Open Access Research

Chætognath transcriptome reveals ancestral and unique features among bilaterians

Ferdinand Marlétaz12, André Gilles34, Xavier Caubit25, Yvan Perez34, Carole Dossat678, Sylvie Samain678, Gabor Gyapay678, Patrick Wincker678 and Yannick Le Parco12*

Author Affiliations

1 CNRS UMR 6540 DIMAR, Station Marine d'Endoume, Centre d'Océanologie de Marseille, Chemin de la Batterie des Lions, 13007, Marseille, France

2 Université de la Méditerranée Aix-Marseille II, Bd Charles Livon, 13284, Marseille, France

3 Université de Provence Aix-Marseille I, place Victor-Hugo, 13331, Marseille, France

4 CNRS UMR 6116 IMEP, Centre St Charles, place Victor-Hugo, 13331, Marseille, France

5 CNRS UMR 6216, IBDML, Campus de Luminy, Route Léon Lachamp, 13288, Marseille, France

6 Genoscope (CEA), rue Gaston Crémieux, BP5706, 91057 Evry, France

7 CNRS, UMR 8030, rue Gaston Crémieux, BP5706, 91057 Evry, France

8 Université d'Evry, Boulevard François Mitterrand, 91025, Evry, France

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Genome Biology 2008, 9:R94  doi:10.1186/gb-2008-9-6-r94

Published: 4 June 2008

Additional files

Additional data file 1:

Figure S1: EST library statistics. Figure S2: Gene Ontology annotation. Figure S3: alignment of GAMT in selected taxa. Figure S4: trees illustrating the divergence between copies of nuclear and mitochondrial genes in the library. Figure S5: transition versus transversion ratios for the five targeted genes. Figure S6: mismatch analyses and testing for the five targeted genes.

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Open Data

Additional data file 2:

Table S1: composition of the composite taxa involved in phylogenomic analyses. Table S2: list of all clusters of transcripts corresponding to alternative forms or not with Ka/Ks ratios. Table S3: list of primers employed for PCR amplifications of alternative forms. Table S4: comparison of molecular evolution trends for four genes retrieved in nine individuals. Table S5: annotation of the BAC 35A21.

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Open Data

Additional data file 3:

Trans-spliced genes conserved between S. cephaloptera and C. elegans and homologous to a SwissProt entry (Figure S6 in Additional data file 1).

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Additional data file 4:

This dataset was employed for phylogenomic reconstruction.

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Additional data file 5:

Transcript sequences of RP L36 exhibiting the alternative forms corresponding to paralogous copies and the position of primers designed to specifically amplify these forms.

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Additional data file 6:

Transcript sequences of RP L40 exhibiting the alternative forms corresponding to paralogous copies and the position of primers designed to specifically amplify these forms.

Format: FAST Size: 34KB Download file

Open Data

Additional data file 7:

Alignment of amino acid sequences of RUX paralogs and variants from S. cephaloptera and some other eukaryotic taxa.

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Additional data file 8:

Primers employed for the specific amplifications are included.

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Additional data file 9:

Alignment of cytochrome oxydase I transcripts retrieved from the EST library.

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Additional data file 10:

Alignment of cytochrome oxydase III transcripts retrieved from the EST library.

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Additional data file 11:

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

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Additional data file 12:

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

Format: FAST Size: 25KB Download file

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Additional data file 13:

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

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Additional data file 14:

Sequences were amplified from the body (B) or head (H) of individuals as indicated in the sequence name.

Format: FAST Size: 16KB Download file

Open Data

Additional data file 15:

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

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Additional data file 16:

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

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Open Data

Additional data file 17:

All the alignments in Additional data files 15, 16, 17 clearly exhibit lack of a SL motif in the genomic sequence.

Format: FAST Size: 4KB Download file

Open Data