Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Trichomycterus rosablanca (Rosablanca cavefish) genome, fTriRos1, sequence data

PROVIDER: PRJNA1147607 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR30228417_subreads.fastq.gz	Fastqsanger.gz
	SRR30228418_subreads.fastq.gz	Fastqsanger.gz
	SRR30228419_subreads.fastq.gz	Fastqsanger.gz
	SRR30228420_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Project description:Trichomycterus rosablanca (Rosablanca cavefish) genome, fTriRos1

| PRJNA971190 | ENA

Trichomycterus rosablanca isolate:fTriRos1

Project description:Trichomycterus rosablanca (Rosablanca cavefish) genome, fTriRos1, haplotype 1

| PRJNA924296 | ENA

Trichomycterus rosablanca isolate:fTriRos1

Project description:Trichomycterus rosablanca (Rosablanca cavefish) genome, fTriRos1, haplotype 2

| PRJNA924297 | ENA

Trichomycterus rosablanca

Project description:Trichomycterus rosablanca overview

| PRJNA924498 | ENA

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

Adaptation to low parasite abundance affects immune investment and immunopathological responses of cavefish

Project description:Reduced parasitic infection rates in the developed world are suspected to underlie the rising prevalence of autoimmune disorders. However, the long-term evolutionary consequences of decreased parasite exposure on an immune system are not well understood. We used the Mexican tetra Astyanax mexicanus to understand how loss of parasite diversity influences the evolutionary trajectory of the vertebrate immune system, by comparing river with cave morphotypes. Here, we present field data affirming a strong reduction in parasite diversity in the cave ecosystem, and show that cavefish immune cells display a more sensitive pro-inflammatory response towards bacterial endotoxins. Surprisingly, other innate cellular immune responses, such as phagocytosis, are drastically decreased in cavefish. Using two independent single-cell approaches, we identified a shift in the overall immune cell composition in cavefish as the underlying cellular mechanism, indicating strong differences in the immune investment strategy. While surface fish invest evenly into the innate and adaptive immune systems, cavefish shifted immune investment to the adaptive immune system, and here, mainly towards specific T-cell populations that promote homeostasis. Additionally, inflammatory responses and immunopathological phenotypes in visceral adipose tissue are drastically reduced in cavefish. Our data indicate that long-term adaptation to low parasite diversity coincides with a more sensitive immune system in cavefish, which is accompanied by a reduction in the immune cells that play a role in mediating the pro-inflammatory response.

2020-07-20 | GSE128306 | 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

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

Project description:Cavefish Genome Sequencing

| PRJNA731843 | ENA

Cavefish

Project description:Cavefish

| PRJNA1137980 | ENA