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Oikopleura dioica

Whole genome shotgun

Genoscope is sequencing the genome of the tunicate Oikopleura dioica, using the whole genome shotgun strategy. The size of this genome has been estimated at 72 Mb by flow cytometry. Two libraries with a mean insert size of 3 kb and 10 kb have been constructed using sperm from a few hundred inbred males (obtained after 15 generations of brother-sister matings). This material should therefore have a high level of homozygosity : among the animal genome sequencing projects, only the projects concerning major model species (Drosophila, mouse, Caenorhabditis elegans) have so far enjoyed such an advantage. Genoscope will perform a total of 1 000 000 reads at the beginning of the year 2004 on these two libraries (3/4 on the first one and 1/4 on the second one) in order to reach a 10 X coverage. A first assembly will be done at 3 X.

The team led by Daniel Chourrout at the Sars center in Bergen, Norway, has a library of 9216 BAC clones (15 - 20 X coverage) with a mean insert size of 135 kb. The Sars center has started physical mapping (fingerprinting) on these clones, whose ends are also being sequenced at the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin. These resources will help in the final assembly stage.

The annotation of the Oikopleura dioica genomic sequence will be facilitated by the very high exon density. Genoscope will undertake an automatic annotation, taking advantage of the comparative genomics resources offered by the availability of the genomic draft of another tunicate, Ciona intestinalis, and of a small collection of ESTs from Oikopleura dioica (more than a thousand clones).

Last update on 16 January 2008

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