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

BMC Genomics, 2004 · DOI: 10.1186/1471-2164-5-54 · Published: August 13, 2004

Simple Explanation

This research developed genomic resources, specifically expressed sequence tags (ESTs), for two closely related salamander species: the Mexican axolotl (Ambystoma mexicanum) and the Eastern tiger salamander (A. tigrinum tigrinum). These salamanders are important models for studying regeneration. The ESTs were isolated from various tissues, including regenerating limbs and tails. This allowed the researchers to identify genes expressed during regeneration and other biological processes. The developed EST resources are valuable for comparative studies, identifying molecular probes, and understanding genome structure and evolution in salamanders and related species.

Study Duration

Not specified

Participants

Mexican axolotl (Ambystoma mexicanum) and Eastern tiger salamander (A. tigrinum tigrinum)

Evidence Level

Level 3: EST sequencing and bioinformatics analysis

Key Findings

1
Approximately 40,000 cDNA sequences were isolated for A. mexicanum and A. t. tigrinum from various tissues.
2
The study identified 21,091 unique contigs overall, representing transcripts for approximately 17,000 different ambystomatid loci.
3
Informatic searches identified over 100 new probes for regeneration research, demonstrating the utility of the EST resources.

Research Summary

The study developed expressed sequence tags (ESTs) for the Mexican axolotl (Ambystoma mexicanum) and the Eastern tiger salamander (A. tigrinum tigrinum) from various tissues, including regenerating limb and tail. Bioinformatic analysis of the ESTs resulted in the identification of over 21,000 unique contigs, representing a significant resource for genomic studies in these species. The utility of the EST resources was demonstrated through the identification of regeneration probes, characterization of nucleotide polymorphism, saturation of a synteny group, and extension of primer sets to a related species.

Practical Implications

Regeneration Research

The EST resources provide a valuable tool for identifying and studying genes involved in salamander regeneration, facilitating comparisons with other vertebrate models.

Conservation Biology

The genomic resources can be used to study population genetics and inform conservation efforts for threatened ambystomatid salamanders.

Comparative Genomics

The ESTs enable comparative genomic studies between salamanders and other vertebrates, providing insights into genome evolution and conserved synteny.

Study Limitations

1
The ESTs only represent a portion of the salamander transcriptome, potentially missing some genes and non-coding regions.
2
The study relied on sequence similarity searches, which may not identify all orthologous genes or accurately annotate novel salamander-specific sequences.
3
The analysis of polymorphism was limited to the largest contigs and may not be representative of the entire genome.

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