Draft Genome Sequences of Two Dickeya dianthicola Isolates from Potato.

Here, we report two annotated draft genome sequences of Dickeya dianthicola isolates from potatoes collected in Delaware and West Virginia. The genomes of strains DE440 and WV516 show 99% similarity to each other and 96% and 95% similarity to the European strains IPO 980 and RNS04.9, respectively.

GENOME ANNOUNCEMENT

Dickeya dianthicola is a phytopathogen that can cause tuber soft rot and blackleg in potatoes. The pathogen has been confirmed by a federal laboratory to be present in 12 states in the United States (Delaware, Florida, Maryland, Massachusetts, New Jersey, New York, North Carolina, Pennsylvania, Rhode Island, Virginia, West Virginia, and Ohio) in the past few years. It has emerged as a considerable threat to potato production due to its potential to cause severe crop losses. Currently, there are five complete genome sequences available, and all are from Europe (1, 2). Here, we report two draft genome sequences of Dickeya dianthicola isolates from potatoes found in the United States, specifically in Delaware and West Virginia.

Dickeya dianthicola was isolated from soft rot potato tubers DE440 and WV516. Genomic DNA was extracted using the DNeasy blood and tissue minikit (Qiagen, Valencia, CA). Paired-end sequencing libraries were prepared using the TruSeq DNA PCR-free DNA library prep kit (Illumina, Inc., San Diego, CA) for the WV516 isolate and the Nextera XT DNA library prep kit (Illumina, Inc.) for the DE440 isolate. The 2 × 300-bp paired-end sequencing was performed on a MiSeq platform (Illumina, Inc.).

There were 2.2 million reads for sample DE440 and 1.2 million reads for WV516. The reads were de novo assembled using the CLC Genomics Workbench 10.1 software, resulting in 55 and 103 contigs, respectively. Sample DE440 contigs (N50, 246,586 bp; maximum, 541,313 bp) had over 100× estimated whole-genome coverage, and sample WV516 contigs (N50, 214,389 bp; maximum, 456,580 bp) had over 50× estimated coverage. Annotations through the Rapid Annotations using Subsystems Technology (RAST) server (http://rast.nmpdr.org) (3–5) identified 4,787 and 4,791 annotated genes and 74 and 71 RNA genes for the DE440 and WV516 strains, respectively.

Pairwise comparison of the sequences revealed 99% similarity between isolates DE440 and WV516. Whole-genome comparisons show 95.78% similarity to Dickeya dianthicola strain IPO 980 for DE440 and 95.79% similarity for WV516. We observed 95.01% (DE440) and 95.04% (WV516) similarity to Dickeya dianthicola strain RNS04.9.

Accession number(s).

The draft genome sequences have been deposited under BioProject PRJNA421738, BioSample numbers SAMN08152918 (DE440) and SAMN08152919 (WV516), and accession numbers PJJB00000000 (DE440) and PJJC00000000 (WV516).