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Molecular analysis of the Oryzias latipes (Medaka) transcriptome.


Berger,  Anja
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Berger, A. (2010). Molecular analysis of the Oryzias latipes (Medaka) transcriptome. PhD Thesis, Freien Universität Berlin, Berlin.

Based on oligonucleotide fingerprinting (OFP) analysis and subsequent EST production a non-redundant set of 10,016 medaka cDNA clones was established from three different embryonic stages (gastrula, neurula and organogenesis) and one adult tissue (ovary) as a resource of high value for further research on the medaka transcriptome. In a first round 26,880 medaka gastrula clones were subjected to OFP cluster analysis and representatives of each cluster or clones left as singletons were chosen for producing ESTs. In total 7680 cDNA clones were sequenced and 6909 high-quality 5'reads were obtained. The advantage of OFP lies not only in the normalisation but it is also possible to get insight into differential expression by subjecting cDNA libraries of different developmental stages or tissues to fingerprinting analysis. Therefore in a second round in addition to the gastrula clones, cDNA inserts from libraries of the ovary tissue and neurula and organogenesis stages were included. From this approach another 11,468 high-quality 5'ESTs were produced. All EST sequence data was published in GenBank EST database with the accession numbers from AM137442 to AM156757. The 18,377 high-quality sequences obtained were, by EST clustering, grouped into 3268 clusters and 7274 singletons providing us with 10542 unique sequences. Further clustering reduced this set to 10,016 unique sequences. High-quality EST clusters and singletons were annotated. To 8155 of these sequences functions were assigned, with many sequences showing similarity to proteins with important functions, e.g. in development. EST data which showed no similarity to any other known proteins includes by a large amount valuable and high-quality sequence information and must therefore be seen as new Medaka sequence data, either protein-coding or non-coding.