Draft genome of a South African strain of Pectobacterium carotovorum subsp. brasiliense.

The draft genome of Pectobacterium carotovorum subsp. brasiliense (Pcb) which causes blackleg of potato was submitted to the NCBI and released with reference number NZ_LGRF00000000.1. The estimated genome size based on the draft genome assembly is 4,820,279bp from 33 contigs ranging in length from 444 to 1,660,019 nucleotides. The genome annotation showed 4250 putative genes, 4114 CDS and 43 pseudo-genes. Three complete rRNA gene species were detected: nine 5S, one 16S and one 23S. Other partial rRNA gene fragments were also identified, nine 16S rRNA and three 23S rRNA. A total of 69 tRNA genes and one ncRNA gene were also annotated in this genome.

A new bacterium species similar to Pectobacterium carotovorum subsp. carotovorum that was recently discovered has been shown to be the cause of blackleg in Brazil, USA, South Africa, Canada, New Zealand and Korea.1, 2, 3, 4, 5 It has been classified as P. carotovorum subsp. brasiliense.6, 7 Very few studies have focussed on studying the complete genome of P. carotovorum subsp. brasiliense and as such, the pathogenicity of this subspecies of P. carotovorum cannot be predicted. Moreover, not much work has been done to characterise the P. carotovorum subsp. brasiliense strain found in South Africa. The work presented here focused on preliminary characterisation of the complete genome of P. carotovorum subsp. brasiliense found in South Africa.

Strain BD255 of P. carotovorum subsp. brasiliense, collected from rotting watermelon in 2002, was selected for this study. Total DNA was isolated using the QIAamp® DNA Mini Kit (Qiagen) and quantified using the Qubit® dsDNA BR Assay kit (Thermo Fisher). The DNA was used to prepare sequencing libraries using the Nextera XT DNA Library Prep Kit (Illumina). Two insert size selections were then performed at 250 and 800 bp respectively and sequenced paired end; 2 × 100 on the Illumina HiScanSQ and 2 × 300 on the Illumina MiSeq respectively. A total of 1 GB of sequencing data was obtained for the 2 × 100 and 3 GB for the 2 × 300 formats. The sequence reads were trimmed for adapters using Trimmomatic, filtered for quality using the FASTX-Toolkit suite of tools (http://hannonlab.cshl.edu/fastx_toolkit/) and the de novo assembly was performed using Velvet v. 1.2.08. The assembly gave an average coverage across the genome of 117X.

The draft genome assembly was submitted to NCBI (www.ncbi.nlm.nih.gov) and can be accessed under project accession number NZ_LGRF01000000 and consists of sequences with accession numbers LGRF01000001-LGRF01000033. The estimated genome size is 4,820,279 nucleotides, about the same size as the complete genome sequence of P. carotovorum subsp. carotovorum NCBI reference NC_012917 submitted in www.ncbi.nlm.nih.gov, and consists of a total of 33 contigs ranging in size from 444 to 1,660,019 nucleotides. Annotation was performed using the NCBI PGAP using the Best-placed reference protein set; GeneMarkS+ method. Results show 4250 genes, 4114 CDS, 43 pseudo-genes, 9 complete 5S rRNA genes, 1 complete 16S rRNA gene and 1 complete 23S rRNA gene. There are also partial rRNA genes 9 (16S rRNA) and 3 (23S rRNA). Additionally, a total of 69 tRNA 1 ncRNA genes were also detected.

Conflicts of interest

The authors declare no conflicts of interest.