High-Quality Draft Genome Sequence of Xanthomonas sp. Strain CPBF 424, a Walnut-Pathogenic Strain with Atypical Features

We report here the draft genome sequence of Xanthomonas sp. strain CPBF 424, isolated from a diseased walnut tree.

Here, we make available the whole-genome sequence of Xanthomonas sp. strain CPBF 424.
Xanthomonas sp. strain CPBF 424 was grown on bacterial culture medium M2 (yeast extract, 2 g liter Ϫ1 ; Bacto peptone, 5 g liter Ϫ1 ; NaCl, 5 g liter Ϫ1 ; KH 2 PO 4 , 0.45 g liter Ϫ1 ; Na 2 HPO 4 12H 2 O, 2.39 g liter Ϫ1 ) at 28°C and 100 rpm for 48 h. DNA was extracted for sequencing using the E.Z.N.A. bacterial DNA purification kit (Omega Bio-tek, Norcross, GA). Genomic library preparation and genome sequencing were outsourced to GATC Biotech, AG (Konstanz, Germany) and conducted using an Illumina HiSeq platform with 2 ϫ 150-bp paired-end reads, which resulted in 12,672,550 reads of raw sequence data with a sequencing coverage of 776ϫ. De novo genome assembly was obtained with MIRA version 4.0 (12) using standard settings in accurate mode. This was followed by contig reassembly using SeqMan Pro from the Lasergene genomics package version 12.1.0 (DNAStar, Madison, WI) with Pro assembler parameters and read mapping using SeqMan NGen with standard settings to check for inconsistencies (overlapping contig extremities with no or low coverage with paired-read inconsistencies). A total of five irregularities were found on which contigs were broken open per the initial de novo assembly. Contigs were ordered using the Move Contigs function in Mauve 20150226 version 10 (13, 14) according to the genome of X. arboricola pv. juglandis CFBP 2528 (GenBank accession number NZ_JZEF00000000) (15). Automatic genome annotation was performed with a Xanthomonas genus database using the Prokka software tool version 1.12 (16).
The Xanthomonas sp. CPBF 424 genome had a total size of 4,896,146 bp and a GϩC content of 65.89% represented by 10 contigs with an N 50 value of 1,029,447 bp. The genome of CPBF 424 is estimated to be composed of 4,143 coding sequences (CDS), including 58 tRNAs and 4 rRNAs. Preliminary analysis with the EDGAR version 2.0 platform (17) allowed us to detect 3,502 coding sequences that are shared between CPBF 424 and X. arboricola pv. juglandis CFBP 2528, which was used as the reference genome.
The whole-genome sequence of strain CPBF 424 may contribute to elucidating new walnut pathoadaptations within the genus Xanthomonas.
Data availability. This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the BioProject accession number PRJEB27248 (SRA accession number ERR2767968), and the sequence accession number is UIHB00000000. The version described in this paper is version UIHB01000000.

ACKNOWLEDGMENTS
This work was cofinanced by the European Structural & Investment Funds (ESIFs) through the Operational Competitiveness and Internationalization Programme-COM-PETE 2020 and by national funds through Fundação para a Ciência e Tecnologia (FCT) within the framework of the project EVOXANT (PTDC/BIA-EVF/3635/2014, POCI-01-0145-FEDER-016600). This article is based on work from European Cooperation in Science and Technology (COST) action CA16107 EuroXanth, supported by COST. C.F. was supported by a fellowship from FCT (SFRH/BD/95913/2013) and a Short-Term Scientific Mission (STSM) from COST action CA16107. The EDGAR platform is funded by Federal Ministry of Education and Research (BMBF) grant FKZ 031A533.
We thank Leonor Cruz for lab support.