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Evolutionary Relationships through Genome Comparisons

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Topiary: Pruning the manual labor from ancestral sequence reconstruction.

Kona N Orlandi^1,2, Sophia R Phillips^1,3, Zachary R Sailer^1,3

¹Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.

Protein Science : a Publication of the Protein Society

|December 24, 2022

Summary

Topiary simplifies ancestral sequence reconstruction (ASR) by automating complex phylogenetic analyses. This pipeline makes studying protein evolution accessible to researchers without extensive bioinformatics expertise.

Keywords:

ASR ancestral sequence reconstruction bioinformatics evolutionary biochemistry phylogenetics protein

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Area of Science:

Evolutionary biology
Computational biology
Bioinformatics

Background:

Ancestral sequence reconstruction (ASR) offers insights into protein evolution, function, and structure.
Current ASR methods are complex, requiring multiple software packages and specialized knowledge, limiting their widespread adoption.

Purpose of the Study:

To introduce Topiary, a user-friendly software pipeline designed to simplify and automate ancestral sequence reconstruction.
To enable researchers, including non-experts, to conduct sophisticated evolutionary analyses of proteins.

Main Methods:

Topiary integrates tools for sequence retrieval (BLAST), quality control, multiple sequence alignment (Muscle5), phylogenetic tree generation (RAxML-NG), gene-species tree reconciliation (GeneRax), and ancestral sequence reconstruction (PastML).
The pipeline utilizes online databases like NCBI and the Open Tree of Life for data retrieval.
User input is simplified to a spreadsheet of protein sequences.

Main Results:

Topiary automates the entire ASR workflow, from sequence acquisition to the generation of annotated evolutionary trees and quality summaries.
The pipeline successfully reconstructs ancestral amino acid sequences and determines branch supports.
Validation using diverse protein families demonstrates the pipeline's robustness and applicability.

Conclusions:

Topiary significantly lowers the barrier to entry for performing ancestral sequence reconstruction.
The software empowers a broader range of scientists to investigate protein evolution and its underlying sequence-structure-function relationships.