative isolates of Cluster A, C1 and C2, respectively, determined that all three isolates can infect pumpkin, squash, watermelon and zucchini var. Eva with different levels of disease severity. Subsequently, type III effectors were investigated and four type III effectors (avrRpt2, hopZ5, hopC1 and hopH1) were associated with host range. The hopZ effector family was also predicted to be associated with disease severity. Conclusions This study refined the taxonomy of the P. syringae clade 2b-a, supported the association between effector profile and pathogenicity in cucurbits established in a previous study and provides new insight into important genomic features of these strains. This study also provided a detailed and comprehensive resource for future genomic and functional studies of these strains.https://doi.org/10.1186/s12866-022-02678-9Pseudomonas syringaeCucurbitaceaeComparative genomics |
| spellingShingle | Noel Djitro Rebecca Roach Rachel Mann Paul R. Campbell Brendan Rodoni Cherie Gambley Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia BMC Microbiology Pseudomonas syringae Cucurbitaceae Comparative genomics |
| title | Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia |
| title_full | Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia |
| title_fullStr | Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia |
| title_full_unstemmed | Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia |
| title_short | Comparative genomics and genomic diversity of Pseudomonas syringae clade 2b-a in Australia |
| title_sort | comparative genomics and genomic diversity of pseudomonas syringae clade 2b a in australia |
| topic | Pseudomonas syringae Cucurbitaceae Comparative genomics |
| url | https://doi.org/10.1186/s12866-022-02678-9 |
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