From biomedicine to natural history research: EST resources for ambystomatid salamanders.
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.
Putta
Srikrishna
S
Department of Biology, University of Kentucky, Lexington, KY 40506, USA. sprutt2@uky.edu
Smith
Jeramiah J
JJ
Walker
John A
JA
Rondet
Mathieu
M
Weisrock
David W
DW
Monaghan
James
J
Samuels
Amy K
AK
Kump
Kevin
K
King
David C
DC
Maness
Nicholas J
NJ
Habermann
Bianca
B
Tanaka
Elly
E
Bryant
Susan V
SV
Gardiner
David M
DM
Parichy
David M
DM
Voss
S Randal
SR
D000557:Ambystoma / Q000235:genetics*; D000558:Ambystoma mexicanum / Q000235:genetics; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D020451:Contig Mapping; D020224:Expressed Sequence Tags; D015723:Gene Library; D006801:Humans; D011110:Polymorphism, Genetic; D051381:Rats; D012038:Regeneration / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D015027:Zebrafish