PANNOTATOR: an automated tool for annotation of pan-genomes

Santos, Anderson; Barbosa, Eudes Guilherme Vieria; Fiaux, Karina; Zurita-Turk, Meritxell; Chaitankar, Vijender; Kamapantula, B; Abdelzaher, A; Ghosh, Preetam; Tiwari, Sandeep; Barve, Neha; Jain, Neha; Barh, Debmalya; Silva, A; Miyoshi, Anderson; Azevedo, Vasco

doi:10.4238/2013.august.16.2

Cited by 24 publications

(13 citation statements)

References 13 publications

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“…pseudotuberculosis MB11 as the reference genome because its assembly was confirmed by the in vitro optical map. The high-quality scaffolds were submitted to the web software Pannotator [ 53 ] for automatic annotation using the C . pseudotuberculosis 316 as the reference genome.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2017

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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.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2017

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“…When specified, an attempt will be made to inherit all annotations from the reference genome and also propagate gene names. Because gene names are used inconsistently across species, neither the SEED nor RAST has ever attempted to propagate them (32). For example, the gene sir A of Salmonella is also known as uvr Y in E. coli or gac A in Pseudomonas .…”

Section: Future Developmentsmentioning

confidence: 99%

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

et al. 2013

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In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

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“…An automatic annotation was first conducted using the online software Pannotator [ 13 ], which provided the .fasta files for the assembled genomes and a reference .embl file for C. pseudotuberculosis 316. The results were then manually curated to meet the gene annotation standards set by UniProt [ 14 ] using Artemis software [ 15 ] to visualize the coding sequences.…”

Section: Genome Sequencing Informationmentioning

confidence: 99%

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

Baraúna

Ramos

Veras

et al. 2017

Stand in Genomic Sci

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The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs). An optical map of the MB11 strain generated using the KpnI restriction enzyme showed that the approach used to assemble the genome was satisfactory, producing good alignment between the sequence observed in vitro and that obtained in silico. In the resulting Neighbor-Joining dendrogram, the C. pseudotuberculosis strains sequenced in this study were clustered into a single clade supported by a high bootstrap value. The structural analysis showed that the genomes of the MB11 and MB14 strains were very similar, while the MB30 and MB66 strains had several inverted regions. The observed genomic characteristics were similar to those described for other strains of the same species, despite the number of inversions found. These genomes will serve as a basis for determining the relationship between the genotype of the pathogen and the type of infection that it causes.

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PANNOTATOR: an automated tool for annotation of pan-genomes

Cited by 24 publications

References 13 publications

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

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

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

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