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

BACKGROUND: Salamanders 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...

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Autores principales: Wu, Cheng-Han, Tsai, Mong-Hsun, Ho, Chia-Chuan, Chen, Chien-Yu, Lee, Hsuan-Shu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702472/
https://www.ncbi.nlm.nih.gov/pubmed/23815514
http://dx.doi.org/10.1186/1471-2164-14-434
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author Wu, Cheng-Han
Tsai, Mong-Hsun
Ho, Chia-Chuan
Chen, Chien-Yu
Lee, Hsuan-Shu
author_facet Wu, Cheng-Han
Tsai, Mong-Hsun
Ho, Chia-Chuan
Chen, Chien-Yu
Lee, Hsuan-Shu
author_sort Wu, Cheng-Han
collection PubMed
description BACKGROUND: Salamanders 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. RESULTS: The 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. CONCLUSION: The 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.
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spelling pubmed-37024722013-07-06 De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration Wu, Cheng-Han Tsai, Mong-Hsun Ho, Chia-Chuan Chen, Chien-Yu Lee, Hsuan-Shu BMC Genomics Research Article BACKGROUND: Salamanders 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. RESULTS: The 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. CONCLUSION: The 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. BioMed Central 2013-07-01 /pmc/articles/PMC3702472/ /pubmed/23815514 http://dx.doi.org/10.1186/1471-2164-14-434 Text en Copyright © 2013 Wu et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Research Article
Wu, Cheng-Han
Tsai, Mong-Hsun
Ho, Chia-Chuan
Chen, Chien-Yu
Lee, Hsuan-Shu
De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title_full De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title_fullStr De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title_full_unstemmed De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title_short De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
title_sort de novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702472/
https://www.ncbi.nlm.nih.gov/pubmed/23815514
http://dx.doi.org/10.1186/1471-2164-14-434
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