Gene expression in Drosophila montana
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila montana
PROVIDER: GSE18475 | GEO | 2010/03/04
SECONDARY ACCESSION(S): PRJNA120261
REPOSITORIES: GEO
Similar Datasets
Project description:We created a custom-made microarray for D. montana with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes. The three samples for the microarray experiments included young females (âyoungâ), 14 days old females cultured under diapause-preventing (âreproducingâ) and 14 days old females cultured under diapause-inducing conditions (âdiapausingâ). Each of these samples had three replicates. The microarray contained 197 unique probe sequences representing 101 candidate genes and seven housekeeping genes. Some of the probes had two copies per array, in which case the averages of their signals were calculated. The Agilent control probes included 77 negative control probes and 200 spike-in probes (10 different probe types, each represented by 20 copies per array).
2010-05-06 | E-GEOD-18475 | biostudies-arrayexpress
Project description:Most northern insect species experience a period of developmental arrest, diapause, which enables them to survive over the winter and postpone reproduction until favorable conditions. We studied the timing of reproductive diapause and its long-term effects on the cold tolerance of Drosophila montana, D. littoralis and D. ezoana females in seasonally varying environmental conditions. At the same time we traced expression levels of 219 genes in D. montana using a custom-made microarray. We show that the seasonal switch to reproductive diapause occurs over a short time period, and that overwintering in reproductive diapause has long-lasting effects on cold tolerance. Some genes, such as Hsc70, Jon25bi and period, were upregulated throughout the diapause, while others, including regucalcin, couch potato and Thor, were upregulated only at its specific phases. Some of the expression patterns induced during the sensitive stage, when the females either enter diapause or not, remained induced regardless of the later conditions. qPCR analyses confirmed the findings of the microarray analysis in D. montana and revealed similar gene expression changes in D. littoralis and D. ezoana. The present study helps to achieve a better understanding of the genetic regulation of diapause and of the plasticity of seasonal responses in general. Custom made DNA microarray for Drosophila montana and D. virilis. Current experiment includes 8 samples (7 to 250 days old diapausing or non-diapausing D. montana females) with two or three biological replicates
2015-06-03 | E-GEOD-69202 | biostudies-arrayexpress
Project description:Most northern insect species experience a period of developmental arrest, diapause, which enables them to survive over the winter and postpone reproduction until favorable conditions. We studied the timing of reproductive diapause and its long-term effects on the cold tolerance of Drosophila montana, D. littoralis and D. ezoana females in seasonally varying environmental conditions. At the same time we traced expression levels of 219 genes in D. montana using a custom-made microarray. We show that the seasonal switch to reproductive diapause occurs over a short time period, and that overwintering in reproductive diapause has long-lasting effects on cold tolerance. Some genes, such as Hsc70, Jon25bi and period, were upregulated throughout the diapause, while others, including regucalcin, couch potato and Thor, were upregulated only at its specific phases. Some of the expression patterns induced during the sensitive stage, when the females either enter diapause or not, remained induced regardless of the later conditions. qPCR analyses confirmed the findings of the microarray analysis in D. montana and revealed similar gene expression changes in D. littoralis and D. ezoana. The present study helps to achieve a better understanding of the genetic regulation of diapause and of the plasticity of seasonal responses in general.
2015-06-03 | GSE69202 | GEO
Project description:Gene expression of two populations was compared at a daylength intermediate to the two population critical photoperiods after 0 and 6 days. Genes with interaction terms are candidates for involvement in long-day response. The mosquito Wyeomyia smithii overwinters in a larval diapause that is initiated, maintained and terminated by day length (photoperiod). We use a forward genetic approach to investigate covert transcriptional events involved in the termination of diapause following exposure to long-days. We incorporate a novel approach that compares two populations (DB - southern, DR - northern) that differentially respond to a single day length. After six long days, 50% of individuals of population DB have terminated diapause and are irrevocably committed to development, though no phenotyping differences are observed. We can compare gene expression between these two populations after six long days and zero long days. The zero long day treatment will control for evolved differences between the populations and the 6 long day treatment allows for the identification of genes that are differentially expressed due to different responses to a single daylength. We identify 30 transcripts associated with differential response to day length. All of the corresponding genes with a previously annotated function are consistent with a role in the termination of diapause, with downstream developmental events, or with the transition from potentially oxygen-poor to oxygen-rich environments; none appears to be specifically part of the photoperiodic switch mechanism itself. However, among 10 unannotated genes, a gene homologous to Drosophila melanogaster CG13043 emerges from three separate forward genetic screens as a leading candidate for a gene contributing to the photoperiodic timing mechanism itself (photoperiodic switch). We name this gene photoperiodic response gene 1 (prg1). Prg1 is up-regulated under long-day response conditions, is located under a QTL for critical photoperiod and is associated with critical photoperiod after 25 generations of recombination from a cross between extreme phenotypes. Three independent forward genetic approaches identify prg1 as a gene either involved in the photoperiodic switch mechanism or very tightly linked to a gene that is. We conclude that continued forward genetic approaches will be central to understanding not only the molecular basis of photoperiodism and diapause, but also the evolutionary potential of temperate and polar animal populations when confronted with rapid climate change. 4 treatments, (Population DR, Day 0; Population DB, Day 0; Population DR, Day 6, Population DB, Day6), one dye swap (treatment Cy3 or Cy5, each replicated three times for a total of 24 arrays
2010-05-14 | E-GEOD-18848 | biostudies-arrayexpress
Project description:Diapause is an environmentally programmed and hormonally regulated period of dormancy which makes an important part of the life-cycle in many species of invertebrates. In this study, using a RNAseq approach, we focused on very early stages of diapause induction in the larvae of drosophilid fly, Chymomyza costata by characterizing global patterns of gene expression associated with photoperiodic induction of diapause.
