Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129545 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using comparative genomics, we discovered that a previously uncharacterized gene (1700011H14RIK/C14ORF105/CCDC198) hereby named FAME (Factor Associated with Metabolism and Energy) shows an unusually high rate of evolutionary divergence in birds and mammals. By comparing SNVs, we identified gene-flow of FAME from Neandertals into modern humans. FAME knockout animals demonstrated increased body weight and decreased energy expenditure, corresponding to GWAS linking FAME with higher BMI, diabetes-related pathologies, and macular degeneration in humans. The analysis of gene expression and subcellular localization revealed that FAME is a membrane-bound protein enriched in kidneys. Although a gene knockout resulted in structurally normal kidneys, we detected higher Albumin in urine and lowered ferritin in the blood. The experiment confirmed interactions between FAME and ferritin and showed co-localization in vesicular and plasma membranes. Overall, our results show that FAME plays a role in tuning metabolite excretion and energy expenditure, partly explaining why it evolves at a high rate in birds and mammals. Here, we provide data related to identification of FAME interactome using the co-immunoprecipitation method.
2023-07-20 | PXD039259 | Pride
Project description:Divergence, gene flow, and the speciation continuum in nine lineages of trans-Beringian birds
| PRJNA393740 | ENA
Project description:Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightly linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence while heterogeneous gene flow flattens the surrounding “sea”, making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.
2018-08-18 | GSE118621 | GEO
Project description:The interplay between phenotypic plasticity and adaptive evolution has long been an important topic of evolutionary biology. This process is critical to our understanding of a species evolutionary potential in light of rapid climate changes. Despite recent theoretical work, empirical studies of natural populations, especially in marine invertebrates, are scarce. In this study, we investigated the relationship between adaptive divergence and plasticity by integrating genetic and phenotypic variation in Pacific oysters from its natural range in China. Genome resequencing of 371 oysters revealed unexpected fine-scale genetic structure that is largely consistent with phenotypic divergence in growth, physiology, thermal tolerance and gene expression across environmental gradient. These findings suggest that selection and local adaptation are pervasive and together with limited gene flow shape adaptive divergence. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and likely favored by selection in organisms facing dynamic environments such as oysters. Divergence in heat response and tolerance implies that the evolutionary potential to a warming climate differs among oyster populations. We suggest that trade-offs in energy allocation are important to adaptive divergence with acetylation playing a role in energy depression under thermal stress.
2018-07-27 | PXD008057 | Pride
Project description:Genomics of Divergence-with-Gene-Flow in an Island Bird
| PRJNA339167 | ENA
Project description:Gene flow and evolutionary divergence between lineages of the Lacerta viridis complex
| PRJEB38736 | ENA
Project description:The storage of lipids as energy in adipose tissue (AT) has been conserved over the course of evolution. However, substantial differences in ATs physiological activities were reported between species. Hence, establishing the mechanisms shaping evolutionarily divergence in ATs transcriptomes could provide a deeper understanding of AT regulation and its roles in obesity-related diseases. While previous studies performed anatomical, physiological and morphological comparisons between ATs across different species, little is currently understood at the molecular phenotypic levels. Here, we characterized transcriptional and lipidomic profiles of available subcutaneous and visceral ATs samples across 15 vertebrate species, spanning more than 300 million years of evolution, including placental mammals, birds and reptiles. We provide detailed descriptions of the datasets produced in this study and report gene expression and lipid profiles across samples. These resources should provide researchers could insights into the molecular and evolutionary mechanisms underlying functional differences between ATs in vertebrate species.
2022-11-17 | MTBLS5943 | MetaboLights