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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Citation and License

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

Published: 4 June 2008

Abstract

Background

The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features.

Results

Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription.

Conclusion

These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes.