| Title | UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction |
|---|---|
| Author | Seong‑In Na1,2, Michael James Bailey1, Mauricio Chalita1, Jae Hyoung Cho1, and Jongsik Chun1,2* |
| Address | 1CJ Bioscience, Seoul 04527, Republic of Korea, 2Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea |
| Bibliography | Journal of Microbiology, 61(7),683-692, 2023, |
| DOI | 10.1007/s12275-023-00064-2 |
| Key Words | Phylogenomics · Archaea · Software · Core gene · Phylogeny · UACG |
| Abstract | In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard method. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https:// www. ezbio cloud. net/ tools/ uacg. |