BMC Genomics Research article BioMed Central Open Access From biomedicine to natural history research: EST resources for ambystomatid salamanders Srikrishna Putta†1, Jeramiah J Smith†1, John A Walker†1, 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 Voss*1 Address: 1Department of Biology, University of Kentucky, Lexington, KY 40506, USA, 2Department of Developmental and Cell Biology and the Developmental Biology Center, University of California, Irvine, CA 92697, USA, 3The Life Sciences Consortium, 519 Wartik Laboratory, Penn State University, University Park, PA 16802, USA, 4Department of Zoology, University of Wisconsin-Madison, 250 N. Mills, Madison, WI 53706, USA, 5Scionics Computer Innovation GmbH, Pfotenhauerstrasse 110, 01307 Dresden, Germany, 6Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany and 7Section of Integrative Biology and Section of Molecular, Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA Email: Srikrishna Putta - sputt2@uky.edu; Jeramiah J Smith - jjsmit3@uky.edu; John A Walker - jawalk2@uky.edu; Mathieu Rondet - mrondet@uci.edu; David W Weisrock - weisrock@uky.edu; James Monaghan - james.monaghan@uky.edu; Amy K Samuels - aksamu2@uky.edu; Kevin Kump - kevinkump@gmail.com; David C King - dck163@psu.edu; Nicholas J Maness - njmaness@wisc.edu; Bianca Habermann - habermann@mpi-cbg.de; Elly Tanaka - tanaka@mpi-cbg.de; Susan V Bryant - svbryant@uci.edu; David M Gardiner - dmgardin@uci.edu; David M Parichy - dparichy@mail.utexas.edu; S Randal Voss* - srvoss@uky.edu * Corresponding author †Equal contributors Published: 13 August 2004 BMC Genomics 2004, 5:54 doi:10.1186/1471-2164-5-54 This article is available from: http://www.biomedcentral.com/1471-2164/5/54 Received: 19 July 2004 Accepted: 13 August 2004 © 2004 Putta et al; licensee BioMed Central Ltd. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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. Page 1 of 17 (page number not for citation purposes)