Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1068324 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:Transcription profiling by array of mouse Brd mutant at different Zeitgeber times
2015-10-22 | E-MEXP-3493 | ExpressionAtlas
Project description:Expression data from MCF7 cells treated with Neuregulin (NRG) at different times
2025-01-24 | E-GEOD-69540 | ExpressionAtlas
Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.
2013-05-09 | GSE46733 | GEO
Project description:Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia
| PRJDB15354 | ENA
Project description:Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes' cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic program in the context of their morphological divergence. Our analysis revealed substantial differences in transcriptional landscapes across somitogenesis, an embryonic period coinciding with NC development and migration. This included dozens of genes with described functions in the vertebrate NC gene regulatory network, several of which showed signatures of positive selection. Among candidates showing between-species expression divergence, we focused on teleost-specific paralogs of the NC-specifier sox10 (sox10a and sox10b) as prime candidates to influence NC development. These genes, expressed in NC cells, displayed remarkable spatio-temporal variation in cichlids, suggesting their contribution to interspecific morphological differences, such as craniofacial structures and pigmentation. Finally, through CRISPR/Cas9 mutagenesis, we demonstrated the functional divergence between cichlid sox10 paralogs, with the acquisition of a novel skeletogenic function by sox10a. When compared with teleost models zebrafish and medaka, our findings reveal that sox10 duplication, although retained in most teleost lineages, had variable functional fates across their phylogeny. Altogether, our study suggests that NC-related processes—particularly those controlled by sox10s—are involved in generating morphological diversification between species and lays the groundwork for further investigations into the mechanisms underpinning vertebrate NC diversification.
2024-08-18 | GSE250387 | GEO
Project description:Transcription profiling by array of Arabidopsis after drought conditions sampled at different times of day
2014-11-24 | E-GEOD-19700 | ExpressionAtlas
Project description:Parallels between phylogeny and ontogeny have been discussed since almost two centuries and a number of theories have been proposed to explain such patterns. Especially elusive is the so-called phylotypic stage, a phase during development where species within a phylum are particularly similar to each other. While this has formerly been interpreted as a recapitulation of phylogeny, it is nowadays thought to reflect an ontogenetic progression phase, where strong constraints on developmental regulation and gene interactions exist. Several studies have shown that genes expressed during this stage evolve slower, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage. We use here a combination of phylostratigraphy and stage specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Intriguingly, aging animals express also increasingly older genes. Comparisons with similar datasets from flies and nematodes show that this pattern occurs across phyla. Our results suggest that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.
2010-12-14 | GSE24616 | GEO