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Marlétaz F
Gilles A
Caubit X
Perez Y
Dossat C
Samain S
Gyapay G
Wincker P
Le Parco Y

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Marlétaz F
Gilles A
Caubit X
Perez Y
Dossat C
Samain S
Gyapay G
Wincker P
Le Parco Y
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Chætognath transcriptome reveals ancestral and unique features among bilaterians

Ferdinand Marlétaz¹^,2 , André Gilles³^,4 , Xavier Caubit²^,5 , Yvan Perez³^,4 , Carole Dossat⁶^,7^,8 , Sylvie Samain⁶^,7^,8 , Gabor Gyapay⁶^,7^,8 , Patrick Wincker⁶^,7^,8 and Yannick Le Parco¹^,2

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

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

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

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

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

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

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

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

author email corresponding author email

Genome Biology 2008, 9:R94doi:10.1186/gb-2008-9-6-r94


Published:	4 June 2008

Subject areas: Evolution, Genetics, Genome studies

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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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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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.

Format: FAST Size: 333KB Download file

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.

Format: FAST Size: 36KB Download file

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

Additional data file 7:

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

Format: FAST Size: 1KB Download file

Additional data file 8:

Primers employed for the specific amplifications are included.

Format: FAST Size: 21KB Download file

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.

Format: FAST Size: 27KB Download file

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

Additional data file 13:

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

Format: FAST Size: 17KB Download file

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

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.

Format: FAST Size: 6KB Download file

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