Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734
Abstract Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced a...
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BMC
2022-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08966-y |
| _version_ | 1798018195253100544 |
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| author | Arburon Sulja Joël F. Pothier Jochen Blom Chiaraluce Moretti Roberto Buonaurio Fabio Rezzonico Theo H. M. Smits |
| author_facet | Arburon Sulja Joël F. Pothier Jochen Blom Chiaraluce Moretti Roberto Buonaurio Fabio Rezzonico Theo H. M. Smits |
| author_sort | Arburon Sulja |
| collection | DOAJ |
| description | Abstract Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5′396′424 bp, containing one circular chromosome and four large circular plasmids. The aim of this study was to identify genomic features that could play a potential role in the interaction between P. agglomerans DAPP-PG 734 and P. savastanoi pv. savastanoi DAPP-PG 722. For this purpose, a comparative genomic analysis between the genome of P. agglomerans DAPP-PG 734 and those of related Pantoea spp. was carried out. In P. agglomerans DAPP-PG 734, gene clusters for the synthesis of the Hrp-1 type III secretion system (T3SS), type VI secretion systems (T6SS) and autoinducer, which could play an important role in a plant-pathogenic community enhancing knot formation in olive trees, were identified. Additional gene clusters for the biosynthesis of two different antibiotics, namely dapdiamide E and antibiotic B025670, which were found in regions between integrative conjugative elements (ICE), were observed. The in-depth analysis of the whole genome suggested a characterization of the P. agglomerans DAPP-PG 734 isolate as endophytic bacterium with biocontrol activity rather than as a plant pathogen. |
| first_indexed | 2024-04-11T16:20:02Z |
| format | Article |
| id | doaj.art-7425d5cf3d3a4bb78a7c1cf5b569f754 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T16:20:02Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7425d5cf3d3a4bb78a7c1cf5b569f7542022-12-22T04:14:25ZengBMCBMC Genomics1471-21642022-11-0123111510.1186/s12864-022-08966-yComparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734Arburon Sulja0Joël F. Pothier1Jochen Blom2Chiaraluce Moretti3Roberto Buonaurio4Fabio Rezzonico5Theo H. M. Smits6Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW)Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW)Bioinformatics and Systems Biology, Justus-Liebig-University GiessenDipartimento Di Scienze Agrarie, Alimentari E Ambientali, Università Degli Studi Di PerugiaDipartimento Di Scienze Agrarie, Alimentari E Ambientali, Università Degli Studi Di PerugiaEnvironmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW)Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW)Abstract Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5′396′424 bp, containing one circular chromosome and four large circular plasmids. The aim of this study was to identify genomic features that could play a potential role in the interaction between P. agglomerans DAPP-PG 734 and P. savastanoi pv. savastanoi DAPP-PG 722. For this purpose, a comparative genomic analysis between the genome of P. agglomerans DAPP-PG 734 and those of related Pantoea spp. was carried out. In P. agglomerans DAPP-PG 734, gene clusters for the synthesis of the Hrp-1 type III secretion system (T3SS), type VI secretion systems (T6SS) and autoinducer, which could play an important role in a plant-pathogenic community enhancing knot formation in olive trees, were identified. Additional gene clusters for the biosynthesis of two different antibiotics, namely dapdiamide E and antibiotic B025670, which were found in regions between integrative conjugative elements (ICE), were observed. The in-depth analysis of the whole genome suggested a characterization of the P. agglomerans DAPP-PG 734 isolate as endophytic bacterium with biocontrol activity rather than as a plant pathogen.https://doi.org/10.1186/s12864-022-08966-yGenomeBiocontrolOlive knot diseaseAntibiotics biosynthesisIntegrative conjugative elementICE |
| spellingShingle | Arburon Sulja Joël F. Pothier Jochen Blom Chiaraluce Moretti Roberto Buonaurio Fabio Rezzonico Theo H. M. Smits Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 BMC Genomics Genome Biocontrol Olive knot disease Antibiotics biosynthesis Integrative conjugative element ICE |
| title | Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 |
| title_full | Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 |
| title_fullStr | Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 |
| title_full_unstemmed | Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 |
| title_short | Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734 |
| title_sort | comparative genomics to examine the endophytic potential of pantoea agglomerans dapp pg 734 |
| topic | Genome Biocontrol Olive knot disease Antibiotics biosynthesis Integrative conjugative element ICE |
| url | https://doi.org/10.1186/s12864-022-08966-y |
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