@inbook{d9f2210fb8574a0cb3d94b4d1b76106c,
title = "Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond",
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.",
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",
author = "Barlow, {Lael D.} and William Maciejowski and Kiran More and Kara Terry and Romana Vargov{\'a} and Krist{\'i}na Z{\'a}honov{\'a} and Dacks, {Joel B.}",
note = "Funding Information: 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{\textquoteright}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 {\'e}t{\'e} financ{\'e}e par le Conseil de recherches en sciences naturelles et en g{\'e}nie du Canada (CRSNG). Copyright: {\textcopyright} 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2023",
doi = "10.1007/978-1-0716-2639-9_26",
language = "English",
isbn = "9781071626382",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "431--452",
editor = "Yanzhuang Wang and Lupashin, {Vladimir V.} and Graham, {Todd R.}",
booktitle = "Golgi",
address = "United States",
}