ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 57 citations in OpenAlex.
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- Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol forbioRxiv : the preprint server for biology · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- Introns as Protective Buffers Against Transposable Elements Invasion During Genome Gigantism in a Newt.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians.iScience · 2025Article
- Genomic Insights into Fertilization: Tracing PLCZ1 Orthologs Across Amphibian Lineages.Genome biology and evolution · 2025Article
- Sustained induction of autophagy enhances survival during prolonged starvation in newt cells.Life science alliance · 2025Article
- Simulation of adult limb regeneration with lizard tail spinal cord implants reveals distinct roles of radial glia and microglia populations.Research square · 2025Article
- Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.Cell genomics · 2025Article
- Improved transcriptome assembly and functional annotation of Pleurodeles waltl for regeneration research.PloS one · 2025Article
- Novel function of Hox13 in regulating outgrowth of the newt hindlimb bud through interaction with Fgf10 and Tbx4.Development, growth & differentiation · 2025Article
- Development of an AI-Assisted Embryo Selection System Using Iberian Ribbed Newts for Embryo-Fetal Development Toxicity Testing.Yonago acta medica · 2024Article
- Macrophages modulate fibrosis during newt lens regeneration.Stem cell research & therapy · 2024Article
- hoxc12/c13 as key regulators for rebooting the developmental program in Xenopus limb regeneration.Nature communications · 2024Article
- FGF-stimulated tendon cells embrace a chondrogenic fate with BMP7 in newt tissue culture.Development, growth & differentiation · 2024Article
- Comparison of hypoxia- and hyperoxia-induced alteration of epigene expression pattern in lungs of Pleurodeles waltl and Mus musculus.PloS one · 2024Article
- Macrophages modulate fibrosis during newt lens regeneration.Research square · 2023Article
- Cellular and Molecular Triggers of Retinal Regeneration in Amphibians.Life (Basel, Switzerland) · 2023Review
- Evaluation of genetic demultiplexing of single-cell sequencing data from model species.Life science alliance · 2023Article
- Resistance Is Not Futile: Widespread Convergent Evolution of Resistance to Alpha-Neurotoxic Snake Venoms in Caecilians (Amphibia: Gymnophiona).International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
15 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic and genome editing methods. However, limited genetic information is available for P. waltl. We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. We generated 1.2 billion Illumina reads from a wide variety of samples across 12 different tissues/organs, unfertilized egg, and embryos at eight different developmental stages. These reads were assembled into 1,395,387 contigs, from which 202,788 non-redundant ORF models were constructed. The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Our transcriptome resource is expected to enhance future research employing this emerging model animal for regeneration research as well as for investigations in other areas including developmental biology, stem cell biology, and cancer research. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.