title: Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds.
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.
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal.
authors.forename: Daniela
authors.initials: D
authors.lastname: Almeida
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.
authors.forename: Emanuel
authors.initials: E
authors.lastname: Maldonado
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal.
authors.forename: Imran
authors.initials: I
authors.lastname: Khan
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal.
authors.forename: Liliana
authors.initials: L
authors.lastname: Silva
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzen, China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark Howard Hughes Medical Institute, Chevy Chase, Maryland.
authors.forename: Erich D
authors.initials: ED
authors.lastname: Jarvis
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia Oceanographic Center, Nova Southeastern University, Ft Lauderdale.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.affiliation: National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC.
authors.forename: Warren E
authors.initials: WE
authors.lastname: Johnson
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Portugal aantunes@ciimar.up.pt.
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
mesh_terms: D025041:Animal Migration; D000818:Animals; D030161:Avian Proteins / Q000235:genetics*; D001717:Birds / Q000235:genetics* / Q000502:physiology; D000072467:Cytochrome P450 Family 2 / Q000235:genetics*; D019143:Evolution, Molecular; D005247:Feeding Behavior; D016678:Genome; D008958:Models, Molecular; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D030161:Avian Proteins; D000072467:Cytochrome P450 Family 2
keywords: avian genomes; cytochrome P450 (CYPs); heme binding areas (HEM); positive selection; substrate recognition sites (SRS)