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Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond
Lael D Barlow1,2, William Maciejowski3, Kiran More3
1Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada. lbarlow001@dundee.ac.uk.
Methods in Molecular Biology (Clifton, N.J.)
|December 13, 2022
Summary
AMOEBAE is a new workflow for comparative genomic analysis, aiding evolutionary cell biology research. It reveals the Golgi protein AP4 Epsilon as the sole AP4 complex subunit in basidiomycete fungi.
Area of Science:
- Evolutionary cell biology
- Comparative genomics
- Bioinformatics
Background:
- An evolutionary approach offers novel insights into cellular mechanisms and their development.
- Comparative genomics is vital for this research but faces technical hurdles.
- The Golgi apparatus, like other cellular systems, benefits from evolutionary study.
Purpose of the Study:
- Introduce AMOEBAE, a customizable workflow for mid-range comparative genomic analyses.
- Provide a protocol for using AMOEBAE, including its rationale, application, and limitations.
- Demonstrate the utility of AMOEBAE with an example dataset.
Main Methods:
- Developed AMOEBAE, a flexible workflow for comparative genomic and transcriptomic data analysis.
- Enabled user customization of parameters, queries, and taxonomic sampling.
- Included a protocol and example dataset for practical application.
Main Results:
- The Golgi protein AP4 Epsilon was identified as the sole retained subunit of the AP4 complex in basidiomycete fungi.
- AMOEBAE facilitates reproducible and efficient comparative genomic studies.
- The workflow balances analytical rigor with user interpretation.
Conclusions:
- AMOEBAE enhances the integration of evolutionary context into cell biology research.
- The tool supports researchers in overcoming technical challenges in comparative genomics.
- Further adoption of such tools can advance evolutionary cell biology studies.
Keywords:
AdaptinBLASTBasidiomyceteComparative genomicsComputational pipelineEvolutionary Cell BiologyGolgiHomology searchingMolecular evolutionWorkflowMore Related Videos
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