Louise Teixeira Cerdeira,1 Maria Paula Cruz Schneider,1 Anne Cybelle Pinto,2 Sintia Silva de Almeida,2
Anderson Rodrigues dos Santos,2Eudes Guilherme Vieira Barbosa,2Amjad Ali,2 Fla´via Figueira Aburjaile,2
Vinicius Augusto Carvalho de Abreu,2 Luis Carlos Guimara˜es,2 Siomar de Castro Soares,2
Fernanda Alves Dorella,2Fla´via Souza Rocha,2 Erick Bol,1Pablo Henrique Caracciolo Gomes de Sa´,1
Thiago Souza Lopes,1 Maria Silvanira Barbosa,1 Adriana Ribeiro Carneiro,1
Rommel Thiago Juca´ Ramos,1 Nilson Antoˆnio da Rocha Coimbra,1
Alex Ranieri Jeroˆnimo Lima,1 Debmalya Barh,3 Neha Jain,3
Sandeep Tiwari,3 Rathiram Raja,3 Vasudeo Zambare,3,4
Preetam Ghosh,3,6 Eva Trost,5 Andreas Tauch,5
Anderson Miyoshi,2 Vasco Azevedo,2and Artur Silva1*
Instituto de Cieˆncias Biolo´gicas, Universidade Federal do Para´, Bele´m, Brazil1; Instituto de Cieˆncias Biolo´gicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil2; Centre for Genomics and Applied Gene Technology, Institute of
Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India3; Center for Bioprocessing Research and Development (CBRD), South Dakota School of Mines and
Technology, South Dakota4; Institute for Genome Research and Systems Biology, Center for Biotechnology, Germany Institute for Genome Research, Bielefeld University, Bielefeld,
Germany5; and Department of Computer Science and Center for the Study of Biological Complexity, Virginia Commonwealth University,
401 West Main Street, Room E4234, P.O. Box 843019, Richmond, Virginia 23284-30196
Received 30 September 2011/Accepted 10 October 2011
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.
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, caus- ing 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, be- longs 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 deter- mined 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 con- sists 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 se- quence obtained in this study has been deposited in the GenBank database under the accession number CP003061 (chromosome).
* Corresponding author. Mailing address: Instituto de Cieˆncias Bi- olo´gicas. Universidade Federal do Para´. Av. Augusto Correˆa 01, Guama´, CEP 66075-110. Bele´m, PA, Brazil. Phone and fax: 55 91 3201-8426. E-mail: [email protected].
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This work was part of the Rede Paraense de Genoˆmica e Pro- teoˆmica, supported by FAPESPA, Nu´cleo Amazoˆnico de Exceleˆn- cia em Genoˆmica de Microorganismos—Pronex/CNPq/FAPESPA, CAPES, and FAPEMIG.
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