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Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention
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Giannakis, Konstantinos, Arrowsmith, Samuel J., Richards, Luke, Gasparini, Sara, Chustecki, Joanna M., Røyrvik, Ellen C. and Johnston, Iain G. (2022) Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention. Cell Systems, 13 (11). 874-884.E5. doi:10.1016/j.cels.2022.08.007 ISSN 2405-4712.
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WRAP-Evolutionary-inference-across-eukaryotes-identifies-universal-features-shaping-organelle-gene-retention-Richards-2022.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (8Mb) | Preview |
Official URL: http://dx.doi.org/10.1016/j.cels.2022.08.007
Abstract
Mitochondria and plastids power complex life. Why some genes and not others are retained in their organelle DNA (oDNA) genomes remains a debated question. Here, we attempt to identify the properties of genes and associated underlying mechanisms that determine oDNA retention. We harness over 15k oDNA sequences and over 300 whole genome sequences across eukaryotes with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection. Previously hypothesized features, including the hydrophobicity of a protein product, and less well-known features, including binding energy centrality within a protein complex, predict oDNA retention across eukaryotes, with additional influences of nucleic acid and amino acid biochemistry. Notably, the same features predict retention in both organelles, and retention models learned from one organelle type quantitatively predict retention in the other, supporting the universality of these features—which also distinguish gene profiles in more recent, independent endosymbiotic relationships. A record of this paper’s transparent peer review process is included in the supplemental information.
Item Type: | Journal Article | |||||||||
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Subjects: | Q Science > QH Natural history | |||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
Library of Congress Subject Headings (LCSH): | Eukaryotic cells, Eukaryotic cells -- Genetics, Cell organelles, Mitochondria , Plastids | |||||||||
Journal or Publication Title: | Cell Systems | |||||||||
Publisher: | Cell Press | |||||||||
ISSN: | 2405-4712 | |||||||||
Official Date: | November 2022 | |||||||||
Dates: |
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Volume: | 13 | |||||||||
Number: | 11 | |||||||||
Number of Pages: | 11 | |||||||||
Page Range: | 874-884.E5 | |||||||||
DOI: | 10.1016/j.cels.2022.08.007 | |||||||||
Status: | Peer Reviewed | |||||||||
Publication Status: | Published | |||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||
Date of first compliant deposit: | 10 October 2022 | |||||||||
Date of first compliant Open Access: | 11 October 2022 | |||||||||
RIOXX Funder/Project Grant: |
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