ITEP: An integrated toolkit for exploration of microbial pan-genomes

Abstract

BackgroundComparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large numbers of related genomes in a single project, requiring computational tools for their integrated analysis. In particular, accurate annotations and identification of gene presence and absence are critical for understanding and modeling the cellular physiology of newly sequenced genomes. Although many tools are available to compare the gene contents of related genomes, new tools are necessary to enable close examination and curation of protein families from large numbers of closely related organisms, to integrate curation with the analysis of gain and loss, and to generate metabolic networks linking the annotations to observed phenotypes.ResultsWe have developed ITEP, an Integrated Toolkit for Exploration of microbial Pan-genomes, to curate protein families, compute similarities to externally-defined domains, analyze gene gain and loss, and generate draft metabolic networks from one or more curated reference network reconstructions in groups of related microbial species among which the combination of core and variable genes constitute the their "pan-genomes". The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. ITEP’s capabilities include de novo protein family prediction, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, annotation curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.ConclusionsITEP is a powerful, flexible toolkit for generation and curation of protein families. ITEP's modular design allows for straightforward extension as analysis methods and tools evolve. By integrating comparative genomics with the development of draft metabolic networks, ITEP harnesses the power of comparative genomics to build confidence in links between genotype and phenotype and helps disambiguate gene annotations when they are evaluated in both evolutionary and metabolic network contexts.

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

“…SnpEff (16) was used to annotate SNPs as falling into protein-encoding (coding DNA sequence [CDS]) or non-protein-encoding regions, with the former also designated synonymous or nonsynonymous SNPs. The CDS SNPs were also annotated as core genome versus accessory genome by searching against a list of core genes obtained from a Markov clustering (MCL) method implemented in ITEP (Integrated Toolkit for Exploration of microbial Pan-genomes) (17). In short, a gene presence-absence matrix was constructed for finished genomes used in this study, using an MCL inflation value of 2.0 and a BLAST maxbit score of 0.4.…”

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

“…Conservation of the genes that are differentially expressed between MeOH and acetate growth. Each vertical bar indicates that a homolog for the differentially expressed gene exists in the indicated species (computed as the bidirectional best hits functionality in the ITEP software [92] with an E-value cut-off of 10 −5 for a database of ∼125000 proteins). Most differentially expressed genes are highly conserved among the Methanosarcinales ; however a core set of genes are conserved across all methanogens …”

“…The Integrated Toolkit for Exploration of Microbial Pan-genomes (ITEP) was used to compare conservation of differentially expressed genes [92]. ITEP was used to construct a database of ∼60 methanogens with published complete or nearly complete genomes.…”

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

“…An ITEP database [45] of 221 archaea, including each of the organisms in Table 1, was constructed using the default parameters. Briefly, ITEP is a software toolkit for examining microbial pan-genomes that provides functionality for constructing a BLAST database and querying protein family prediction, ortholog detection, and analysis of functional domains.…”