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RNA sequencing of oocytes at different developmental stages in Astyanax mexicanus

ABSTRACT: We performed bulk RNA sequencing on different cell size categories to capture different oocyte developmental stages in surface fish, Pachón cavefish and Molino cavefish, allowing us to investigate the differences in reproductive abilities between surface fish and cavefish.

ORGANISM(S): Astyanax mexicanus

PROVIDER: GSE284643 | GEO | 2025/04/15

REPOSITORIES: GEO

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Single cell RNA sequencing reveals the functions of ovary in Astyanax mexicanus

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

Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish

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

Small RNAseq to identify miRNAs in four different morphs of Astyanax mexicanus - Pachón, Tinaja, Molino, and surface fish

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

Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity

Project description:To test wheather cavefish have higher lipogenesis capability than surface fish, we used liver sample from fasted and refed fish to do RNA-seq to compare their transcriptome responding to feeding in surface fish and Pachón cavefish. Moreover, we did the Pparγ ChIP-seq with liver from fed surface fish and Pachón cavefish. We amied to test whether Pparγ in Pachón cavefish have more biding sites and higher binding peaks than surface fish.

2022-02-10 | GSE173494 | GEO

Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression

Project description:Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachón cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab‐raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.

2020-02-19 | GSE139490 | GEO

Ovary transciptomic profiles of starved surface fish and Pachón females

Project description:We performed bulk RNA sequencing on the ovaries from control and starved females of surface fish and Pachón cavefish, allowing us to study the effects of starvation on reproduction between surface fish and cavefish.

2025-04-15 | GSE284646 | GEO

RNA-Seq Analysis of liver cells of Astyanax mexicanus.

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.

2021-09-07 | GSE153050 | GEO

Astyanax mexicanus strain:Pachon cavefish and Surface fish

Project description:Astyanax mexicanus strain:Pachon cavefish and Surface fish Transcriptome or Gene expression

| PRJNA183542 | ENA

Astyanax mexicanus

Project description:Pachon cavefish Astyanax mexicanus genome sequencing and assembly

| PRJNA734455 | ENA

Genome-wide maps of chromatin state in liver cells of Astyanax mexicanus [ChIP-seq]

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.

2021-09-07 | GSE153049 | GEO

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