Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production

Soares, Siomar C.; Trost, Eva; Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Santos, Anderson; Pinto, Anne C.; Barbosa, Eudes Guilherme Vieria; Aburjaile, Flávia Figueira; Ali, Amjad; Diniz, Carlos; Hassan, Syed Shah; Fiaux, Karina; Guimarães, Luís Carlos; Bakhtiar, Syeda Marriam; Pereira, Ulisses de Pádua; Almeida, Síntia; Abreu, Vinícius Augusto Carvalho de; Rocha, Flávia Souza; Dorella, Fernanda Alves; Miyoshi, Anderson; Silva, Artur M. S.; Azevedo, Vasco; Tauch, Andreas

doi:10.1016/j.jbiotec.2012.11.003

Cited by 40 publications

(31 citation statements)

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“…ovis strain was analyzed using RNA-seq, and genes involved in the molecular responses of the bacterium to different stresses during infection were identified (8). A study of reverse vaccinology reported by Soares et al (9) identified 49 possible antigens from the genome of the C. pseudotuberculosis bv. equi strain 258 that may serve as targets for the development of effective vaccines.…”

Section: Genome Announcementmentioning

confidence: 99%

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California

et al. 2014

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Section: Genome Announcementmentioning

confidence: 99%

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California

et al. 2014

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“…The new assembly of Cp258 (length: 2,369,817 bp) detected an increase of ~60 Kbp over the original genome (length: 2,314,404 bp; GenBank: NC_017945; [17]). The SIMBA’s genomic visualization confirmed and extended the MapSolver results, allowing a detailed comparison between the old assembly and the new assembly (Fig.…”

Section: Resultsmentioning

confidence: 99%

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

et al. 2016

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BackgroundThe evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects.ResultsIn order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM.ConclusionBesides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net.

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“…9 (3) virulence factors are better targets. 10 The results of vaccine targets prediction (34 potential vaccine candidates are marked in red) and virulence genes annotation are summarized in Table S1 and Table S2, respectively. These results are useful to predict possible effective targets and helpful for development of DNA and subunit vaccines.…”

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confidence: 99%

Complete genome sequence ofVibrio mimicusstrain SCCF01 with potential application in fish vaccine development

Geng

Wang

et al. 2016

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Vibrio mimicus strain SCCF01 was isolated from the yellow catfish (Pelteobagrus fulvidraco) during a mass mortality event at an aquaculture facility. We sequenced the genome of strain SCCF01, then predicted possible effective targets for subunit vaccine and identified possible virulence genes for live attenuated vaccine. The genome of SCCF01 consists of 2 circular chromosomes of 3,213,040 and 1,272,975 bp with G+C content of 46.61% and 45.88%, respectively. Subcellular localization, number of transmembrane helices and adhesion probability were predicted by Vaxign programs. Several candidate virulence genes were identified using the Virulence Factors Database. The genomic information presented herein will be useful for future studies investigating the pathogenesis of V. mimicus and with vaccine development.Vibrio mimicus is an enteric pathogen that is widely distributed in aquatic environments that can infect and cause disease in fish.1,2 Additionally, the pathogen is zoonotic and can cause bacterial gastroenteritis and food poisoning in humans if infected fish are consumed.2 Hence, understanding the pathogenesis of V. mimicus and developing a vaccine to treat infected fish hosts is an important research direction. In this study, we revived V. mimicus strain SCCF01 from the farmed yellow catfish (Pelteobagrus fulvidraco) in Sichuan Province, China, during a mass mortality event.3 Our objectives were to: (1) characterize the SCCF01 genome, (2) predict possible effective targets for subunit vaccine, (3) identify possible virulence genes that could lead to development of attenuated V. mimicus for vaccine development, and (4) identify the ability of colonization and adhesion of V. mimicus infection in yellow catfish.The whole-genome sequence of SCCF01 strain was determined with single molecule real-time (SMRT) sequencing platform PacBio RS II. Single SMRT cells produced 35,089 reads for 306,431,068 bases (N50 size 12,135 bp and mean read length 8,732 bp). Subsequently, the sequence reads were assembled using the PacBio SMRT Analysis (ver. 2.3.0) with default options.

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Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production

Cited by 40 publications

References 51 publications

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Complete genome sequence ofVibrio mimicusstrain SCCF01 with potential application in fish vaccine development

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