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Related Experiment Video

Updated: May 1, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Phylogenomic Tree Reconstruction from Bacterial Genomes.

Kyung Mo Kim1, Kyuin Hwang2

  • 1Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea. kmkim@kopri.re.kr.

Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2026
PubMed
Summary
This summary is machine-generated.

This study presents a bioinformatics protocol for bacterial phylogenomics, using Docker and GTDB-Tk for accurate tree reconstruction from prokaryotic genomes.

Keywords:
16S ribosomal RNAMaximum-likelihoodPhylogenetic analysisSequence alignmentSubstitution model

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Area of Science:

  • Microbial Ecology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • The rapid growth of prokaryotic genome data has advanced phylogenomics.
  • Comprehensive protocols for bacterial phylogenomic tree reconstruction are lacking.

Purpose of the Study:

  • To provide a detailed bioinformatics protocol for bacterial phylogenomic tree reconstruction.
  • To address challenges in genome-level phylogenetic analyses, such as gene duplication and horizontal gene transfer.

Main Methods:

  • Utilized a Docker environment for consistent implementation.
  • Employed Genome Taxonomy Database (GTDB) toolkits for genome retrieval and quality checking (CheckM).
  • Performed alignment with GTDB-Tk and tree reconstruction with RAxML.

Main Results:

  • Successfully reconstructed phylogenomic trees from five bacterial genomes.
  • Demonstrated the utility of orthologous gene concatenation for accuracy.

Conclusions:

  • The presented protocol offers a robust framework for bacterial phylogenomics.
  • Orthologous gene concatenation is crucial for accurate phylogenetic analyses in the face of genomic complexities.