ArticleBMC genomics2013
De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
37 citing papers in PubMed, 76 citations in OpenAlex.
- A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration.Genome biology and evolution · 2024Article
- hoxc12/c13 as key regulators for rebooting the developmental program in Xenopus limb regeneration.Nature communications · 2024Article
- Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity.Animals : an open access journal from MDPI · 2023Article
- De Novo Transcriptome Sequencing and Analysis of Differential Gene Expression among Various Stages of Tail Regeneration inJournal of developmental biology · 2022Article
- Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum).Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- Animal regeneration in the era of transcriptomics.Cellular and molecular life sciences : CMLS · 2021Review
- A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration.Bioelectricity · 2021Article
- Towards comparative analyses of salamander limb regeneration.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2021Review
- An ATAC-seq Dataset Uncovers the Regulatory Landscape During Axolotl Limb Regeneration.Frontiers in cell and developmental biology · 2021Article
- Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb Regeneration.Frontiers in cell and developmental biology · 2021Article
- Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.Systematic biology · 2021Article
- von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration.Evolution & development · 2020Article
- Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution.Developmental cell · 2020Article
- Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues.Scientific reports · 2019Article
- Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma.Genomics · 2019Article
- Deep evolutionary origin of limb and fin regeneration.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamanderEcology and evolution · 2019Article
- Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research.BMC genomics · 2018Article
- Regeneration in distantly related species: common strategies and pathways.NPJ systems biology and applications · 2018Article
- A microRNA-mRNA expression network during oral siphon regeneration inDevelopment (Cambridge, England) · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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