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UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

  • Systems and Synthetic Microbiology and Bioinformatics
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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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Authors and Affiliations

  1. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 00826, Republic of Korea

    Seong-In Na, Yeong Ouk Kim & Jongsik Chun

  2. Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 00826, Republic of Korea

    Seong-In Na, Yeong Ouk Kim, Inwoo Baek & Jongsik Chun

  3. School of Biological Sciences, Seoul National University, Seoul, 00826, Republic of Korea

    Sung-min Ha, Inwoo Baek & Jongsik Chun

  4. ChunLab, Inc., Seoul, 06725, Republic of Korea

    Seok-Hwan Yoon, Sung-min Ha & Jongsik Chun

Authors
  1. Seong-In Na
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  2. Yeong Ouk Kim
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  3. Seok-Hwan Yoon
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  4. Sung-min Ha
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  5. Inwoo Baek
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  6. Jongsik Chun
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Correspondence to Jongsik Chun.

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Supplemental material for this article may be found at http://www.springerlink.com/content/120956

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Na, SI., Kim, Y.O., Yoon, SH. et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol. 56, 280–285 (2018). https://doi.org/10.1007/s12275-018-8014-6

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  • DOI: https://doi.org/10.1007/s12275-018-8014-6

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