Ontology highlight
ABSTRACT:
PROVIDER: PRJNA857690 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Seasonal variation of bacterial endophytes in urban trees
| PRJNA277035 | ENA
Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.
2012-04-18 | GSE37342 | GEO
Project description:The ability to cope with infection by a parasite is one of the major challenges for any host species and is a major driver of evolution. Parasite pressure differs between habitats. It is thought to be higher in tropical regions compared to temporal ones. We infected Drosophila melanogaster from two tropical (Malaysia and Zimbabwe) and two temperate populations (the Netherlands and North Carolina) with the generalist entomopathogenic fungus Beauveria bassiana to examine if adaptation to local parasite pressures led to differences in resistance. Contrary to previous findings we observed increased survival in temperate populations. This, however, is not due to increased resistance to infection per se, but rather the consequence of a higher general vigor of the temperate populations. We also assessed transcriptional response to infection within these flies eight and 24 hours after infection. Only few genes were induced at the earlier time point, most of which are involved in detoxification. In contrast, we identified more than 4,000 genes that changed their expression state after 24 hours. This response was generally conserved over all populations with only few genes being uniquely regulated in the temperate populations. We furthermore found that the American population was transcriptionally highly diverged from all other populations concerning basal levels of gene expression. This was particularly true for stress and immune response genes, which might be the genetic basis for their elevated vigor. mRNA profiles of whole Drosophila melanogaster adult males from an African, American, Asian and European population after infection with Beauveria bassiana. Samples include uninfected controls, 8h after infection and 24h after infection. 3 biological replicates each (2 in the case of American controls).
2015-06-19 | E-GEOD-67177 | biostudies-arrayexpress
Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. 204 samples were analysed with the Illumina platform Human610-Quad v 1.0 and are described herein.
2012-04-17 | E-GEOD-37342 | biostudies-arrayexpress
Project description:BACKGROUND: Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes. In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour. RESULTS: Strong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level. We identified 607 heat responsive genes as well as 39 heat tolerance genes. CONCLUSION: Our findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress. We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.
2016-10-20 | GSE88917 | GEO
Project description:Seasonal nitrogen (N) storage and reuse is important to the N-use efficiency of temperate deciduous trees. In poplar, bark storage proteins (BSPs) accumulate in protein storage vacuoles of the bark parenchyma and xylem ray cells in the fall. During spring growth, N from stored BSPs is remobilized and utilized by growing shoots. The goal of this study is to investigate global gene expression changes in the bark during BSP remobilization and shoot regrowth under long-day conditions.
2014-03-01 | GSE49982 | GEO
Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.
2019-09-27 | GSE133502 | GEO
Project description:Seasonal adaptation to changes in light:dark regimes (i.e., photoperiod) allows organisms living at temperate latitudes to anticipate environmental change and adjust their physiology and behavior accordingly. The circadian system has been implicated in measurement and response to changes in photoperiod in nearly all animals studied so far (Saunders, 2011). The use of both traditional and non-traditional model insects with robust seasonal responses has recently genetically demonstrated the central role that clock genes play in photoperiodic response. Yet, the molecular pathways involved in insect photoperiodic responses remain largely unknown. Here, using the Eastern North American monarch butterfly (Reppert et al, 2016; Denlinger et al, 2017), we identified the vitamin A pathway as a novel pathway downstream of the circadian clock mediating insect photoperiod responsiveness. We found that interrupting clock function by disrupting circadian activation and repression abolishes photoperiodic responses in reproductive output, providing a functional link between clock genes and photoperiodic responsiveness in the monarch. Through transcriptomic approaches, we identified a molecular signature of seasonal-specific rhythmic gene expression in the brain, the organ known to function in photoperiodic reception in both Lepidoptera and some flies (Bowen et al, 1984; Saunders & Cymborowski, 1996). Among genes differentially expressed between both long and short photoperiods and between seasonal forms, several were belonging to the vitamin A pathway. The rhythmic expression of all of these genes was abolished in clock-deficient mutants. We also showed that a CRISPR/Cas9-mediated loss-of-function mutation in the pathway’s rate-limiting enzyme, ninaB1, impaired the monarch ability to respond to the photoperiod independently of visual function in the compound eye and without affecting circadian rhythms. Our finding that the vitamin A pathway is a key mediator of photoperiodic responses in insects could have broad implications for understanding the molecular mechanisms underlying photoperiodism.
2019-11-13 | GSE126336 | GEO
Project description:We investigated the gene expression changes associated with skin pigmentation variation between Virginia opossum populations inhabiting tropical and temperate environments. We found that gene expression variation in genes with melanocytic and immune functions is associated with the degree of skin pigmentation variation. Further, we found evidence suggesting that the Wnt/ß-catenin signaling pathway might be regulating the depigmentation observed in temperate populations. We present several alternative hypotheses that may explain Gloger’s rule pattern of skin pigmentation variation in the Virginia opossum.
2018-03-31 | GSE112562 | GEO