ArticleGenome biology2004
An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 74 citations in OpenAlex.
- Whole body regeneration deploys a rewired embryonic gene regulatory network logic.Nature communications · 2025Article
- The Axolotl's journey to the modern molecular era.Current topics in developmental biology · 2022Article
- Salamanders: The molecular basis of tissue regeneration and its relevance to human disease.Current topics in developmental biology · 2021Review
- Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum).Nature protocols · 2018Article
- Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.Scientific reports · 2018Article
- Advances in Decoding Axolotl Limb Regeneration.Trends in genetics : TIG · 2017Review
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- A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration.Regeneration (Oxford, England) · 2014Article
- De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration.BMC genomics · 2013Article
- Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.PloS one · 2013Article
- Germline transgenic methods for tracking cells and testing gene function during regeneration in the axolotl.Stem cell reports · 2013Article
- Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins.Nature communications · 2012Article
- Gene expression profile of the regeneration epithelium during axolotl limb regeneration.Developmental dynamics : an official publication of the American Association of Anatomists · 2011Article
- EST-based identification of genes expressed in skeletal muscle of the mandarin fish (Siniperca chuatsi).Genomics, proteomics & bioinformatics · 2011Article
- Cdkn1c drives muscle differentiation through a positive feedback loop with Myod.Developmental biology · 2011Article
- Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags.Molecular vision · 2010Article
- Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish.BMC genomics · 2010Article
- Proteomic analysis of blastema formation in regenerating axolotl limbs.BMC biology · 2009Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsTwo 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.
conclusionsOur 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.
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