Complete Genome Sequence Resource for a Recently Isolated Potato Ring Rot Pathogen, Clavibacter sepedonicus K496

Potato ring rot caused by Clavibacter sepedonicus has been a devastating disease in the U.S. since 1930. In this study, we isolated a recent C. sepedonicus strain, K496, from potato tubers showing discolorations of the vascular cylinder or pith tissues. We de novo assembled the genome sequence of K496 with 1,924,544,313 bp of Nanopore reads (N-50 = 13,785 bp) using Flye v2.9 and polished it with 2 x 150 bp paired-end Illumina reads (855,788,703 bp in total). The resulting genome of K496 consists of a single circular chromosome 3,266,016 bp long and a linear plasmid of 135,489 bp. Using the NCBI PGAP v5.3, this genome was predicted to have 3,301 genes, encompassing 3,247 protein-coding genes, 90 pseudogenes, two 5S rRNA-coding, two 16S rRNA-coding, two 23S rRNA-coding sequences, 45 tRNAs, and three noncoding RNAs. The chromosome and plasmid sequences have been deposited at the NCBI GenBank database under the accession numbers CP088266 and CP088267, respectively.

Automated summary

In this study, a recent strain of Clavibacter sepedonicus, K496, was isolated from potato tubers with vascular cylinder or pith tissue discolorations. The genome sequence of K496 was de novo assembled using Nanopore reads and polished with Illumina reads. The resulting K496 genome consists of a circular chromosome of 3,266,016 bp and a linear plasmid of 135,489 bp. Bioinformatics analysis predicted a total of 3,301 genes in the K496 genome, including protein-coding genes, pseudogenes, rRNA-coding genes, tRNAs, and noncoding RNAs.