Ortholog-Finder: A Tool for Constructing an Ortholog Data Set

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Ortholog identification is crucial for species phylogeny but challenged by horizontal gene transfer (HGT) and out-paralogs.
• Distinguishing true orthologs from these confounding factors is essential for accurate evolutionary reconstructions.

Purpose of the Study:

• To develop and present Ortholog-Finder, a novel program designed to generate high-quality ortholog datasets for phylogenetic analysis.
• To minimize the impact of horizontal gene transfer (HGT) and out-paralogs on phylogenetic tree construction.

Main Methods:

• Ortholog-Finder employs five key processes: HGT filtering based on base composition, out-paralog filtering via sequence similarity, phylogenetic tree classification (monophyletic/polyphyletic), tree splitting, and threshold adjustment.
• The program utilizes all open-reading frame data for comprehensive analysis.
• Validation involved simulation data and phylogenetic reconstruction for 12 Gram-positive bacteria.

Main Results:

• Ortholog-Finder effectively filters out genes affected by horizontal gene transfer (HGT) and out-paralogs.
• The program successfully generated reliable ortholog datasets, leading to accurate phylogenetic trees.
• Phylogenetic analysis of 12 Gram-positive bacteria using Ortholog-Finder-derived data demonstrated validated tree nodes.

Conclusions:

• Ortholog-Finder provides a robust solution for obtaining accurate ortholog data sets, essential for reliable phylogenetic analyses.
• The developed methods effectively mitigate the challenges posed by horizontal gene transfer (HGT) and out-paralogs in evolutionary studies.
• The program's application in bacterial phylogeny highlights its utility and accuracy in reconstructing evolutionary relationships.