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Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2557))

Abstract

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.

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Acknowledgments

The authors wish to thank Igor Sinelnikov, Information Services and Technology University of Alberta for his technical expertise in setting up and maintaining the computational cluster on which the Dacks lab AMOEBAE version is housed and on which the beta testing of this version was performed. His technical support over the years for the Dacks Lab computational resources has been invaluable.

AMOEBAE was initially developed at the Dacks Laboratory at the University of Alberta, and was supported by National Sciences and Engineering Council of Canada (NSERC) Discovery grants RES0021028, RES0043758, and RES0046091 awarded to Joel B. Dacks, as well as an NSERC Postgraduate Scholarship-Doctoral awarded to Lael D. Barlow. Kara Terry was supported by an Alberta Innovates Health Solutions Summer Research Studentship. Will Maciejowski was supported by an Office of the Provost and VP (Academic) Summer Studentship Award. Kiran More was supported by an NSERC Alexander Graham Bell Canada Graduate Scholarship - Master’s and a Walter H. Johns Graduate Fellowship.

We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC). Cette recherche a été financée par le Conseil de recherches en sciences naturelles et en génie du Canada (CRSNG).

The authors gratefully acknowledge helpful discussion with many additional past members of the Dacks laboratory, as well as numerous colleagues around the globe particularly in the fields of protistology and evolutionary cell biology.

Author Contributions

LDB conceived of and wrote the AMOEBAE workflow. JBD conceived of the manuscript and directed the collaboration. LDB, WM, KM, KT, RV, and KZ tested the workflow on example datasets as well as other datasets (data not shown) and provided feedback for iterative improvement or identification of problematic dataset types. LDB and JBD drafted the manuscript, and all authors contributed to editing the manuscript.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada

    Lael D. Barlow, William Maciejowski, Kiran More & Joel B. Dacks

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

    Lael D. Barlow

  3. Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada

    Kara Terry & Joel B. Dacks

  4. Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia

    Romana Vargová

  5. Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia

    Kristína Záhonová & Joel B. Dacks

  6. Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia

    Kristína Záhonová

  7. Centre for Life’s Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, London, UK

    Joel B. Dacks

Authors
  1. Lael D. Barlow
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  2. William Maciejowski
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  3. Kiran More
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  4. Kara Terry
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  5. Romana Vargová
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  6. Kristína Záhonová
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  7. Joel B. Dacks
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Corresponding authors

Correspondence to Lael D. Barlow or Joel B. Dacks .

Editor information

Editors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA

    Yanzhuang Wang

  2. Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA

    Vladimir V Lupashin

  3. Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA

    Todd R. Graham

1 Electronic Supplementary Material

Supplementary file 1

Detailed summary of similarity search results output by AMOEBAE (CSV 1849 kb)

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Barlow, L.D. et al. (2023). Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond. In: Wang, Y., Lupashin, V.V., Graham, T.R. (eds) Golgi. Methods in Molecular Biology, vol 2557. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2639-9_26

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  • DOI: https://doi.org/10.1007/978-1-0716-2639-9_26

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2638-2

  • Online ISBN: 978-1-0716-2639-9

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