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Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds
Genome Biology and Evolution
  • Daniela Almeida, Universidade do Porto - Portugal
  • Emanuel Maldonado, Universidade do Porto - Portugal
  • Imran Khan, Universidade do Porto - Portugal
  • Liliana Silva, Universidade do Porto - Portugal
  • M. Thomas P. Gilbert, University of Copenhagen - Denmark
  • Guojie Zhang, BGI-Shenzhen - China; University of Copenhagen - Denmark
  • Erich D. Jarvis, Duke University; Howard Hughes Medical Institute
  • Stephen J. O'Brien, St. Petersburg State University - Russia; Nova Southeastern University
  • Warren E. Johnson, Smithsonian Conservation Biology Institute
  • Agostinho Antunes, Universidade do Porto - Portugal
Document Type
Article
Publication Date
11-1-2016
Keywords
  • Avian genomes,
  • Cytochrome P450 (CYPs),
  • Substrate recognition sites (SRS),
  • Heme binding areas (HEM),
  • Positive selection
Abstract

The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall,12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K, and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3, and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins.Additionally,we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J, and CYP2K), and migratory behaviors (CYP2D, CYP2H, and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds.

Comments

©The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Additional Comments
Fundacao para a Ciencia e a Tecnologia grant #s: SFRH/BD/79766/2011, SFRH/BD/48518/2008; Russian Ministry of Science Mega-grant # 11.G34.31.0068
Creative Commons License
Creative Commons Attribution-NonCommercial 4.0 International
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
DOI
10.1093/gbe/evw041
Citation Information
Daniela Almeida, Emanuel Maldonado, Imran Khan, Liliana Silva, et al.. "Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds" Genome Biology and Evolution Vol. 8 Iss. 4 (2016) p. 1115 - 1131 ISSN: 1759-6653
Available at: http://works.bepress.com/stephen-obrien/693/