2015-08-03 | E-MTAB-3620 | biostudies-arrayexpress
Project description:Gene expression of two populations was compared at a daylength intermediate to the two population critical photoperiods after 0 and 6 days. Genes with interaction terms are candidates for involvement in long-day response. The mosquito Wyeomyia smithii overwinters in a larval diapause that is initiated, maintained and terminated by day length (photoperiod). We use a forward genetic approach to investigate covert transcriptional events involved in the termination of diapause following exposure to long-days. We incorporate a novel approach that compares two populations (DB - southern, DR - northern) that differentially respond to a single day length. After six long days, 50% of individuals of population DB have terminated diapause and are irrevocably committed to development, though no phenotyping differences are observed. We can compare gene expression between these two populations after six long days and zero long days. The zero long day treatment will control for evolved differences between the populations and the 6 long day treatment allows for the identification of genes that are differentially expressed due to different responses to a single daylength. We identify 30 transcripts associated with differential response to day length. All of the corresponding genes with a previously annotated function are consistent with a role in the termination of diapause, with downstream developmental events, or with the transition from potentially oxygen-poor to oxygen-rich environments; none appears to be specifically part of the photoperiodic switch mechanism itself. However, among 10 unannotated genes, a gene homologous to Drosophila melanogaster CG13043 emerges from three separate forward genetic screens as a leading candidate for a gene contributing to the photoperiodic timing mechanism itself (photoperiodic switch). We name this gene photoperiodic response gene 1 (prg1). Prg1 is up-regulated under long-day response conditions, is located under a QTL for critical photoperiod and is associated with critical photoperiod after 25 generations of recombination from a cross between extreme phenotypes. Three independent forward genetic approaches identify prg1 as a gene either involved in the photoperiodic switch mechanism or very tightly linked to a gene that is. We conclude that continued forward genetic approaches will be central to understanding not only the molecular basis of photoperiodism and diapause, but also the evolutionary potential of temperate and polar animal populations when confronted with rapid climate change.
2010-02-13 | GSE18848 | GEO
Project description:Daylength is an important seasonal cue, and genetic variation in the regulation of photoperiodism has been selected for in adapting wheat and barley to northern latitudes. Despite the importance of this trait, the mechanism by which monocot plants sense photoperiod is not known. We find in Brachypodium distachyon that photoperiodism is mediated by phytochromeC (phyC), a chromophore that acts as a molecular timer and measures the length of the night. The phyC signal is directly communicated to the circadian clock via the activity of EARLY FLOWERING3 (ELF3). ELF3 is a central regulator of photoperiodism, and elf3 mutants display a constitutive long day transcriptome. By coordinating an endogenous timer for night length perception with rhythmical circadian clock controlled gene expression, this mechanism resolves how Brachypodium, and likely other monocots, perceive photoperiod. Using ChIP-Seq, we detected that occupancy of ELF3 at various genomic regions varies in response to photoperiod and ZTime.
2020-02-29 | GSE128206 | 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:In Drosophila, the rapid shortening of the day during the autumn induces an arrest of ovarian development (diapause) in females. The molecular basis underlying this photoperiodic seasonal response is yet unknown. Here we analyse the global expression changes in transcripts and microRNA (miRNA) associated with photoperiodic diapause response, focusing on the head transcriptome as the putative location of the photoperiodic timer.
2014-07-18 | GSE28246 | GEO
Project description:In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L. sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.
2018-02-02 | E-MTAB-6454 | biostudies-arrayexpress