Draft Genome Sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, Isolated from an Infected Field Corn Plant in Manitoba, Canada

Abstract

In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated from symptomatic corn leaves in Manitoba, Canada. We report the draft genome sequence of C. michiganensis subsp. nebraskensis DOAB 397, consisting of 3.059 Mb with 73.0% G+C content, 2,922 predicted protein-coding sequences, 45 tRNAs, 3 rRNAs, and 37 pseudogenes.

GENOME ANNOUNCEMENT

Clavibacter michiganensis subsp. nebraskensis (CMN) is the causal agent of Goss’s wilt and blight disease of corn. The disease was first reported in 1969 in south-central Nebraska, USA, but became sporadic after partially resistant cultivars were identified in field corn (1). Goss’s wilt has reemerged and is spreading rapidly in major corn-growing regions of the United States and Canada. This pathogen is a concern to corn growers given the potential high yield losses (up to 50%) that could be incurred from systemic infections as well as its phytosanitary risk to nonendemic international trade partners such as Europe and China. In 2014, we isolated Clavibacter michiganensis subsp. nebraskensis DOAB 397 from symptomatic corn leaves in Manitoba, Canada, confirming the establishment of the disease in this Canadian province. We report the draft genome sequence of Clavibacter michiganensis subsp. nebraskensis DOAB 397. Genomic DNA shearing, library preparation, and the whole-genome shotgun sequence of Clavibacter michiganensis subsp. nebraskensis DOAB 397 were performed by the Génome-Québec Innovation Centre (Montreal, Canada). The draft genome was determined by paired-end sequencing using Illumina MiSeq technology (Génome-Québec, Montreal, Canada). A total of 1,078,908 paired-end reads, each 250 bp in length, totaling 269,727,000 bp, were obtained. The quality of the reads was checked by using FastQC version 0.11.3 (2). De novo assembly was performed using ABySS version 1.5.2 (3) at different k-mer values (75–113). A k-mer value of 97 gave the best assembly quality (no misassembled scaffolds) based on QUAST version 2.3 (4). Scaffolds with length <300 bp were discarded. The draft genome comprises 28 scaffolds (minimum, 3,207 bp; maximum, 428,173 bp; N₅₀, 142,187 bp; total size, 3,059,794 bp). The G+C content of the draft genome is 73.0% with an overall estimated coverage of 89×.

The 28 scaffolds of Clavibacter michiganensis subsp. nebraskensis DOAB 397 were ordered and oriented based on the complete genome sequence of the type strain, Clavibacter michiganensis subsp. nebraskensis NCPPB 2581^T (NC_020891) using the CAR software (5). The NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) revealed that the draft genome of Clavibacter michiganensis subsp. nebraskensis DOAB 397 contains 2,922 predicted protein-coding sequences, 45 tRNAs, 37 pseudogenes, 3 rRNAs, and 1 other RNA. Compared to PGAAP, CMG-Biotools (6) predicted 2,903 genes based on Prodigal (7), whereas RNAmmer version 1.2 (8) predicted 3 rRNAs containing one copy each of 16S rRNA, 5S rRNA, and 23S rRNA. The number of predicted tRNAs genes was confirmed by tRNAscan-SE version 1.3.1 software (9). Analysis of the draft genome of strain DOAB 397 revealed that it has 14 more genes than the complete genome sequence of Clavibacter michiganensis subsp. nebraskensis NCPPB 2581^T, the type strain isolated in 1969. A more detailed analysis of strain DOAB 397 will be included in a future publication.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LAKL00000000. The version described in this paper is the first version, LAKL01000000.