Computational protocol: High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae Isolates

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Protocol publication

[…] Xanthomonas arboricola pv. fragariae was described in 2001 as the causal agent of strawberry bacterial leaf blight (). The first symptoms related to this bacterium were observed in 1993 in strawberry cultivations in northern Italy (). Afterward, the disease has only been reported in plantlets from Turkey in 2004 (). The bacterium was under quarantine status in Europe starting in 2002 (), but it was derestricted in 2007 (see https://www.eppo.int/MEETINGS/2007_meetings/phytomeasures.htm). This was partly due to the observation that the pathogen was sometimes coisolated with Xanthomonas fragariae (, ), which is the causal agent of bacterial angular leaf spot and is under quarantine status in Europe (, ). Also, the reported pathogenicity of X. arboricola pv. fragariae upon artificial inoculation on strawberry has often been ambiguous (, , ; M. Gétaz and J. F. Pothier, unpublished data). This could be related to the important heterogeneity among X. arboricola pv. fragariae strains, as observed in previous studies (, , ). Very recently, the pathogenicity of the pathotype strain was proved to produce typical symptoms in the strawberry cultivars Candonga, Sabrina, and Murano ().Until now, no whole-genome data for this bacterium were available in GenBank. In this study, whole-genome sequences of five X. arboricola pv. fragariae strains isolated from strawberry plants in Italy and France between 1986 and 1993 were obtained ().Genomic DNA was extracted using the NucleoSpin tissue kit (Macherey-Nagel AG, Düren, Germany) following the manufacturer’s protocol. Paired-end libraries constructed by the Nextera XT DNA library prep kit (Illumina, San Diego, CA) were sequenced on a MiSeq system (Illumina) using a 600-cycle MiSeq reagent kit v3 (Illumina). De novo assemblies were created using SeqMan NGen from the Lasergene genomics package version 12.1.0 (DNAStar, Madison, WI). This was followed by contig reassembly using SeqMan Pro and read mapping using SeqMan NGen to check for inconsistencies.The five genomes displayed an overall size between 4,692,498 and 4,906,785 bp, which is in the range previously observed with other X. arboricola genomes (). The G+C contents in all the genomes were similar (65.75 to 65.95%). Genomes were annotated automatically using GenDB (), and a total of 3,852 to 4,044 coding sequences (CDSs) were detected (). Using EDGAR 2.0 (), a total of 3,523 CDSs were found to be shared between these five genomes.Average nucleotide identities (ANIs) between these five genomes ranged from 96.57% to 97.69%, thus confirming the species designation but also suggesting some genome content heterogeneity.The X. arboricola pv. fragariae draft genome sequences presented here add to the existing genomic information and further clarify the complexity of the species X. arboricola. […]

Pipeline specifications

Software tools DNASTAR Molecular Biology Suite, GenDB
Application WGS analysis
Organisms Xanthomonas arboricola, Bacteria