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A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network
Ehdieh Khaledian1, Kelly A Brayton1,2,3, Shira L Broschat1,2,3
1School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164, USA.
Microorganisms
|February 28, 2020
Summary
This study introduces a novel phylogenetic tree construction method using whole bacterial proteomes. It identifies conserved protein sequences to reveal evolutionary relationships and detect horizontal gene transfer events.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Phylogenetic tree reconstruction historically relied on single genes (e.g., rRNA) or ad hoc gene combinations.
- Limited gene sets can lead to less robust evolutionary inferences.
- Increasing availability of complete genomes enables whole-genome-based phylogenetic analyses.
Purpose of the Study:
- To develop a systematic approach for constructing phylogenetic trees using complete bacterial proteomes.
- To identify conserved protein sequences for robust evolutionary analysis.
- To detect horizontal gene transfer events in bacterial species.
Main Methods:
- Clustering of complete proteomes from 360 bacterial species.
- Identification of 49 protein sequences shared by 99% of the organisms.
- Construction of a phylogenetic tree using these conserved proteins.
- Network analysis of homologous clusters to identify horizontal gene transfer.
Main Results:
- A phylogenetic tree was constructed based on 49 conserved protein sequences from 360 bacterial species.
- 47 of these sequences showed homology across bacteria, archaea, and eukarya.
- A network analysis successfully identified bacterial species with horizontally transferred genes.
Conclusions:
- Whole-proteome analysis offers a more robust method for phylogenetic reconstruction than traditional gene-based approaches.
- The identified conserved proteins are valuable markers for bacterial phylogeny.
- The method effectively detects horizontal gene transfer, providing insights into bacterial evolution.
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