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ABSTRACT: Engystomops pustulosus (Tungara frog) genome, aEngPut4, sequence data

PROVIDER: PRJNA1145948 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30176131_subreads.fastq.gz	Fastqsanger.gz
	SRR30176132_subreads.fastq.gz	Fastqsanger.gz

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Project description:Engystomops pustulosus (Tungara frog) genome, aEngPut1, sequence data

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Project description:Engystomops pustulosus (Tungara frog) genome, aEngPut4, paternal haplotype

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Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

2022-03-30 | GSE199671 | GEO

Engystomops pustulosus

Project description:Engystomops pustulosus Organism overview

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Project description:Engystomops pustulosus Genome sequencing and assembly

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Principles of nucleation of H3K27 methylation during embryonic development

Project description:During embryonic development, maintenance of cell identity and lineage commitment requires the Polycomb-group PRC2 complex, which catalyzes histone H3 K27 trimethylation (H3K27me3). However, the developmental origins of this regulation are unknown. Here, we report on H3K27me3 deposition dynamics in Xenopus embryos, on sequence elements that initiate deposition during pluripotency, and the sequence characteristics that segregate Polycomb-regulated domains from the rest of the genome. Strikingly, although PRC2 binds widely to active enhancers, H3K27me3 is only deposited at a small subset of these sites. Using a Support Vector Machine algorithm these sequences can be predicted accurately on basis of DNA sequence alone, with a sequence signature conserved between humans, frog and fish. The results suggest a genetic-default model in which genomic sequence constrains Polycomb regulation.

2013-11-28 | GSE41161 | GEO

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