ArticleGenome biology2013
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 114 citations in OpenAlex.
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- Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut.BMC biology · 2024Article
- A Novel Approach to Comparative RNA-Seq Does Not Support a Conserved Set of Orthologs Underlying Animal Regeneration.Genome biology and evolution · 2024Article
- Comparative proteomic analysis of tail regeneration in the green anole lizard,Natural sciences (Weinheim, Germany) · 2024Article
- Molecular Signatures Integral to Natural Reprogramming in the Pigment Epithelium Cells after Retinal Detachment inInternational journal of molecular sciences · 2023Article
- 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
- Comparative transcriptional profiling of regenerating damaged knee joints in two animal models of the newt Notophthalmus viridescens strengthens the role of candidate genes involved in osteoarthritis.Osteoarthritis and cartilage open · 2022Article
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- Relationship between the Phenylpropanoid Pathway and Dwarfism ofInternational journal of molecular sciences · 2021Article
- Towards comparative analyses of salamander limb regeneration.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2021Review
- Single-cell RNA-seq reveals novel mitochondria-related musculoskeletal cell populations during adult axolotl limb regeneration process.Cell death and differentiation · 2021Article
- From Autonomy to Integration, From Integration to Dynamically Balanced Integrated Co-existence: Non-aging as the Third Stage of Development.Frontiers in aging · 2021Article
- Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System.Molecular & cellular proteomics : MCP · 2020Article
- Insights into regeneration tool box: An animal model approach.Developmental biology · 2019Review
- Model systems for regeneration: salamanders.Development (Cambridge, England) · 2019Review
- The First Transcriptome Assembly of Yenyuan Stream Salamander (International journal of molecular sciences · 2019Article
- Article
- Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research.BMC genomics · 2018Article
- Novel erythrocyte clumps revealed by an orphan gene Newtic1 in circulating blood and regenerating limbs of the adult newt.Scientific reports · 2018Article
- Lens regeneration: a historical perspective.The International journal of developmental biology · 2018Review
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundNotophthalmus viridescens, an urodelian amphibian, represents an excellent model organism to study regenerative processes, but mechanistic insights into molecular processes driving regeneration have been hindered by a paucity and poor annotation of coding nucleotide sequences. The enormous genome size and the lack of a closely related reference genome have so far prevented assembly of the urodelian genome.
resultsWe describe the de novo assembly of the transcriptome of the newt Notophthalmus viridescens and its experimental validation. RNA pools covering embryonic and larval development, different stages of heart, appendage and lens regeneration, as well as a collection of different undamaged tissues were used to generate sequencing datasets on Sanger, Illumina and 454 platforms. Through a sequential de novo assembly strategy, hybrid datasets were converged into one comprehensive transcriptome comprising 120,922 non-redundant transcripts with a N50 of 975. From this, 38,384 putative transcripts were annotated and around 15,000 transcripts were experimentally validated as protein coding by mass spectrometry-based proteomics. Bioinformatical analysis of coding transcripts identified 826 proteins specific for urodeles. Several newly identified proteins establish novel protein families based on the presence of new sequence motifs without counterparts in public databases, while others containing known protein domains extend already existing families and also constitute new ones.
conclusionsWe demonstrate that our multistep assembly approach allows de novo assembly of the newt transcriptome with an annotation grade comparable to well characterized organisms. Our data provide the groundwork for mechanistic experiments to answer the question whether urodeles utilize proprietary sets of genes for tissue regeneration.
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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 Socratic graph.