Astyanax mexicanus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA734455 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR14729057_1.fastq.gz | Fastqsanger.gz | |||
| SRR14729057_2.fastq.gz | Fastqsanger.gz | |||
| SRR14729058_1.fastq.gz | Fastqsanger.gz | |||
| SRR14729058_2.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Astyanax mexicanus isolate:Pachon cavefish Genome sequencing and assembly
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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: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.
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Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. In parallel, we performed RNA Seq as a read out of gene expression. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
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Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
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