UBCG: Up-to-date Bacterial Core Gene Set and Pipeline for Phylogenomic Tree Reconstruction

Overview

Journal J Microbiol

Specialty Microbiology

Date 2018 Mar 2

PMID 29492869

Citations 380

Authors

Seong-In Na

Yeong Ouk Kim

Seok-Hwan Yoon

Sung-Min Ha

Inwoo Baek

Jongsik Chun

Affiliations

Soon will be listed here.

Abstract

Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.

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