| Title | UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction |
|---|---|
| Author | Seong-In Na1,2, Yeong Ouk Kim1,2, Seok-Hwan Yoon3, Sung-min Ha3,4, Inwoo Baek2,4, and Jongsik Chun1,2,4* |
| Address | 1Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea, 2Institute of Molecular Biology & Genetics, Seoul National University, Seoul 00826, Republic of Korea, 3ChunLab, Inc., Seoul 06725, Republic of Korea, 4School of Biological Sciences, Seoul National University, Seoul 00826, Republic of Korea |
| Bibliography | Journal of Microbiology, 56(4),280–285, 2018, |
| DOI | 10.1007/s12275-018-8014-6 |
| Key Words | phylogeny, phylogenetic analysis, phylogenomics, bacterial core gene |
| 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. |