The 16S rRNA gene has played an essential role in bacterial taxonomy by providing a universally applicable phylogenetic framework. However, this single gene contains only about 1,500 bp which inheritably limits the resolution of the analysis. Here, we present the set of bacterial core genes that covers all phyla, which we named UBCG (up-to-date bacterial core gene). The current UBCG set was calculated using complete genomes of 1,492 species covering 28 phyla, consisting of 92 genes .
The package provides the following features:
- Extraction of UBCGs from genome assemblies
- Multiple-alignment of 92 gene sequences
- Concatenation of 92 gene sequences
- Filtering positions of multiple-alignments
- Phylogenetic analysis using RAxML and FastTree
- Calculation of Gene Support Index (GSI) which indicates how many genes support the branch in the concatenated phylogenetic tree (named UBCG tree)
Citing this software
Na, S. I., Kim, Y. O., Yoon, S. H., Ha, S. M., Baek, I. & Chun, J. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56, (in press).
UBCG can be used without any restrictions. However, its redistribution in any way, form, shape, or derivative is strictly prohibited.