Daphnia pulex
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REPOSITORIES: ENA
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Project description:Under favorable conditions, the micro-crustacean Daphnia pulex produces female offspring by parthenogenesis, whereas in response to various unfavorable external cues, they produce male offspring to induce sexual reproduction (environmental sex determination: ESD). We recently established a suitable experimental system for ESD studies using D. pulex WTN6 strain, in which the sex of the offspring can be regulated simply by alterations in day-length; long-day and short-day conditions can induce female and male offspring respectively. Taking advantage of this system, we have already demonstrated that methyl farnesoate (MF) synthesis is necessary for male offspring production. Further, we identified ionotropic glutamate receptors as an upstream regulator of MF signaling by transcriptome analysis. Despite these findings, the molecular mechanisms associated with MF signaling have not yet been well elucidated in D. pulex. To more comprehensively understand the molecular mechanisms of ESD, we analyzed the whole metabolic profiles of mother daphniids reared under long-day (female-producing) and short-day (male-producing) conditions using mass spectrometry based metabolomics. We discovered that pantothenate (vitamin B5), a known precursor to coenzyme A, was significantly accumulated in response to the short-day condition. To confirm the role of pantothenate in D. pulex ESD, this metabolite was administered to mother daphniids (under long-day conditions) resulting in a significantly increased proportion of male offspring producing mothers. This study not only provides several candidates for further investigations into the molecular changes involved in male offspring production, but also novel insights into the metabolic mechanisms of the ESD system in D. pulex.
2017-04-03 | MTBLS259 | MetaboLights
Project description:Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. Results In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. Conclusions The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.
2019-10-18 | GSE124427 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE25841: Evolutionary Diversification of Duplicated Genes; Experiment A GSE25843: Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P GSE25845: Evolutionary Diversification of Duplicated Genes; Experiments B-I GSE25850: Evolutionary Diversification of Duplicated Genes; Experiment J GSE25851: Evolutionary Diversification of Duplicated Genes; Experiment L, K GSE25852: Empirical Annotation of the Daphnia pulex genome; Experiment B GSE25855: Empirical Annotation of the Daphnia pulex genome; Experiment A GSE25856: Empirical Annotation of the Daphnia pulex genome; Experiment C Refer to individual Series
2011-02-01 | E-GEOD-25823 | biostudies-arrayexpress
Project description:We report the application of CAGE (Cap Analysis of Gene Expression) on collections of Daphnia pulex individuals representing three major developmental states. This submission comes from a project of Michael Lynch and was funded by a grant from the National Institutes of Health entitled 'Population Genomics of Daphnia pulex' (Project Number: 1R01GM101672-01A1).
2016-09-12 | GSE80141 | GEO
Project description:Investigation of gene expression level changes in Daphnia pulex MFP strain between in the presence or absence of Chaoborus kairomone.
2015-05-13 | GSE63275 | GEO
Project description:Investigation of gene expression level changes in Daphnia pulex MFP strain between in the presence or absence of Chaoborus kairomone. 12 samples (4 conditions x 3 replicates) in one 12-plex NimbleGen array GPL11278
2015-05-13 | E-GEOD-63275 | biostudies-arrayexpress
Project description:We use a custom microarray for the crustacean Daphnia pulex to investigate gene expression in males, juvenile females and pregnant females. Keywords: sex-biased, developmental
2006-10-06 | GSE5908 | GEO