Brazilian Journal of Microbiology Brazilian Journal of Microbiology
Braz J Microbiol 2016;47:529-30 - Vol. 47 Num.3 DOI: 10.1016/j.bjm.2016.04.023
Genome Announcements
Draft genome sequences of five Pseudomonas syringae pv. actinidifoliorum strains isolated in France
Amandine Cuntya,b, Sophie Cesbrona, Martial Brianda, Sébastien Carrèrec,d, Françoise Poliakoffb, Marie-Agnès Jacquesa, Charles Manceaub,,
a Institut National de la Recherche Agronomique, IRHS, Beaucouzé, France
b Agence Nationale de la Sécurité sanitaire, de l’alimentation, de l’environnement et du travail, Plant Health Laboratory, Angers, France
c INRA, LIPM, Castanet-Tolosan, France
d Centre National de la Recherche Scientifique, LIPM, Castanet-Tolosan, France
Received 18 January 2016, Accepted 17 February 2016
Abstract

Pseudomonas syringae pv. actinidifoliorum causes necrotic spots on the leaves of Actinidia deliciosa and Actinidia chinensis. P. syringae pv. actinidifoliorum has been detected in New Zealand, Australia, France and Spain. Four lineages were previously identified within the P. syringae pv. actinidifoliorum species group. Here, we report the draft genome sequences of five strains of P. syringae pv. actinidifoliorum representative of lineages 1, 2 and 4, isolated in France. The whole genomes of strains isolated in New Zealand, representative of P. syringae pv. actinidifoliorum lineages 1 and 3, were previously sequenced. The availability of supplementary P. syringae pv. actinidifoliorum genome sequences will be useful for developing molecular tools for pathogen detection and for performing comparative genomic analyses to study the relationship between P. syringae pv. actinidifoliorum and other kiwifruit pathogens, such as P. syringae pv. actinidiae.

Keywords
Pseudomonas syringae, Actinidia, Kiwifruit pathogen, Leaf necrotic spots
Introduction

The Pseudomonas syringae species group comprises plant-pathogenic bacteria with a vast host range. The multiple strains of this species cause diseases on more than 180 plant species.1P. syringae is divided into 8 genomospecies2,3 and 13 phylogroups.4P. syringae is further divided into more than 50 pathovars, according to the disease that the strain causes on plants. Two pathovars have been described for kiwifruit: P. syringae pv. actinidiae,5 which causes bacterial canker on kiwifruit, and P. syringae pv. actinidifoliorum6–8), which causes bacterial spots on kiwifruit. Both P. syringae pv. actinidiae and P. syringae pv. actinidifoliorum are classified into phylogroup 1 and genomospecies 3. Phylogenetic analysis conducted by MLSA has classified P. syringae pv. actinidifoliorum strains isolated in Australia, New Zealand and France into four different lineages.7 Strain genomes belonging to lineages 1 and 3 of P. syringae pv. actinidifoliorum (CFBP 7812 and CFBP 7951, respectively), isolated in New Zealand, were sequenced.9,10 Here, we briefly describe the genome sequencing of five P. syringae pv. actinidifoliorum strains representing three different lineages, lineage 1 (CFBP8161 and CFBP8180), lineage 2 (CFBP8043) and lineage 4 (CFBP8039 and CFBP8160), to provide genome sequences for at least one strain of each MLVA lineage described to date.

DNA Libraries were constructed from extracted DNA using the Nextera XT DNA Sample Preparation Kit with average insert sizes of 1200bp. The sequencing was performed on an Illumina Hi-Seq 2500 platform (Genoscreen, Lille, France) using a TruSeq Rapid SBS kit and a Truseq Rapid paired-end cluster kit v3. The assembly statistics for each genome are reported in Table 1. Reads were assembled in contigs using SOAPdenovo 1.0511 and Velvet.12 Annotation was performed using EuGene-P (v0.3).13 The number of features for each genome are reported in Table 1. Analysis of the five genomes showed that an intact phage was present in the lineage 1 strains only. In all five genomes, in silico analysis confirmed the presence of only one Type III secretion system (hrp 1 type). All specific effector genes (hopO1, hopT1, hopS1, hopAB3, hopF1, hopE1, hopAF1-2) of P. syringae pv. actinidifoliorum that were previously reported by McCann et al.10 were present in all 5 genome sequences. No ICE (Integrative and Conjugative Element) was identified in the genome sequences of P. syringae pv. actinidifoliorum, unlike in P. syringae pv. actinidiae9,10,14). Regarding nucleotide sequence accession numbers, the genome sequences have been deposited at GenBank under the accession numbers listed in Table 1.

Table 1.

Genome characteristics.

Strain code  Lineage  Accession no.  Genome size (Mb)  No. of contigs  N50 (bp)  No. of protein coding genes  G+C content (%) 
CFBP8161  LJFL00000000  6.24  206  111,837  5775  58.72 
CFBP8180  LJFN00000000  6.26  256  98,002  5833  58.69 
CFBP8043  LJFM00000000  6.05  176  132,698  5630  58.80 
CFBP8039  LJJM00000000  6.1  204  116,909  5700  58.75 
CFBP8160  LJJL00000000  6.09  220  113,613  5679  58.76 
Conflicts of interest

The authors declare no conflicts of interest.

Acknowledgements

Support for this work came from in-house funding of the EmerSys team at IRHS. We thank Jerome Gouzy (LIPM-INRA SPE platform, Toulouse) for performing automatic annotation of the genomes. We thank Corinne Audusseau and Sandrine Paillard for the isolation of the P. syringae pv. actinidiae and P. syringae pv. actinidifoliorum strains and Perrine Portier and Géraldine Taghouti at the International Centre for Microbial Resources and Plant-associated Bacteria (CIRM-CFBP) for providing strains and extracted DNAs, respectively. A. Cunty is supported by a fellowship provided by Anses and the Region Pays de la Loire, France.

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Corresponding author. (Charles Manceau charles.manceau@anses.fr)
Copyright © 2016. Sociedade Brasileira de Microbiologia
Braz J Microbiol 2016;47:529-30 - Vol. 47 Num.3 DOI: 10.1016/j.bjm.2016.04.023