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


RESULTS
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.


CONCLUSIONS
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.
Habermann
Bianca
B
Scionics Computer Innovation GmbH, Pfotenhauerstrasse 110, Dresden 01307, Germany. habermann@mpi-cbg.de
Bebin
Anne-Gaelle
AG
Herklotz
Stephan
S
Volkmer
Michael
M
Eckelt
Kay
K
Pehlke
Kerstin
K
Epperlein
Hans Henning
HH
Schackert
Hans Konrad
HK
Wiebe
Glenis
G
Tanaka
Elly M
EM
D000557:Ambystoma / Q000196:embryology* / Q000235:genetics*; D000818:Animals; D001482:Base Composition / Q000235:genetics; D002453:Cell Cycle / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D002454:Cell Differentiation / Q000235:genetics; D049109:Cell Proliferation; D017124:Conserved Sequence / Q000235:genetics; D020451:Contig Mapping / Q000379:methods; D050759:Cyclin-Dependent Kinase Inhibitor p21; D030541:Databases, Genetic; D004625:Embryo, Nonmammalian / Q000737:chemistry / Q000378:metabolism; D020224:Expressed Sequence Tags; D015723:Gene Library; D005796:Genes / Q000235:genetics; D018816:Genes, cdc; D005810:Multigene Family / Q000235:genetics; D009432:Neural Crest / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D012313:RNA / Q000378:metabolism; D012038:Regeneration / Q000235:genetics*; D012100:Reproduction, Asexual / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013623:Tail / Q000196:embryology
D018797:Cell Cycle Proteins; D050759:Cyclin-Dependent Kinase Inhibitor p21; D012313:RNA