Astyanax mexicanus strain:Pachon cavefish and Surface fish
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA183542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR639083.fastq.gz | Fastqsanger.gz | |||
| SRR639085.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:We performed single cell RNA sequencing to capture all somatic cell types and early germ cells in the ovary of surface fish, Pachón cavefish and Molino cavefish, allowing us to investigate the differences in reproductive abilities between surface fish and cavefish. This study represents the first transcriptomic characterization at the single cell level of the ovary in Astyanax mexicanus.
2025-04-15 | GSE282933 | GEO
Project description:Transcriptional changes underlie not only adaptations of animals to novel or changing environments, but also to human disease phenotypes, such as insomnia. Linking specific transcriptional variations to observable traits can reveal the genetic basis of adaptive trait evolution and disease. To link genetic variation to phenotypic differences, we constructed the first single nucleus RNA sequencing (snRNA seq) brain atlas in a uniquely suited model system, the Mexican tetra Astyanax mexicanus. We made comparisons between surface and cavefish A. mexicanus morphs, which despite having dramatically different life histories, physiologies, and morphologies, can nevertheless interbreed. Here we show a suite of genetic changes that underlie specific differences in phenotypes, including synaptic and neural rewiring, as well as circadian dysregulation between surface and cave-dwelling morphs that may underlie human sleep disorders. Our comprehensive snRNA seq brain atlas revealed widespread divergence in the abundance and molecular signatures of neurons and glia between surface and cavefish and establishes a platform for uncovering the genetic underpinnings of cavefish disease phenotypes.
2026-07-27 | GSE328673 | GEO
Project description:In this pioneering study, we present the first comprehensive catalog of 683 small non-coding miRNAs for Astyanax mexicanus. Focusing on an early developmental stage, miRNAs were extracted and sequenced from 24hpf embryos of surface fish and three distinct cavefish morphs (Pachón, Tinaja, and Molino). We utilized in silico analyses to predict putative 3’UTR targets of these miRNAs, revealing a unique and extensive miRNA landscape in cavefish. Small RNA sequencing identified over 100 differentially expressed miRNAs in each cave morph compared to surface fish at 24hpf, suggesting early activation of miRNA-mediated silencing pathways. Notably, a subset of miRNAs was common across all three cave morphs, constituting cave-specific miRNAs potentially instrumental in cave adaptation. To unravel the functional implications of these cave-specific miRNAs, we analyzed their predicted target genes. Gene Ontology (GO) term analysis unveiled pathways which align with known adaptations in cavefish, primarily affecting development and metabolism. Further, cross-validating with a sample mRNAseq data from Pachón and surface fish also strongly suggested impact of these miRNAs on cave adaptation associated pathways. This study establishes a foundation for exploring miRNA-mediated gene regulation in cavefish, shedding light on their potential role in regulating early developmental and metabolic adaptations crucial for troglomorphic features. The comprehensive miRNA catalog provided will also guide future investigations into the intricate world of miRNA-mediated evolution in cave-adapted species.
2025-01-03 | GSE254598 | GEO
Project description:We found higher substitution rates in cavefish compared with surface fish, in accordance with a smaller cavefish population size which has allowed more rapid fixation of derived alleles present in the ancestral population. This result also implies that the Pachn cave population is much younger than previously estimated. The comparison of these data with simulations suggests that the Pachn cavefish population has probably been underground less than 30,000 years. This new time frame, together with other evidence, indicate that the evolution of cave phenotypes mainly involves the fixation of cryptic genetic variants present in surface fish populations within a short period of time.
2016-06-27 | E-MTAB-5142 | biostudies-arrayexpress
Project description:Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with a comprehensive biochemical and molecular characterization of the cell lines, which reflects key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.
2022-02-02 | GSE195950 | GEO
Project description:Astyanax mexicanus isolate:Pachon cavefish Genome sequencing and assembly
| PRJNA533584 | ENA
Project description:Adaptation of organisms to extreme environments, such as caves, requires dramatic phenotypic changes. Studying these changes can elucidate mechanisms underlying phenotypic differences in the context of both evolution and human disease. The Mexican tetra, Astyanax mexicanus, is a useful model of extreme adaptation over a short evolutionary time scale. This fish species includes surface- and cave-dwelling ecotypes, with cavefish displaying many adaptations to subterranean life, including behavioral changes such as sleep loss, increased appetite, and reduced aggression. Unraveling the mechanisms underlying these changes has been challenging, presumably because they are complex traits that required coordinated changes across multiple cell types to evolve. Here, we present a spatially integrated comparative cell atlas of whole adult brains of surface and cavefish. After establishing the molecular signatures of 35 cell types, we show that cave colonization drove canalized regulatory changes to gene expression that persist in the laboratory environment. Cavefish brains show shifts in cell type composition compared to their surface counterparts, as well as complex regulatory changes to pathways governing hypoxia response and circadian rhythm. Microglia in the cavefish brain underwent extensive transcriptional remodelling, including changes in senescence and AMPK pathways. Further, cell-cell communication analysis identified a cave-enriched ligand-receptor communication pattern centered on signals sent from glial cells to diverse populations of neurons. This atlas highlights discoveries on how brains adapt to new environments and provides a resource for future studies of brain evolution in A. mexicanus, an emerging model for translational research into neurodegenerative disease in humans.
2026-08-10 | GSE335564 | GEO
Project description:This study seeks to investigate genome-wide, circadian-regulated gene expression within the skeletal muscle of the Astyanax mexicanus – comprised of the river-dwelling surface fish and troglobitic cavefish – providing novel insights into the evolutionary consequence of circadian disruption on skeletal muscle physiology
2026-02-28 | GSE213401 | GEO
Project description:This study seeks to investigate the temporal, genome-wide response of skeletal muscle following cardiotoxin injection within the skeletal muscle of the Astyanax mexicanus – comprised of the river-dwelling surface fish and troglobitic cavefish – providing novel insights into the evolutionary consequence of skeletal muscle regernation.
2024-07-31 | GSE223617 | GEO
Project description:Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish, Astyanax mexicanus provides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and aging, we compared the transcriptional response to aging between surface and cave morphs of A. mexicanus
2024-10-13 | GSE272611 | GEO