We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosome and two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pantocin A biosynthesis genes was identified

Abelli, Azzurra

Blom, Jochen

Duffy, Brion

Goesmann, Alexander

Kron Morelli, Roberto

Rezzonico, Fabio

Smits, Theo H.M.

Vanneste, Joël L.

PubMed

ZHAW digitalcollection

Draft Genome Sequence of the Commercial Biocontrol Strain Pantoeaagglomerans P10cTheo H. M. Smits,a Fabio Rezzonico,a Jochen Blom,b Alexander Goesmann,b Azzurra Abelli,c Roberto Kron Morelli,c Joël L. Vanneste,dBrion DuffyaEnvironmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zürich University of Applied Sciences ZHAW, Wädenswil,Switzerlanda; Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germanyb; Agrifutur, Alfianello (Brescia), Italyc; The New Zealand Institute for Plant &Food Research Limited, Ruakura, Hamilton, New ZealanddWe report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosomeand two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pan-tocin A biosynthesis genes was identified.Received 19 October 2015 Accepted 23 October 2015 Published 10 December 2015Citation Smits THM, Rezzonico F, Blom J, Goesmann A, Abelli A, Kron Morelli R, Vanneste JL, Duffy B. 2015. Draft genome sequence of the commercial biocontrol strainPantoea agglomerans P10c. Genome Announc 3(6):e01448-15. doi:10.1128/genomeA.01448-15.Copyright © 2015 Smits et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Theo H. M. Smits, theo.smits@zhaw.ch.Pantoea agglomerans is a ubiquitous bacterial species oftenfound in association with plants. Several strains of P. agglo-merans have been found to control fungal or bacterial postharvestdiseases (1, 2) and to reduce disease incidence in the orchards andfields, for example, basal kernel blight of barley caused by Pseu-domonas syringae pv. syringae (3) or fire blight caused by Erwiniaamylovora (2, 4, 5). P. agglomerans is one of the most commonbacteria isolated fromfire blight-susceptible plant species (4). Themechanisms by which P. agglomerans suppresses plant pathogensinclude nutritional competition and preemptive exclusion incombination with a variety of antibacterial organic acids and pep-tide antibiotics (5–9).P. agglomerans P10c was isolated from pear blossoms in NewZealand. Selected for its exceptional ability to rapidly colonizeapple and pear flowers and to suppress fire blight disease (10), ithas been developed as a commercial biocontrol agent (BlossomBless; Agrinova NZ Limited). Whole-genome sequencing (Illu-mina MiSeq 2  300-bp shotgun sequencing) yielded 2,693,476reads representing ~160 genome coverage. The genomes wereassembled using a combination of de novo assembly with NGenversion 4 (DNAStar, Madison, WI) and comparisons with avail-able P. agglomerans genomes (11–13) using Mauve version 2.3.1(14). The final assembly consists of a draft chromosome (16 contigsfor a total 4,034,977bp) and twoclosedplasmids, pPag1 (182,134bp)and pPag3 (558,805 bp). All sequenceswere annotated automaticallyusing GenDB (15), with manual optimization (16).The plasmids pPag1 and pPag3 are relatives of the respectivePantoea vagans C9-1 plasmids (16). Plasmid pPag3 is a group Imember of the large Pantoea plasmid 1 family (LPP-1) of plas-mids, most closely related to the plasmids of other sequencedP. agglomerans strains (11). Plasmid pPag1 is present in all P.agglomerans genomes studied to date but also shows some varia-tion between strains.Comparative analysis using EDGAR (17) confirmed that thegenomes of P. agglomerans strains are highly collinear. A distinctgenomic island integrated in the mutS N-terminus was identifiedcontaining the pantocin A biosynthetic genes (18), one potentialmechanism of action in biocontrol. Overall, this genomic island isrelated to the pantocin A genomic island of P. vagans C9-1, withslight variations (16).The genome sequence of P. agglomerans P10c will give us theopportunity to improve strain-specific fingerprinting importantfor registration and intellectual property protection of active bio-logical agents in commercial biocontrol products. Moreover, thisprovides a foundation to elucidate mechanisms of action and theregulation of antimicrobial compound biosynthesis, which inturn can be exploited to improve practical and commercial valuethrough the optimization of formulation technology, perfor-mance reliability, and efficacy of this biocontrol strain.Nucleotide sequence accession numbers. The whole-genomeshotgun project of P. agglomerans P10c has been deposited atDDBJ/EMBL/GenBank under the accession no. LIME00000000.The version described in this paper is version LIME01000000.The finished plasmid sequences received accession numbersLIME01000017 (P10c pPag1) and LIME01000018 (P10c pPag3).ACKNOWLEDGMENTSThis genome project was supported by the European Union’s SeventhFramework Programme for Research, Technological Development andDemonstration under grant agreement no. 613678 (DROPSA), theEUPHRESCO Era-Net