bcgTree: automatized phylogenetic tree building from bacterial core genomes

• Published in: Genome Vol. 59; no. 10; pp. 783 - 791
• Main Authors: Ankenbrand, Markus J, Keller, Alexander
• Format: Journal Article
• Language: English
• Published: Canada NRC Research Press 01.10.2016; Canadian Science Publishing NRC Research Press
• Subjects: Analysis; Bacteria; Bacteria - classification; Bacteria - genetics; Bacterial genetics; bactéries; bioinformatics; Computational Biology - methods; Deoxyribonucleic acid; DNA; DNA barcoding; Forecasts and trends; Genes; Genetic research; genome; Genome, Bacterial; Genomes; génome; high-throughput nucleotide sequencing; Lactobacillus; Lactobacillus - classification; Lactobacillus - genetics; Markov analysis; Markov chain; Markov Chains; multi-gene; multigénique; Phylogenetics; phylogenomics; Phylogeny; phylogénie; phylogénomique; Reproducibility of Results; ribosomal DNA; RNA, Ribosomal, 16S - genetics; Software; taxonomy; Web Browser; Workflow; genome; génome; bacteria; bactéries; multigénique; phylogeny; phylogénie; multi-gene; phylogenomics; phylogénomique
• ISSN: 0831-2796; 1480-3321; 1480-3321
• DOI: 10.1139/gen-2015-0175

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).