Ontology highlight
ABSTRACT:
PROVIDER: PRJNA700772 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, to unravel the influence of phylogenetic divergence and biogeography in shaping the composition and activity of Daboia venoms, we comparatively investigated the venoms of D. russelii from western India and D. palaestinae from Israel.
2023-03-11 | PXD031190 | Pride
Project description:Despite their early evolutionary divergence, reef-building corals exhibit complex circadian responses to diurnal, lunar and annual changes in the conditions around them. Understanding circadian regulation in reef-building corals is, however, complicated by the presence of photosynthetic endosymbionts that have a profound physiochemical influence on the intracellular environment. How corals tune their animal-based clock machinery to respond to external cues while at the same time responding to internal physiological changes imposed by the symbiont is not clear. We explore this issue using microarray analysis to dissect genes governed directly by the circadian machinery from those responding indirectly as a consequence of changing internal oxygen tensions.
2011-04-21 | GSE21658 | GEO
Project description:Reproductive proteins evolve rapidly, which is predicted to cause postmating-prezygotic (PMPZ) reproductive isolation between divergent populations. While most previous studies have focused on protein sequence divergence as a likely driver of PMPZ incompatibilities, reproductive proteomes may also diverge compositionally and/or quantitatively. Here, we characterize extensive protein sequence, compositional, and quantitative divergence of male and female reproductive proteomes in two species exhibiting strong PMPZ isolation (D. mojavensis and D. arizonae). We further demonstrate that three divergent male seminal fluid proteins affect the size of the insemination reaction mass and/or fertilization success in D. arizonae. Using quantitative data and protein-protein interaction modeling of proteases and protease inhibitors, we predict the relative importance of protein sequence divergence, compositional changes, and quantitative divergence to the evolution of PMPZ incompatibilities between the species. We find that predicted interspecies protein incompatibilities arise from proteome compositional changes rather than protein sequence divergence, at least for the subset of the interactome that we tested. Furthermore, extensive quantitative divergence, particularly for proteases and inhibitors, suggests pervasive stoichiometric mismatches in heterospecific matings. Altogether, our findings provide novel insights into how the reproductive interactome diverges, and the consequences of this divergence for the evolution of PMPZ reproductive isolation.
2026-04-02 | PXD065290 | Pride
Project description:Genes involved in chromatin remodeling during sperm development are under strong evolutionary pressure to optimize reproductive fitness In mice, the histone H3.4 variant, encoded by the single copy H3f4 gene, is essential for spermatogenesis. H3.4 is highly expressed in spermatogonia and replaces progressively canonical H3 histones during spermatogonial expansion and differentiation. Phylogenetic analysis shows that H3f4 is specific to the placental lineage and originates from an ancestral H3.2 gene existing prior to the divergence of placental and marsupial mammals over 100 million years ago. Situated in a majorly truncated histone cluster, placental H3f4 orthologs show increased synonymous and non-synonymous substitution rates compared to analogous marsupial H3.2 genes. H3f4 carries four non-synonymous substitutions relative to H3.2 genes. To understand the impact of evolutionary sequence divergence on reproductive fitness, we reverted three of four non-synonymously substituted residues in H3f4 to those present in H3.1 (H3f4V24A, H3f4H42R, H3f4S98A) while leaving H3f4C96 intact which is identical to H3.1C96. When expressed from both alleles, neither single nor triple reversion of diverged residues affected spermatogenesis much. In contrast, hemizygous expression of the triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed that residues V24 and H42 of H3.4 promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.
2026-04-06 | GSE291272 | GEO
Project description:Despite their early evolutionary divergence, reef-building corals exhibit complex circadian responses to diurnal, lunar and annual changes in the conditions around them. Understanding circadian regulation in reef-building corals is, however, complicated by the presence of photosynthetic endosymbionts that have a profound physiochemical influence on the intracellular environment. How corals tune their animal-based clock machinery to respond to external cues while at the same time responding to internal physiological changes imposed by the symbiont is not clear. We explore this issue using microarray analysis to dissect genes governed directly by the circadian machinery from those responding indirectly as a consequence of changing internal oxygen tensions. Three coral colonies were sampled at 4 hr intervals during two consecutive days under an ambient light/dark (LD) cycle and under constant darkness (DD). In total 72 arrays were hybridized, as each array represented a sample from a treatment and a time point (n=3).
2011-04-20 | E-GEOD-21658 | biostudies-arrayexpress
Project description:We applied numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the biogeography of mucosa-associated bacteria along the human colon. The microbial DNA associated with matched biopsy tissue samples taken from the cecum, transverse colon, sigmoid colon and rectum of 10 healthy patients was examined. Consistent with previous studies, the profiles revealed a marked inter-subject variability; however, the numerical ecology methods of analysis allowed the subtraction of the subject effect from the data and revealed, for the first time, evidence of a longitudinal gradient for specific microbes along the colorectum: with Streptococcus, Comamonadaceae, Enterococcus and Lactobacillus in greatest abundance at the cecum, with a gradual decline in their relative abundance through to the rectum. Conversely, the analyses suggest that members of the Enterobacteriaceae increase in relative abundance towards the rectum. These differences were validated by quantitative PCR. We were also able to identify significant differences in the profiles, especially for the Streptococci, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive, and suggestive that the biogeography of the colonic mucosa can be monitored for changes via cross-sectional and/or inception cohort studies.
2010-03-01 | GSE18933 | GEO
Project description:The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.
2026-02-11 | GSE319137 | GEO