| Title | UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis |
|---|---|
| Author | Jihyeon Kim1,2, Seong-In Na1, Dongwook Kim1,2, and Jongsik Chun1,2,3* |
| 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, 3School of Biological Sciences, Seoul National University, Seoul 00826, Republic of Korea |
| Bibliography | Journal of Microbiology, 59(6),609–615, 2021, |
| DOI | 10.1007/s12275-021-1231-4 |
| Key Words | phylogeny, phylogenetic analysis, phylogenomics, bacterial core genes |
| Abstract | Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2. |