Open Access Research article

Molecular adaptation and resilience of the insect’s nuclear receptor USP

Arnaud Chaumot2, Jean-Luc Da Lage3, Oscar Maestro4, David Martin4, Thomas Iwema5, Frederic Brunet1, Xavier Belles4, Vincent Laudet1 and François Bonneton1*

Author Affiliations

1 Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Université Lyon 1; CNRS; INRA; Ecole Normale Supérieure de Lyon, 32-34 avenue Tony Garnier, Lyon, 69007, France

2 Irstea, UR MALY, Lyon, F-69336, France

3 UPR9034, Laboratoire Evolution, génomes et spéciation (LEGS), CNRS, Gif sur Yvette, 91198, France

4 Institute of Evolutionary Biology (CSIC-UPF), Passeig Marítim de la Barceloneta 37, Barcelona, 08003, Spain

5 Groupe de recherche "immunopathologie et maladies infectieuses (GRI), Universite de la Réunion, Centre CYROI, Cyclotron Réunion Ocean Indien, Sainte Clotilde Ile de la Réunion, 97491, France

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BMC Evolutionary Biology 2012, 12:199  doi:10.1186/1471-2148-12-199

Published: 5 October 2012

Additional files

Additional file 1:

Table S1. Accession numbers of sequences used for alignments.

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Additional file 2:

Table S3. dN/dS of usp in Drosophilidae, Diptera, Lepidoptera, Tenebrionidae and Blattaria.

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Additional file 3:

Table S4. Standard errors [SE] associated to the parameters of the models fitted in the likelihood analysis reported in Table 1.

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Additional file 4:

Figure S1. Robustness of dN/dS estimates to saturation in Diptera usp dataset. The accuracy of the estimate of the β distribution function was tested by re-performing the Codeml analysis (under model M7) on 50 simulated alignments, which were generated with Evolver in the PAML package using the global parameters established for the real usp Diptera dataset (number of sequences, sequence length, topology and branch lengths of the tree, β distribution function for dN/dS, Ts/Tv ratio, codon usage). Bold lines are the same as in Figure 2: Drosophilidae: red; Diptera: purple; Lepidoptera: orange; Tenebrionidae: green; Blattaria: blue. A thin pink line was added for each ones of the 50 re-analysis of the simulated alignments.

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Additional file 5:

Table S5. Comparison between usp and cox1 substitution rates.

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Additional file 6:

Figure S2. Evolutionary rates on the surface of USP structures in four extant groups of insects. Site-specific dN/dS were projected onto the crystal structure of the USP LBD domain of Tribolium (2NXX, ECR-USP) for Blattaria (A) and Tenebrionidae (B), of Drosophila (1HG4, USP) for Diptera (C) and of Heliothis (1R1K, ECR-USP) for Lepidoptera (D). The values are distributed along a colour scale from blue (low dN/dS) to red (high dN/dS). Sequences not available for the estimation of evolutionary rates are in white. Views on the left show the side of the LBD that is near ECR, while views on the right show the same structure after a rotation of 180°.

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Additional file 7:

Table S6. Posterior probabilities for each site to belong to the site-class under positive selection (along branch A or branch B) or relaxation (along branch C).

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Additional file 8:

Figure S3. Selection in the putative coactivation surface during the radiation of Mecopterida. Posterior probabilities for each site to belong to the site-class under positive selection (along branch A or branch B) or relaxed evolution (along branch C) were projected onto the crystal structure of the USP LBD domain of Drosophila (1HG4). Probabilities are distributed along a colour scale from yellow (p=0) to red (p=1). Sequences not available for the estimation of evolutionary rates are in white. (A) Branch A, stem lineage of Mecopterida. (B) Branch B, subdivision between Amphiesmenoptera (Lepidoptera, Trichoptera) and Antliophora (Diptera, Mecoptera, Siphonaptera). (C) Branch C, subdivision of Diptera into the suborders Brachycera and Nematocera. (D) The coactivation surface, defined by homology with RXR, is shown in pink. The helix H12 is showed in green.

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Additional file 9:

Table S2. Relative synonymous codon usage (RSCU).

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Additional file 10:

Table S7. Degenerated primers used to clone usp and cox1 genes.

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