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Open Access Research article

From biomedicine to natural history research: EST resources for ambystomatid salamanders

Srikrishna Putta1, Jeramiah J Smith1, John A Walker1, Mathieu Rondet2, David W Weisrock1, James Monaghan1, Amy K Samuels1, Kevin Kump1, David C King3, Nicholas J Maness4, Bianca Habermann5, Elly Tanaka6, Susan V Bryant2, David M Gardiner2, David M Parichy7 and S Randal Voss1*

  • * Corresponding author: S Randal Voss srvoss@uky.edu

  • † Equal contributors

Author Affiliations

1 Department of Biology, University of Kentucky, Lexington, KY 40506, USA

2 Department of Developmental and Cell Biology and the Developmental Biology Center, University of California, Irvine, CA 92697, USA

3 The Life Sciences Consortium, 519 Wartik Laboratory, Penn State University, University Park, PA 16802, USA

4 Department of Zoology, University of Wisconsin-Madison, 250 N. Mills, Madison, WI 53706, USA

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

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

7 Section of Integrative Biology and Section of Molecular, Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA

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BMC Genomics 2004, 5:54  doi:10.1186/1471-2164-5-54

Published: 13 August 2004

Abstract

Background

Establishing genomic resources for closely related species will provide comparative insights that are crucial for understanding diversity and variability at multiple levels of biological organization. We developed ESTs for Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum), species with deep and diverse research histories.

Results

Approximately 40,000 quality cDNA sequences were isolated for these species from various tissues, including regenerating limb and tail. These sequences and an existing set of 16,030 cDNA sequences for A. mexicanum were processed to yield 35,413 and 20,599 high quality ESTs for A. mexicanum and A. t. tigrinum, respectively. Because the A. t. tigrinum ESTs were obtained primarily from a normalized library, an approximately equal number of contigs were obtained for each species, with 21,091 unique contigs identified overall. The 10,592 contigs that showed significant similarity to sequences from the human RefSeq database reflected a diverse array of molecular functions and biological processes, with many corresponding to genes expressed during spinal cord injury in rat and fin regeneration in zebrafish. To demonstrate the utility of these EST resources, we searched databases to identify probes for regeneration research, characterized intra- and interspecific nucleotide polymorphism, saturated a human – Ambystoma synteny group with marker loci, and extended PCR primer sets designed for A. mexicanum / A. t. tigrinum orthologues to a related tiger salamander species.

Conclusions

Our study highlights the value of developing resources in traditional model systems where the likelihood of information transfer to multiple, closely related taxa is high, thus simultaneously enabling both laboratory and natural history research.