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Astyanax mexicanus isolate:Pachon cavefish

ABSTRACT: Astyanax mexicanus isolate:Pachon cavefish Genome sequencing and assembly

PROVIDER: PRJNA533584 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR608878_1.fastq.gz	Fastqsanger.gz
	SRR608878_2.fastq.gz	Fastqsanger.gz
	SRR608890_1.fastq.gz	Fastqsanger.gz
	SRR608890_2.fastq.gz	Fastqsanger.gz

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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.

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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.

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Cavefish Mount a Rapid and Sustained Regenerative Response Following Skeletal Muscle Injury

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.

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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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