Transcriptional landscapes of Axolotl (Ambystoma mexicanum)

Juan Caballero-Pérez, Annie Espinal-Centeno, Francisco Falcon, Luis F. García-Ortega, Everardo Curiel-Quesada, Andrés Cruz-Hernández, Laszlo Bako, Xuemei Chen, Octavio Martínez, Mario Alberto Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez

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Abstract

The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.

Original languageEnglish
Pages (from-to)227-239
Number of pages13
JournalDevelopmental Biology
Volume433
Issue number2
DOIs
StatePublished - Jan 15 2018

Keywords

  • Axolotl
  • Coding and non-coding RNAseq
  • MicroRNAs
  • Regenerative tissues

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    Caballero-Pérez, J., Espinal-Centeno, A., Falcon, F., García-Ortega, L. F., Curiel-Quesada, E., Cruz-Hernández, A., Bako, L., Chen, X., Martínez, O., Alberto Arteaga-Vázquez, M., Herrera-Estrella, L., & Cruz-Ramírez, A. (2018). Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Developmental Biology, 433(2), 227-239. https://doi.org/10.1016/j.ydbio.2017.08.022