ArticleBMC genomics2018
Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- Transcriptomic analysis of spinal cord regeneration after injury inNeural regeneration research · 2023Article
- Unravelling the limb regeneration mechanisms of Polypedates maculatus, a sub-tropical frog, by transcriptomics.BMC genomics · 2023Article
- Ramosin: The First Antibacterial Peptide Identified onPharmaceutics · 2022Article
- Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2022Article
- Rebuilding limbs, one cell at a time.Developmental dynamics : an official publication of the American Association of Anatomists · 2022Article
- Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra.EvoDevo · 2022Article
- Animal regeneration in the era of transcriptomics.Cellular and molecular life sciences : CMLS · 2021Review
- Towards comparative analyses of salamander limb regeneration.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2021Review
- Developmental Biology in Central America, the northern region of South America and the Caribbean.The International journal of developmental biology · 2021Review
- Anatomical and histological analyses reveal that tail repair is coupled with regrowth in wild-caught, juvenile American alligators (Alligator mississippiensis).Scientific reports · 2020Article
- AData in brief · 2020Article
- Deep evolutionary origin of limb and fin regeneration.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Model systems for regeneration: salamanders.Development (Cambridge, England) · 2019Review
- The First Transcriptome Assembly of Yenyuan Stream Salamander (International journal of molecular sciences · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundTissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration.
resultsUsing paired-end Illumina sequencing technology and Trinity assembly, a total of 433,809 transcripts were recovered and we obtained functional annotation for 142,926 non-redundant transcripts of the B. ramosi de novo reference transcriptome. Among the annotated transcripts, 602 genes were identified as differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor from approximately 180 million years ago.
conclusionsWe identified genes from B. ramosi that are differentially expressed during limb regeneration, including multiple conserved protein-coding genes and possible putative species-specific genes. Comparative analyses reveal a subset of genes that show similar patterns of expression with ambystomatid species, which highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.