Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.

Centre for Life's Origin and Evolution Department of Genetics Evolution and Environment University College of London London UK

Department of Biological Sciences University of Alberta Edmonton AB Canada

Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czechia

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec Czechia

Division of Biological Chemistry and Drug Discovery School of Life Sciences University of Dundee Dundee UK

Division of Infectious Diseases Department of Medicine University of Alberta Edmonton AB Canada

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czechia

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