Project description:Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vertebrate species Xenopus tropicalis. We selected approximately 3500 sites highly correlated with age from WGBS data from 9 frogs of 3 different age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old - GSE221656) and designed probes for the development of cost effective targeted bisulfite sequencing (TBSeq) assay. Here, we present the TBSeq assay in sixteen different frogs as a pilot experiment to validate our previous findings.

2023-04-28 | GSE222107 | GEO

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

Gut microbiome of hibernating frogs

Project description:Gut microbiome of hibernating frogs Targeted loci environmental

| PRJNA432152 | ENA

Mitogenomics of historical type specimens of Australasian turtles

Project description:Mitogenomics of historical type specimens of Australasian turtles

| PRJEB31010 | ENA

Arctic fox mitogenomics

Project description:Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

| PRJEB34472 | ENA

Sexy fingers: pheromones in the glands of male dendrobatid frogs

Project description:Sexual pheromones in dendrobatid frogs

| PRJEB76881 | ENA

Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion zone

Project description:Functional modifications shape the ability of populations to cope with anthropogenic environmental changes. These modifications are mediated by complex interactions between transmitted and non-transmitted changes which limit their prediction. To study how these changes are intertwined with evolutionary processes in a case of persistent anthropogenic environmental change, we characterized population structure, genetic diversity and individual response on gene expression of the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant. We detected lower effective population size in populations most exposed to ionizing radiation that is not compensated by migrations from surrounding areas. We also highlight a decreased body condition of frogs living in the most contaminated area, a peculiar transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. Population most exposed to ionizing radiation in the Chernobyl exclusion zone experience both genetic drift and functional changes that collectively point towards deleterious effects of ionizing radiation on tree frogs and potential difficulty to adapt to this novel environment.

2023-06-15 | GSE211060 | GEO

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