UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction

Seong-In Na; Michael James Bailey; Mauricio Chalita; Jae Hyoung Cho; Jongsik Chun

doi:10.1007/s12275-023-00064-2

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UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction: Seong-In Na ^1,2, Michael James Bailey ¹, Mauricio Chalita ¹, Jae Hyoung Cho ¹, Jongsik Chun ^1,2; Journal of Microbiology 2023;61(7):683-692.
DOI: https://doi.org/10.1007/s12275-023-00064-2
Published online: August 11, 2023

¹CJ Bioscience, Seoul 04527, Republic of Korea, ²Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea

Corresponding author: Jongsik Chun ,

Received: 15 May 2023 • Revised: 19 June 2023 • Accepted: 23 June 2023

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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.

Keywords: Phylogenomics · Archaea · Software · Core gene · Phylogeny · UACG

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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
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International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

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UACG: Up‑to‑Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction

J. Microbiol. 2023;61(7):683-692. Published online August 11, 2023

DOI: https://doi.org/10.1007/s12275-023-00064-2

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