Abstract
Pseudomonas syringae pv. persicae is a pathogen that causes bacterial decline of stone fruit. Here, we report the draft genome sequence for P. syringae pv. persicae, which was isolated from Prunus persica.
GENOME ANNOUNCEMENT
Pseudomonas syringae is responsible for causing diseases in more than 180 plant species, including fruit trees, vegetable crops, and flowers (1). The P. syringae complex comprises plant pathogens in eight closely related Pseudomonas spp., including 64 pathovars in P. syringae (2). P. syringae pv. persicae, the pathogen causing bacterial decline of stone fruit, which was first noted almost simultaneously in France and New Zealand, is now under quarantine control in Europe and China (3, 4). Here, we briefly describe the genome sequencing of P. syringae pv. persicae strain NCPPB 2254.
Three DNA libraries were constructed from the extracted genomic DNA using a NEB E7370L DNA library preparation kit for Illumina, with average insert sizes of 330 bp, 460 bp, and 600 bp, respectively. The sequencing was performed on an Illumina MiSeq platform using a MiSeq reagent kit v3, 600 cycles. A total of 2,931,855 × 2 × 301 bp generated reads were subjected to the skewer (5) program (version 0.1.123) with a quality threshold of 9 and an error threshold of 0.25 for adapter trimming, and then de novo assembled using the ABySS program (6) (version 1.5.2) with a k-mer size of 128. Fragments <300 bp long were removed from the final assembly. Annotations were made via the RAST (7) and xBASE2 (8) servers. As declared from the xBASE2 server, protein-coding gene finding, tRNA gene scanning, and rRNA gene identification were performed using Glimmer (9), tRNAscan-SE (10), and RNAmmer (11), respectively.
The draft genome comprises 201 contigs, with a G+C content of 58.44%, an N50 length of 69,352 bp, an N90 length of 19,310 bp, and a total length of 6.34 Mb. As annotated by the RAST server, it contains 5,625 protein-coding sequences (CDSs) and 86 RNA-coding sequences, among which 65 tRNA sequences and 21 rRNA clusters were found.
Nucleotide sequence accession numbers.
The genome sequence has been deposited at GenBank under the accession no. LAZV00000000. The version described in this paper is version LAZV01000000.
ACKNOWLEDGMENTS
This work was supported primarily by the 12th Five Years Key Programs for Science and Technology Development of China (2012BAK11B02, 2012BAK11B06) and the Basic Scientific Research Foundation of the Chinese Academy of Inspection and Quarantine (CAIQ) (2013JK003).
Footnotes
Citation Zhao W, Jiang H, Tian Q, Hu J. 2015. Draft genome sequence of Pseudomonas syringae pv. persicae NCPPB 2254. Genome Announc 3(3):e00555-15. doi:10.1128/genomeA.00555-15.
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