pilot project “PhytFire,” and the Department ofLife Sciences and Facility Management of ZHAW.REFERENCES1. Bonaterra A, Mari M, Casalini L, Montesinos E. 2003. Biological controlof Monilinia laxa and Rhizopus stolonifer in postharvest of stone fruit byPantoea agglomerans EPS125 and putative mechanisms of antagonism.Int J Food Microbiol 84:93–104. http://dx.doi.org/10.1016/S0168-1605(02)00403-8.2. Vanneste JL, Cornish DA, Yu J, Voyle MD. 1998. A microcin producedby a strain of Erwinia herbicola is involved in biological control of firecrossmarkGenome AnnouncementsNovember/December 2015 Volume 3 Issue 6 e01448-15 genomea.asm.org 1blight and soft rot caused by Erwinia sp. Acta Hortic 513:39–46. http://dx.doi.org/10.17660/ActaHortic.1998.513.3.3. Braun-Kiewnick A, Jacobsen BJ, Sands DC. 2000. Biological control ofPseudomonas syringae pv. syringae, the causal agent of basal kernel blightof barley, by antagonistic Pantoea agglomerans. Phytopathology 90:368–375. http://dx.doi.org/10.1094/PHYTO.2000.90.4.368.4. Johnson KB, Stockwell VO. 1998. Management of fire blight: a case studyin microbial ecology. Annu Rev Phytopathol 36:227–248. http://dx.doi.org/10.1146/annurev.phyto.36.1.227.5. Vanneste JL. 1996. Honey bees and epiphytic bacteria to control fireblight, a bacterial disease of apple and pear. Biocontrol News Inform 17:67N–78N.6. Vanneste JL, Yu J, Beer SV. 1992. Role of antibiotic production byErwinia herbicola Eh252 in biological control of Erwinia amylovora. J Bac-teriol 174:2785–2796.7. Stockwell VO, Johnson KB, Sugar D, Loper JE. 2010. Control of fireblight by Pseudomonas fluorescens A506 and Pantoea vagans C9-1 appliedas single strains and mixed inocula. Phytopathology 100:1330–1339.http://dx.doi.org/10.1094/PHYTO-03-10-0097.8. WilsonM, Lindow SE. 1994. Coexistence among epiphytic bacterial pop-ulations mediated through nutritional resource partitioning. Appl Envi-ron Microbiol 60:4468–4477.9. Stockwell VO, Johnson KB, Sugar D, Loper JE. 2002. Antibiosis con-tributes to biological control of fire blight by Pantoea agglomerans strainEh252 in orchards. Phytopathology 92:1202–1209. http://dx.doi.org/10.1094/PHYTO.2002.92.11.1202.10. Vanneste JL, Cornish DA, Yu J, Voyle MD. 2002. P10c: a new biologicalcontrol agent for control of fire blight which can be sprayed or distributedusing honey bees. Acta Hortic 590:231–236. http://dx.doi.org/10.17660/ActaHortic.2002.590.33.11. De Maayer P, Chan W, Blom J, Venter SN, Duffy B, Smits THM,Coutinho TA. 2012. The large universal Pantoea plasmid LPP-1 plays amajor role in biological and ecological diversification. BMC Genomics13:625. http://dx.doi.org/10.1186/1471-2164-13-625.12. Matsuzawa T, Mori K, Kadowaki T, Shimada M, Tashiro K, Kuhara S,Inagawa H, Soma G-I, Takegawa K. 2012. Genome sequence of Pantoeaagglomerans IG1. J Bacteriol 194:1258–1259. http://dx.doi.org/10.1128/JB.06674-11.13. Smith DDN, Kirzinger MWB, Stavrinides J. 2013. Draft genome se-quence of the antibiotic-producing cystic fibrosis isolate Pantoea agglo-merans Tx10. Genome Announc 1(5):e00904-13. http://dx.doi.org/10.1128/genomeA.00904-13.14. Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiplealignment of conserved genomic sequence with rearrangements. GenomeRes 14:1394–1403. http://dx.doi.org/10.1101/gr.2289704.15. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J,Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A. 2003.GenDB—an open source genome annotation system for prokaryote ge-nomes. Nucleic Acids Res 31:2187–2195. http://dx.doi.org/10.1093/nar/gkg312.16. Smits THM, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, FreyJE, Stockwell VO, Duffy B. 2011. Metabolic versatility and antibacterialmetabolite biosynthesis are distinguishing genomic features of the fireblight antagonist Pantoea vagans C9-1. PLoS One 6:e22247. http://dx.doi.org/10.1371/journal.pone.0022247.17. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F, ZakrzewskiM, Goesmann A. 2009. Edgar: a software framework for the comparativeanalysis of prokaryotic genomes. BMC Bioinformatics 10:154. http://dx.doi.org/10.1186/1471-2105-10-154.18. Jin M, Liu L, Wright SAI, Beer SV, Clardy J. 2003. Structural andfunctional analysis of pantocin A: an antibiotic from Pantoea agglomeransdiscovered by heterologous expression of cloned genes. Angew Chem IntEd 42:2898–2901. http://dx.doi.org/10.1002/anie.200351053.Smits et al.Genome Announcements2 genomea.asm.org November/December 2015 Volume 3 Issue 6 e01448-15

Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c

We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosome
and two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pantocin
A biosynthesis genes was identified

ZHAW Zürcher Hochschule für Angewandte Wissenschaften

https://digitalcollection.zhaw.ch/bitstream/11475/1576/1/2015_Smits_Draft%20Genome%20Sequence_Genome%20Announcements.pdf

Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c

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