Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya

Abstract

In this work, we report the whole-genome sequence of Corynebacterium pseudotuberculosis bv. equi strain CIP 52.97 (Collection Institut Pasteur), isolated in 1952 from a case of ulcerative lymphangitis in a Kenyan horse, which has evidently caused significant losses to agribusiness. Therefore, obtaining this genome will allow the detection of important targets for postgenomic studies, with the aim of minimizing problems caused by this microorganism.

GENOME ANNOUNCEMENT

Corynebacterium pseudotuberculosis is an intracellular pathogen which causes significant losses in the goat, sheep, horse, and cattle breeding industries, since infected animals demonstrate wounds on the skin and internal organs, causing damage to the pelt and even the flesh (4). This bacterium is classified into two biovars, ovis (type I) and equi (type II). The biochemical difference between the types is the ability to reduce nitrate. C. pseudotuberculosis bv. ovis is negative for nitrate reduction, while C. pseudotuberculosis bv. equi is positive. CIP 52.97, the strain described in this paper, belongs to biovar type II. Ulcerative lymphangitis (also known as chest abscess, pigeon breast, and pigeon fever) is one of the most common and economically threatening infectious diseases of young-adult horses of all breeds and both sexes in California (3). In equine ulcerative lymphangitis, there are two forms of the disease, one characterized by external abscesses and one which affects the internal organs (1). To best understand the molecular and genetic basis of virulence of this bacterium, it was necessary to perform sequencing and genome analysis by using the SOLiD platform. We generated 60,342,023 mate-paired short reads (25 bp), with 580-fold coverage. The assembly process was based on the strategy of Cerdeira et al. (2), which allowed us to close gaps without the bench work time. The structural annotation was done automatically by a multipronged approach using the following programs: for gene prediction, FgenesB (http://www.softberry.com); for rRNA prediction, RNAmmer (5); for tRNA prediction, tRNA-scan-SE (6); and for repetitive DNA prediction, Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html). Protein domains and motifs were determined by InterProScan analysis (8). Manual curation was achieved using Artemis (7). Identification and confirmation of pseudogene in the genome were carried out using CLCBio Workbench 4.0.2. The genome of CIP 52.97 consists of a 2,320,595-bp circular chromosome, and the average G+C content of the chromosome is 52,14%. The genome was predicted to contain 2,057 coding sequences, four rRNA operons, 47 tRNAs, and 78 pseudogenes.

Nucleotide sequence accession number.

The genome sequence obtained in this study has been deposited in the GenBank database under the accession number CP003061 (chromosome).