Open Access Research article

The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula

Mélanie Debiais-Thibaud135, Silvan Oulion136, Franck Bourrat4, Patrick Laurenti12, Didier Casane12 and Véronique Borday-Birraux12*

Author Affiliations

1 Evolution des familles multigéniques, Laboratoire Evolution Génome et Spéciation, UPR9034 CNRS, 1 avenue de la terrasse, 91198 Gif-sur-Yvette, France

2 UFR des Sciences du Vivant, Université Paris Diderot Sorbonne Paris Cité, 5 rue Marie-Andrée Lagroua Weill-Hallé, 75205 Paris Cedex 13, France

3 UFR Sciences, Université Paris-Sud 11, 91405 Orsay Cedex, France

4 Laboratoire Neurobiologie et Développement, Institut de Neurobiologie Alfred Fessard, UPR3294 CNRS, 1 avenue de la terrasse, 91198 Gif-sur-Yvette, France

5 Département Forme, Institut des Sciences de l'Evolution - Montpellier, UMR5554 CNRS/Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier cedex05, France

6 Evolution et développement des chordés, Biologie Intégrative des Organismes Marins, UMR7232 CNRS/UMPC Université Paris 6, Observatoire océanologique, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France

For all author emails, please log on.

BMC Evolutionary Biology 2011, 11:307  doi:10.1186/1471-2148-11-307

Published: 18 October 2011

Additional files

Additional file 1:

Assignment of the Dlx probes to their group of orthologues. In order to assign each Dlx probe to an orthologous group, phylogenetic analyses were performed. The Dlx gene sequences of Triakis semifiasciata (leopard shark), Homo sapiens (human), Gallus gallus (chicken), Xenopus tropicalis (xenopus), Danio rerio (zebrafish) were retrieved from Ensembl release 49 and GenBank release 164. Multiple Dlx amino acid sequences were aligned using ClustalX (Thompson et al. 1997) with manual optimization using MUST software (Philippe 1993). Regions of ambiguous homology were removed. Evolutionary distances were computed using the Poisson correction and a neighbor-joining tree was obtained using MEGA4 (Tamura et al. 2007). The robustness of the tree nodes was estimated by a bootstrap test (1000 replicates). Philippe H. 1993. MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21:5264-5272. Tamura K, Dudley J, Nei M, and Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.

Format: PDF Size: 98KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Position of Dlx probes on the coding sequences of T. semifasciata. The position of a probe is indicated by a grey line. The position of introns (I), the position of homeobox sequences (black box) and the length of each coding sequence (cds) and of each probe are indicated.

Format: PDF Size: 178KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Test of Dlx probes activity during early stages of embryogenesis in the dogfish. Lateral view of whole mount in situ hybridized embryos with the Dlx probes designed for the 6 dogfish Dlx genes. For each panel, the name of the probe is indicated up right and the stage of the hybridized embryo down right.

Format: PDF Size: 503KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Statistical evaluation of differences between Dlx expression patterns in gnathostome odontode development. A. Matrix describing the expression pattern of each Dlx gene from the mouse, zebrafish, medaka and dogfish, during all four odontode developmental stages (see text for a description), either in the epithelial (e) or mesenchymal (m) compartment. Data are as of Table 3, but different columns were made for oral (o) versus pharyngeal (p) teeth in medaka, or scales (s) versus oral teeth (o) in dogfish. B. Neighbor Joining tree inferred with a pairwise distance (number of differences) matrix estimated with the matrix of characters shown in A.

Format: PDF Size: 74KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Primer sequences. Primer names follow the description in the Additional file 2.

Format: PDF Size: 48KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data