title: PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.
abstract: A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study.
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: sandipp@u.washington.edu.
authors.forename: Sandip
authors.initials: S
authors.lastname: Paul
authors.affiliation: CSIR - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. Electronic address: archana2287@gmail.com.
authors.forename: Archana
authors.initials: A
authors.lastname: Bhardwaj
authors.affiliation: CSIR - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. Electronic address: sumit.bag@nbri.res.in.
authors.forename: Sumit K
authors.initials: SK
authors.lastname: Bag
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: evs@u.washington.edu.
authors.forename: Evgeni V
authors.initials: EV
authors.lastname: Sokurenko
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: sujayc@u.washington.edu.
authors.forename: Sujay
authors.initials: S
authors.lastname: Chattopadhyay
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D022761:Gene Transfer, Horizontal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D064349:Genome, Microbial / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D015203:Reproducibility of Results; D019779:Salmonella enterica / Q000145:classification / Q000235:genetics; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins
keywords: Core-genome; Draft-genome annotation; Pan-genome; Protein-coding genes