Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1124553 | ENA |
REPOSITORIES: ENA
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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
Project description:DNA methylation clocks have been widely used for accurate age prediction, but most studies have been carried out on mammals. Here we present an epigenetic clock for the aquatic frog Xenopus tropicalis, a widely used model organism in developmental biology and genomics. To construct the clock, we collected DNA methylation data from 192 frogs using targeted bisulfite sequencing at genomic regions containing CpG sites previously shown to have age-associated methylation in Xenopus. We found highly positively and negatively age-correlated CpGs are enriched in heterochromatic regions marked with H4K20me3 and H3K9me3. Positively age-correlated CpGs are enriched in bivalent chromatin and gene bodies with H3K36me3, and tend to be proximal to lowly expressed genes. These epigenetic features of aging are similar to those found in mammals, suggesting evolutionary conservation of epigenetic aging mechanisms. Our clock enables future aging biology experiments that leverage the unique properties of amphibians.
2025-05-17 | GSE292839 | GEO
Project description:The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.
2018-03-10 | GSE111639 | GEO
Project description:Amphibian populations around the world are threatened by an emerging infectious pathogen, the chytrid fungus Batrachochytrium dendrobatidis (Bd). How can a fungal skin infection kill such a broad range of amphibian hosts? And why are certain species particularly susceptible to the impacts of Bd? Here we use a genomics approach to understand the genetic response of multiple susceptible frog species to Bd infection. We characterize the transcriptomes of two closely-related endangered frog species (Rana muscosa and Rana sierrae) and analyze whole genome expression profiles from frogs in controlled Bd-infection experiments. We integrate the Rana results with a comparable dataset from a more distantly-related susceptible species (Silurana tropicalis). We demonstrate that Bd-infected frogs show massive disruption of skin function and show no evidence of a robust immune response. The genetic response to infection is shared across the focal susceptible species, suggesting a common effect of Bd on susceptible frogs.
2012-05-01 | GSE34235 | GEO
Project description:Expression of known and predicted genes in tissues of Xenopus tropicalis (frog) pooled from multiple healthy individuals.
2009-04-16 | GSE12975 | GEO
Project description:We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesodermal stem cells and determine their bipotential fates in the Xenopus tropicalis frog embryo.
2013-09-19 | GSE48560 | GEO
Project description:Brachyury (Xbra/Xbra3) knock-down embryos of the frog Xenopus tropicalis were profiled to quantify neuro-mesodermal cell fate switches at a transcriptional level.
2013-09-19 | GSE48663 | GEO
Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species.
2015-12-09 | GSE58420 | GEO
Project description:We defined genome-wide regulatory inputs of the T-box transcription factors Brachyury (Xbra), Eomesodermin (Eomes) and VegT that maintain neuro-mesodermal stem cells and determine their bipotential fates in the Xenopus tropicalis frog embryo. Binding profiles for Xbra, Eomes and VegT in X. tropicalis embryos (ChIP-Seq)
2013-09-19 | E-GEOD-48560 | biostudies-arrayexpress
Project description:Evolutionary genomics of Australian Treefrogs (genus Litoria)
| PRJNA912233 | ENA