An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

Genome Biology
Bianca HabermannElly M Tanaka

Abstract

The 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. Two 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 fami...Continue Reading

References

Jun 12, 1981·Neuroscience Letters·B Fritzsch, W Himstedt
Oct 24, 1995·Proceedings of the National Academy of Sciences of the United States of America·J Y SuJ L Maller
May 1, 1996·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Y B ShiM A Stolow
Jul 1, 1997·Brain, Behavior and Evolution·G RothD B Wake
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 12, 1998·Trends in Biochemical Sciences·F JeanmouginT J Gibson
Oct 6, 1999·Genome Research·X Huang, A Madan
Dec 26, 2001·Nucleic Acids Research·Aron Marchler-BauerStephen H Bryant
Apr 16, 2003·Molecular Ecology·S R VossH B Shaffer
Jun 7, 2003·Science·Elizabeth Pennisi
Jun 26, 2003·Evolution & Development·Andrew D JohnsonBrian I Crother
Mar 1, 1961·The Journal of Biophysical and Biochemical Cytology·J E EDSTROM, J KAWIAK
Sep 23, 2003·Methods in Molecular Biology·Pablo D Rabinowicz
Dec 20, 2003·Science·Lance E PalmerW Richard McCombie

❮ Previous
Next ❯

Citations

Oct 19, 2006·Nature Reviews. Genetics·Alejandro Sánchez Alvarado, Panagiotis A Tsonis
Jun 21, 2007·Physiological Genomics·Carmencita Rojas-CartagenaJosé E García-Arrarás
Jun 10, 2009·BMC Genomics·Pablo A Ortiz-PinedaJosé E García-Arrarás
Dec 2, 2009·BMC Biology·Nandini RaoDavid L Stocum
Dec 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ricardo M ZayasPhillip A Newmark
Feb 19, 2008·Developmental and Comparative Immunology·Bérénice Schaerlinger, Jean-Pol Frippiat
Nov 17, 2006·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Jamie I MorrisonAndrás Simon
Dec 13, 2012·Nature Communications·Natalia TapiaHans R Schöler
Apr 15, 2014·Animal Science Journal = Nihon Chikusan Gakkaihō·Ning DingQigui Wang
Apr 15, 2010·Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes·Martha P García de LlaseraLuz E Vera-Avila
Feb 4, 2011·Developmental Dynamics : an Official Publication of the American Association of Anatomists·David L Stocum, Jo Ann Cameron
Jun 8, 2011·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Leah J CampbellCraig M Crews
Jun 1, 2006·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Francie E CoblentzThomas H Shafer
Mar 15, 2008·Reproductive Biomedicine Online·R G Edwards
Dec 15, 2010·Developmental Biology·Daniel P S OsbornSimon M Hughes

❮ Previous
Next ❯

Methods Mentioned

BETA
18,432 sequencing
ubiquitination
GTPases
aminoacetylation
EST sequencing
PCR

Software Mentioned

- Assembler
BLASTN
ClustalX
protdist
BLAST
ESTScan
TIGR
fitch
Cap3
nj

Related Concepts

Related Feeds

Candida albicans

Candida albicans is an opportunistic, fungal pathogen of humans that frequently causes superficial infections of oral and vaginal mucosal surfaces of debilitated and susceptible individuals. Discover the latest research on Candida albicans here.

Cell Checkpoints & Regulators

Cell cycle checkpoints are a series of complex checkpoint mechanisms that detect DNA abnormalities and ensure that DNA replication and repair are complete before cell division. They are primarily regulated by cyclins, cyclin-dependent kinases, and the anaphase-promoting complex/cyclosome. Here is the latest research.

Cadherins and Catenins

Cadherins (named for "calcium-dependent adhesion") are a type of cell adhesion molecule (CAM) that is important in the formation of adherens junctions to bind cells with each other. Catenins are a family of proteins found in complexes with cadherin cell adhesion molecules of animal cells: alpha-catenin can bind to β-catenin and can also bind actin. β-catenin binds the cytoplasmic domain of some cadherins. Discover the latest research on cadherins and catenins here.

Candidiasis

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Cell Cycle Pathways

Cell cycle is a complex process regulated by several signal transduction pathways and enzymes. Here is the latest research on regulation of cell cycle and cell cycle pathways.

Candidiasis (ASM)

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Cell Cycle Control & Proteolysis

Key regulators of cell cycle, including cyclins, cyclin dependent kinase inhibitors, DNA replication factors, are controlled by proteolysis. Discover the latest research on cell cycle control and proteolysis.