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

Lael D. Barlow (Lead / Corresponding author), William Maciejowski, Kiran More, Kara Terry, Romana Vargová, Kristína Záhonová, Joel B. Dacks (Lead / Corresponding author)

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review

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.

Original languageEnglish
Title of host publicationGolgi
Subtitle of host publicationMethods and Protocols
EditorsYanzhuang Wang, Vladimir V. Lupashin, Todd R. Graham
Place of PublicationNew York
PublisherHumana Press
Pages431-452
Number of pages22
ISBN (Electronic)9781071626399
ISBN (Print)9781071626382
DOIs
Publication statusPublished - 2023

Publication series

NameMethods in Molecular Biology
Volume2557
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Amoeba/genetics
  • Reproducibility of Results
  • Genomics/methods
  • Biological Evolution
  • Golgi Apparatus/metabolism
  • Computational Biology/methods
  • Basidiomycete
  • Adaptin
  • Comparative genomics
  • Workflow
  • Computational pipeline
  • Molecular evolution
  • Homology searching
  • Evolutionary Cell Biology
  • Golgi
  • BLAST

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