Open Access Research article

Rapid birth-and-death evolution of the xenobiotic metabolizing NAT gene family in vertebrates with evidence of adaptive selection

Audrey Sabbagh128*, Julie Marin34, Charlotte Veyssière34, Emilie Lecompte34, Sotiria Boukouvala5, Estella S Poloni6, Pierre Darlu7 and Brigitte Crouau-Roy34

Author Affiliations

1 Institut de Recherche pour le Développement (IRD), UMR216-Mère et enfant face aux infections tropicales, Paris, France

2 PRES Paris Sorbonne Cité, Université Paris Descartes, Paris, France

3 CNRS, Université Paul Sabatier, ENFA, UMR5174EDB (Laboratoire Évolution & Diversité Biologique), Toulouse F-31062, France

4 Université de Toulouse 3, UMR5174EDB, Toulouse F-31062, France

5 Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece

6 Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland

7 UMR 7206 Eco-anthropologie et ethnobiologie, MNHN-CNRS-Université Denis Diderot, Paris, France

8 IRD UMR 216, Université Paris Descartes, Paris, France

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BMC Evolutionary Biology 2013, 13:62  doi:10.1186/1471-2148-13-62

Published: 7 March 2013

Additional files

Additional file 1:

Alignment result for the set of 77 vertebrate NAT nucleotide sequences.

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Open Data

Additional file 2: Figure S1:

Maximum likelihood tree of vertebrate NATs obtained using PhyML after removing all regions affected by gene conversion from the multiple nucleotide alignment (converted fragments were replaced by ‘?’ characters in the alignment). A general time reversible model with a proportion of invariant sites and gamma distributed among-site rate variation (GTR + I + G) was used, as selected by Akaike information criterion in Modeltest 3.04. The tree is rooted with the three fish species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes) and bootstrap values of 1,000 replicates are shown as percentages at nodes. Bootstrap values are only shown for nodes with greater than 50% support. The clades of Afrotheria, Laurasiatheria, Lagomorpha, Rodentia and Primates are shown in aqua blue, purple, green, blue and red, respectively.

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Additional file 3: Figure S2:

Gene order and orientation in regions surrounding the NAT genes on human (Homo sapiens) and mouse (Mus musculus) chromosome 8. Gene lengths and intergenic distances are not drawn to scale. Double slashes (//) indicate continuing sequence data extending toward the centromeric (cen) and telomeric (tel) parts of the chromosome. Grey boxes indicate NAT-like sequences. The region encompassing the three NAT loci spans approximately 190 kb in human, but less than 60 kb in mouse. In humans, two of the loci are functional (NAT1 and NAT2) and one is a pseudogene (NATP). In mice, all three appear to generate functional transcripts, although no apparent specific substrate for the product of the third locus (Nat3) has been identified. Interestingly, Mouse Nat2 is considered as the functional equivalent of human NAT1, based on substrate profile, tissue distribution and expression during development (see [10] for review).

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Additional file 4: Table S1:

Patterns of nucleotide substitutions along the four branches showing evidence of positive selection in the Pteropus vampyrus clade of NAT genes.

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Additional file 5:

Alignment result for the set of 58 primate NAT nucleotide sequences.

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Additional file 6: Table S2:

Posterior mean of ω as estimated by the codeml program for different regions and different categories of sites in the NAT protein for the four datasets investigated.

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Additional file 7: Table S3:

Comparisons of the mean ω between different regions and categories of sites within the NAT protein sequence.

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Additional file 8: Table S4:

Primers for amplification and sequencing of primate NAT genes.

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Additional file 9: Table S5:

Primer pairs and annealing temperatures used for each primate species for the PCR amplification of the three NAT genes.

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