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An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

Bianca Habermann1*, Anne-Gaelle Bebin2, Stephan Herklotz2, Michael Volkmer1, Kay Eckelt2, Kerstin Pehlke3, Hans Henning Epperlein3, Hans Konrad Schackert4, Glenis Wiebe2 and Elly M Tanaka2*

Author Affiliations

1 Scionics Computer Innovation GmbH, Pfotenhauerstrasse 110, Dresden 01307, Germany

2 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany

3 Institute of Anatomy, Medical Faculty of the Carl Gustav Carus Technical University, Dresden, Fetscherstrasse 74, Dresden 01307, Germany

4 Department of Surgical Research, Medical Faculty of the Carl Gustav Carus Technical University, Dresden, Fetscherstrasse 74, Dresden 01307, Germany

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Genome Biology 2004, 5:R67  doi:10.1186/gb-2004-5-9-r67

Published: 13 August 2004



The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum.


Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians.


Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online.