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

Background The 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. Results In 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. Conclusion Besides 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

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

The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi

Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.

Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer

Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays.

Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods

Assessing the Genotypic Differences between Strains of <i>Corynebacterium pseudotuberculosis</i> biovar <i>equi</i> through Comparative Genomics

<div><p>Seven genomes of <i>Corynebacterium pseudotuberculosis</i> biovar <i>equi</i> were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as “pigeon fever” which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within <i>Corynebacterium</i> genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, <i>C</i>. <i>pseudotuberculosis</i> was divided into two distinct clades, one formed by nitrate non-reducing species (biovar <i>ovis</i>) and another formed by nitrate-reducing species (biovar <i>equi</i>). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar <i>equi</i>. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar <i>equi</i> of <i>C</i>. <i>pseudotuberculosis</i>. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of <i>C</i>. <i>pseudotuberculosis</i> were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.</p></div

Map of the circular genomes of <i>C</i>. <i>pseudotuberculosis</i>, <i>C</i>. <i>ulcerans</i> and <i>C</i>. <i>diphtheriae</i> and the analysis of GEIs.

<p>The genomes were compared by blastn, and the percentage of identity between them was determined by the intensity of the color in the circular map. The genomes of <i>C</i>. <i>pseudotuberculosis</i> were identified only by the name of the lineage. (a) The innermost ring to the outermost is presented in this figure, as follows: the GC skew of the MB14 strain; the GC contents of the MB14 strain, the genomes of the <i>C</i>. <i>pseudotuberculosis</i> strains MB14, MB20, MB30, MB44, MB66, MB122, MB154, MB278, MB295, MB302, and MB336, and the genomes of <i>C</i>. <i>ulcerans</i> BR-AD22 and <i>C</i>. <i>diphtheriae</i> NCTC 13129. The two outermost rings comprise CDSs identified in the genome of <i>C</i>. <i>pseudotuberculosis</i> MB14. The graph displayed by GC skew is common to chromosomes that have bidirectional replication. (b) A circular genome map of the MB20 strain was constructed by comparing the position of 18 PAIs in the MB122 strain and 21 PAIs the in MB336 strain through tblastx. The PAIs shown in black were detected in both strains by GIPSy, while the PAIs in green were detected only in MB122 and the PAIs in red were detected only in MB336. A later comparison using blastn showed that the conservation of these PAIs was higher than that observed by GIPSy. (c) A dendrogram was calculated with the Neighbor-Joining model from the comparison of the nucleotide sequences of the RIs of 12 Californian isolated genomes.</p

Phylogenomic analysis of the <i>Corynebacterium</i> genus.

<p>(a) The entire Neighbor-Joining tree containing the <i>Corynebacterium</i> RefSeq genomes, demonstrating the closeness between the species <i>C</i>. <i>diphtheriae</i>, <i>C</i>. <i>ulcerans</i> and <i>C</i>. <i>pseudotuberculosis</i>. This latter species comprises two distinct clades composed of strains from biovar <i>ovis</i> (marked in orange) and biovar equi (marked in purple). (b) An expanded view of the biovar <i>equi</i> tree. Strains isolated in California (in color) are closely related to each other. The strains CIP 52.97 and 1/06-A formed the outermost clade of biovar <i>equi</i>. The colors of the names from strains isolated in California distinguish the types of infection caused by the pathogen. (c) Dendrogram calculated with the Neighbor-Joining model from heatmap values generated in the Gegenees program. The values shown in the heatmap indicate the percentage of similarity between the analyzed genomes. The name of the species isolated in California is colored according to the type of infection caused by the pathogen.</p

Synteny analysis of <i>C</i>. <i>pseudotuberculosis</i> pili gene clusters.

<p>From top to the bottom of the figure the genome of strains 1002, MB11, MB14, MB30 and CIP 52.97 are shown. Genes are represented by arrows of different color. Genes without standardized names are identified as gene_1, gene_2, and so on. Conserved genes are connected by lines. (a) <i>spaA</i> cluster. (b) <i>spaD</i> cluster.</p