De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration

BMC Genomics

Research Article

Chien-Yu Chen¹  Chia-Chuan Ho²  Cheng-Han Wu³  Mong-Hsun Tsai⁴  Hsuan-Shu Lee⁵ 

[1] Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, 106, Taipei, Taiwan;Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, 106, Taipei, Taiwan;Institute of Biotechnology, National Taiwan University, 106, Taipei, Taiwan;Institute of Biotechnology, National Taiwan University, 106, Taipei, Taiwan;Agricultural Biotechnology Research Center, Academia Sinica, 115, Taipei, Taiwan;Institute of Biotechnology, National Taiwan University, 106, Taipei, Taiwan;Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, 106, Taipei, Taiwan;Agricultural Biotechnology Research Center, Academia Sinica, 115, Taipei, Taiwan;Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, 100, Taipei, Taiwan;

关键词: Ambystoma mexicanum;    Axolotl;    Transcriptome;    Blastema;    De novo;   

DOI  :  10.1186/1471-2164-14-434

 received in 2012-08-30, accepted in 2013-06-21,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSalamanders are unique among vertebrates in their ability to completely regenerate amputated limbs through the mediation of blastema cells located at the stump ends. This regeneration is nerve-dependent because blastema formation and regeneration does not occur after limb denervation. To obtain the genomic information of blastema tissues, de novo transcriptomes from both blastema tissues and denervated stump ends of Ambystoma mexicanum (axolotls) 14 days post-amputation were sequenced and compared using Solexa DNA sequencing.ResultsThe sequencing done for this study produced 40,688,892 reads that were assembled into 307,345 transcribed sequences. The N50 of transcribed sequence length was 562 bases. A similarity search with known proteins identified 39,200 different genes to be expressed during limb regeneration with a cut-off E-value exceeding 10-5. We annotated assembled sequences by using gene descriptions, gene ontology, and clusters of orthologous group terms. Targeted searches using these annotations showed that the majority of the genes were in the categories of essential metabolic pathways, transcription factors and conserved signaling pathways, and novel candidate genes for regenerative processes. We discovered and confirmed numerous sequences of the candidate genes by using quantitative polymerase chain reaction and in situ hybridization.ConclusionThe results of this study demonstrate that de novo transcriptome sequencing allows gene expression analysis in a species lacking genome information and provides the most comprehensive mRNA sequence resources for axolotls. The characterization of the axolotl transcriptome can help elucidate the molecular mechanisms underlying blastema formation during limb regeneration.

【 授权许可】

Unknown   
© Wu et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.