Ontology highlight
ABSTRACT:
PROVIDER: PRJNA997275 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27920344_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR27920345_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR27920346_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR29059434_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR29059435_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Ambystoma macrodactylum krausei (northern long-toed salamander) genomic and transcriptomic data
| PRJNA1001969 | ENA
Project description:Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
2018-07-04 | GSE116615 | GEO
Project description:Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
2018-07-10 | GSE116777 | GEO
Project description:Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.
2020-12-12 | GSE137607 | GEO
Project description:Tissue 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 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 transcript sequence data and identify 602 genes that are 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 approximately 180 million years ago. Our study highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders. All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.
2018-09-26 | GSE105232 | GEO
Project description:The order Caudata of amphibians has been important in the study of tissue regeneration. The most complete genetic available data from salamanders are from Ambystoma mexicanum (Ambystomidae) and Notophthalmus viridescens (Salamandridae). Transcriptome data obtained with Next-generation sequencing technology has become a useful tool to discover new candidate genes in non-model organisms without a genome of reference. This study highlights the need of performing RNA-sequencing in other salamander species to compare and identify important clusters of genes that could be modulating important biological process in amphibians. Here we describe a de novo reference transcriptome and its annotation of a non-model terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). For this purpose, we utilized genome protein databases from vertebrates, nucleotide sequences obtained for salamander species, and a de novo reference transcriptomes of Bolitoglossa ramosi to conduct a homology analysis. While the majority of the transcripts recovered homologs with Bolitoglossa ramosi, only a minority of the data (22%; n= 94,739) recovered homologs with other vertebrates. We also compared the transcriptome profile of skin tissue between these Bolitoglossa species. We found a group of antimicrobial peptides, such as cathelicidins, which have been not previously described in salamanders and could be important modulators of different biological process. All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.
2019-12-07 | GSE107213 | GEO
Project description:The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray-derived gene expression analysis. In total, 3,510 probes targeted transcripts differentially expressed between the clusters we identified. Genes upregulated in PreM related to organogenesis, and those upregulated in Meta underlie structural proteins and relate to development of anatomical structures and pigmentation. Biosynthesis pathways of pigments (pteridines and melanin) were upregulated during late ProM and Meta. Gas chromatographic analysis of alkaloids indicated the onset of steroidal alkaloid biosynthesis at ProM. When comparing gene expression in the fire salamander to that in other amphibians—three anurans, Xenopus laevis, X. tropicalis, and Michrohyla fissipes, and one caudate, Ambystoma mexicanum—, we identified genes with conserved expression patterns involved in basic metamorphic processes such as skin restructuring and tail fin resorption. Our results support that primary stages of postembryonic development in caudates are homologous to those of anurans, and offer a baseline for the study of the evolution of developmental modes.
2018-02-21 | GSE110893 | GEO
Project description:Plethodontid salamanders are the largest family of salamanders and are classic models for studying the effect of rapidly evolving courtship pheromones on mating behavior and reproductive success. Despite interests in plethodontid reproduction, very little is known about the molecular composition of salamander gametes, as the extraordinary sizes of their genomes have impaired the development of various omic-scale resources. To identify what proteins may be expressed in salamander sperm, we performed DIA-MS on sperm samples from two plethodontid species, Plethodon shermani and Desmognathus ocoee. As the first detailed study of salamander sperm, this study partially fills in a critical taxonomic gap in the study of fertilization proteins in vertebrates.
2022-04-18 | PXD030143 | Pride
Project description:The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.
2012-11-06 | GSE29727 | GEO