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

ANNOUNCEMENT

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 N₅₀ value of 580,527 bp, a G+C content of 54.58%, and 4,786 annotated genes.