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Updated: Jul 28, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Genealogical inference and more flexible sequence clustering using iterative-PopPUNK.

Bin Zhao1, John A Lees2,3, Hongjin Wu1

  • 1The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

Genome Research
|May 30, 2023
PubMed
Summary
This summary is machine-generated.

Iterative-PopPUNK enhances bacterial genealogy inference by rapidly producing flexible, consistent clusters across various sequence identities. This method improves accuracy for large-scale genome data analysis in public health and clinical settings.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Bacterial genome data is rapidly increasing due to widespread sequencing applications.
  • Accurate and efficient genealogical reconstruction from large datasets remains a challenge.

Purpose of the Study:

  • To enhance the PopPUNK method for increased flexibility and interpretability in bacterial genealogy inference.
  • To develop a method for rapid, accurate, and flexible clustering and phylogenetic analysis of large bacterial genome datasets.

Main Methods:

  • Extension of the alignment- and annotation-free PopPUNK method to iterative-PopPUNK.
  • Rapid generation of multiple consistent cluster assignments across a range of sequence identities.
  • Construction of a partially resolved genealogical tree based on cluster assignments.

Main Results:

  • Iterative-PopPUNK demonstrates accuracy in clustering and genealogical inference on simulated and real bacterial datasets.
  • Phylogenetically concordant results were obtained across seven bacterial species.
  • Achieved variable cluster resolutions, from phylogroup to sequence typing (ST), using *Escherichia/Shigella* and *Vibrio parahaemolyticus* examples.

Conclusions:

  • Iterative-PopPUNK offers a flexible and accurate approach for bacterial genealogy reconstruction from large-scale genome data.
  • The method supports user-defined resolution levels for diverse applications in clinical diagnostics and population genetics.
  • The iterative-PopPUNK algorithm is implemented in the 'PopPUNK_iterate' program for accessible use.