# Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

Gabriela Vuletin Selak, Marina Raboteg, Audrey Dubost, Danis Abrouk, Philippe Normand, Petar Pujić

► To cite this version:

Gabriela Vuletin Selak, Marina Raboteg, Audrey Dubost, Danis Abrouk, Philippe Normand, et al. Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot. Microbiology Resource Announcements, 2019, 8 (42), 10.1128/MRA.00978-19. hal-02473982

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Distributed under a Creative Commons Attribution 4.0 International License
# Whole-Genome Sequence of a *Pantoea* sp. Strain Isolated from an Olive (*Olea europaea* L.) Knot

Gabriela Vuletin Selak,ª Marina Raboteg,ª Audrey Dubost,ᵇ Danis Abrouk,ᵇ Katja Žanić,ª Philippe Normand,ᵇ ▸ Petar Pujićᵇ

**ABSTRACT** Here, we present the total genome sequence of *Pantoea* sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of *Pantoea* sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of *Pantoea* spp.

Pantoea is a genus of Gram-negative bacteria belonging to phylum Proteobacteria, class Gammaproteobacteria, order Enterobacteriales, family Erwiniaceae. In the olive knot disease, the nonpathogenic bacterial species *Pantoea agglomerans* and *Erwinia toletana*, olive plant epiphytes and endophytes, coexist with the pathogenic bacterium *Pseudomonas savastanoi* pv. savastanoi, the causal agent of disease (1–3).

*P. agglomerans* strains inhabiting olive trees as nonpathogenic endophytes have been shown to cooperate with strains of *P. savastanoi*, forming a stable bacterial consortium that increases the severity of disease (1). It has been suggested that the indole-3-acetic acid (IAA) and cytokinins produced by *P. agglomerans* may increase the size of the knots on olive caused by *P. savastanoi* and also that the growth of *P. agglomerans* is apparently supported by the copresence of an actively growing population of *P. savastanoi* (2).

Bacterial cells were isolated from olive knots isolated in the central region of Dalmatia, Croatia (global positioning system [GPS] coordinates 43°30′19.6″N, 16°29′55.0″E). Fresh olive knots were surface sterilized by 75% ethanol, sliced with a sterile scalpel, and plated onto King's medium agar plates (4). Plates were kept in the dark at 25°C for 48 h. An isolated single colony was transferred into 10 ml of liquid lysogeny broth (LB) medium and grown at 28°C for 24 h with shaking. DNA was isolated from bacterial cells using a microbial DNA kit (Macherey-Nagel, Hoerdt, France).

Two micrograms of genomic DNA was used for fragmentation and 300-bp library preparation using a Nextera XT DNA library prep kit and protocol (Illumina, Evry, France), and 2 × 150-bp paired-end sequencing was done using Illumina technology at GATC Biotech (Mulhouse, France). Quality controls were made with FastQC (5) and Trimmomatic (6). We obtained a total of 7,822,775 reads, with 462× coverage and a G+C content of 54%. Genome assembly was realized using Unicycler v0.4.3 software, and annotation was done with the MicroScope platform v3.10.0 using default parameters, with a minimum contig length of 200 bp (7–9). The *Pantoea* sp. genome is assembled in 52 contigs, with the largest contigs of 1,219,567 bp. The genome size has 5,077,592 bp, an *N*₅₀ value of 580,527 bp, a G+C content of 54.58%, and 4,786 annotated genes.

**Data availability.** The complete genome sequence described here has been deposited at NCBI/GenBank under BioProject number PRJNA555164, BioSample number

**Citation** Vuletin Selak G, Raboteg M, Dubost A, Abrouk D, Žanić K, Normand P, Pujić P. 2019. Whole-genome sequence of a *Pantoea* sp. strain isolated from an olive (*Olea europaea* L.) knot. Microbiol Resour Announc 8:e00978-19. https://doi.org/10.1128/MRA.00978-19.

**Editor** Irene L. G. Newton, Indiana University, Bloomington

**Copyright** © 2019 Vuletin Selak et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Gabriela Vuletin Selak, gabriela.vuletin selak@krs.hr, or Petar Pujić, petar.pujic@univ-lyon1.fr.

**Received** 13 August 2019

**Accepted** 1 October 2019

**Published** 17 October 2019

<footnote>ªInstitute for Adriatic Crops and Karst Reclamation, Split, Croatia</footnote>

<footnote>ᵇEcologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Villeurbanne, France</footnote>
<figure><img src="image_2.png" /></figure>

SAMN12302724, and GenBank accession number VLTF00000000. Raw reads were de-
posited at NCBI under SRA accession number SRX6799334. The version described in this
paper is the first version. The *Pantoea* sp. paga strain is available on request from the
Institute for Adriatic Crops (IAC).

ACKNOWLEDGMENTS

This work was supported by the Split-Dalmatia County grant for the project "Agents,
transmitters and bio-control of olive knot disease in the olive groves of the Split-
Dalmatia County" and by the Unity Through Knowledge Fund, collaboration grant 2017
olumsensing signals and role of interspecies communities in a bacterial plant
disease. ISME J 5:1857-1870. https://doi.org/10.1038/ismej.2011.65.
Marchi G, Sisto A, Cimmino A, Andolfi A, Cipriani MG, Evidente A, Surico
G. 2006. Interaction between Pseudomonas savastanoi and Pantoea ag-
glomerans in the olive knots. Plant Pathol 55:614-624. https://doi.org/
10.1111/j.1365-3059.2006.01449.x.
Buonaurio R, Moretti C, Passos da Silva D, Cortese C, Ramos C, Venturi V.
2015. The olive knot disease as a model to study the role of interspecies
bacterial communities in plant disease. Front Plant Sci 6:434. https://doi.
org/10.3389/fpls.2015.00434.
King EO, Ward MK, Raney DE. 1954. Two simple media for the demon-
stration of pyocyanin and fluorescin. J Lab Clin Med 44:301-307.
Andrews S. 2010. FastQC: a quality control tool for high throughput se-
quence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

We thank platform Genomique Environnementale PGE, UMR, CNRS 5557, for tech-
nical support.

We declare no conflict of interest.

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