Ontology highlight
ABSTRACT:
PROVIDER: PRJNA518878 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10728577_1.fastq.gz | Fastqsanger.gz | |||
| SRR10728577_2.fastq.gz | Fastqsanger.gz | |||
| SRR10728578_1.fastq.gz | Fastqsanger.gz | |||
| SRR10728578_2.fastq.gz | Fastqsanger.gz | |||
| SRR10728579_1.fastq.gz | Fastqsanger.gz |
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Project description:Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes (Chen et al. 2013)1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome Chen et al. 2012)2. However, the way in which new DNA-binding proteins acquire and co-evolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Our results suggest that evolution of young regulatory genes can be coupled to substantial re-wiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.
2022-01-04 | GSE192880 | GEO
Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)
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Project description:We overexpressed the conspecific miR-975 in the cell lines derived from multiple Drosophila species (i.e. S2 cells from Drosophila melanogaster; ML82-19a cells from Drosophila simulans and WR-Dv-1 cells from Drosophila virilis). Comparison of the miR-975 effect between different cell lines provide insight into the rewiring of regulatory network through the evolution of new microRNA.
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Project description:In order to test the hypothesis that adult hybrid misexpression results from the cascading effect of earlier-expressed developmentally important improperly regulated genes, as well as address whether Von Baer’s 3rd law (suggesting that earlier stages of development should be more similar between species than later stages) holds at the level of gene expression, we conducted whole-transcriptome Drosophila melanogaster cDNA microarray-based expression profiling of males of D. melanogaster, D. sechellia, and D. simulans, at four synchronized developmental time-points (3rd instar larval [larval], early pupal, late pupal, and newly-emerged adult [adult]). D. simulans and D. sechellia shared a most recent common ancestor (MRCA) ~0.5 to 1.0 million years ago (MYA) and form a clade that shared an MRCA with D. melanogaster approximately 5.4 MYA. In addition, we also performed the same analysis on the male interspecific F1 hybrids of the D. simulans (♀) × D. sechellia (♂) cross.
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Project description:We study the relatively unexplored evolutionary consequences of the epigenetic effects of transpoable elements (TEs) by providing the first genome-wide quantification of such effects in wild-derived D. melanogaster and D. simulans strains. Surprisingly, over half of euchromatic TEs show spread of repressive epigenetic marks to nearby DNA, resulting in differential epigenetic states of homologous genic alleles and, in return, selection against TEs. Interestingly, compared to D. melanogaster, the lower TE content in D. simulans is correlated with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. We conclude that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the population dynamics of TEs within and between species.
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Project description:We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed between the sexes and sex-specific alternative splicing events, and examine the evolution of gene expression.
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Project description:Y chromosome from different Drosophila simulans were introgressed into the same genetic background. Strains showing distinct sex-ratio distortion were clustered according to the ratio of males and females observed in the progeny. Strains showing disproportionally high number of female flies in the progeny were contrasted with strains displaying the proportion of male and females flies close to 1:1. In addition, interspecific Y chromosome from Drosophila sechellia (Ysec) was compared with D. simulans Y chromosomes. Total RNA was extracted from whole flies using TRIzol (Life Technologies). The synthesis of cDNA and its labeling with fluorescent dyes (Cy3 and Cy5) as well as hybridization reactions were carried out using 3DNA protocols and reagents (Genisphere). A minimum of 2 biological replicas was used, however this number varied according to the hybridization design (See 'Branco et. al, Natural variation of the Y chromosome suppresses sex ratio distortion and modulates testis-specific gene expression in Drosophila simulans' for details of the hybridization design). Microarrays were ~18,000-feature cDNA arrays spotted with D. melanogaster cDNA PCR products. We have recently annotated these probes using the D. simulans genome. Possible biases introduced by using a D. melanogaster platform for a D. simulans genome are minimized because the probed genomes are essentially identical except for the Y chromosomes. Slides were scanned using Axon 400B scanner (Axon Instruments) and GenePix Pro 6.0 software. Foreground fluorescence of dye intensities was normalized by the Loess method in Bioconductor / Limma.
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