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Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster

ABSTRACT: We used RNA-seq to investigate gene expression variation in Malpighian tubules, which have a function analogous to that of human kidneys. In order to characterize population differentiation, we sequenced the Malpighian tubule transcriptomes of flies derived from two populations, one from sub-Saharan Africa (Zimbabwe) and one from Europe (the Netherlands). Males and females were examined separately. Overall, we found a high amount of differential expression between sexes (2,308 genes) and populations (2,474 genes). Although most of the differentially expressed genes were consistent between sexes and populations, there were 615 genes showed sex-biased expression in only one population and 557 genes showed population-biased expression in only one sex. mRNA expression profiles of Drosophila melanogaster Malpighian tubules from adult males and females from a European and an African population (2 biological replicates per sex and population)

ORGANISM(S): Drosophila melanogaster

SUBMITTER: John Parsch

PROVIDER: E-GEOD-58578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster.

Huylmans Ann Kathrin AK Parsch John J

G3 (Bethesda, Md.) 20140922 12

Within species, levels of gene expression typically vary greatly between tissues, sexes, individuals, and populations. To investigate gene expression variation between sexes and populations in a single somatic tissue, we performed a quantitative analysis of the Malpighian tubule transcriptome in adult males and females of Drosophila melanogaster derived from two distinct populations (one from sub-Saharan Africa and one from northern Europe). We identified 2308 genes that differed in expression b ...[more]

PMID: 25246242

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Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster

Project description:We used RNA-seq to investigate gene expression variation in Malpighian tubules, which have a function analogous to that of human kidneys. In order to characterize population differentiation, we sequenced the Malpighian tubule transcriptomes of flies derived from two populations, one from sub-Saharan Africa (Zimbabwe) and one from Europe (the Netherlands). Males and females were examined separately. Overall, we found a high amount of differential expression between sexes (2,308 genes) and populations (2,474 genes). Although most of the differentially expressed genes were consistent between sexes and populations, there were 615 genes showed sex-biased expression in only one population and 557 genes showed population-biased expression in only one sex.

2014-09-25 | GSE58578 | GEO

Population and sex differences in Drosophila melanogaster brain gene expression

Project description:Background: Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-throughput RNA sequencing of a single Drosophila melanogaster tissue to detect brain-specific differences in gene expression between the sexes and between two populations, one from the ancestral species range in sub-Saharan Africa and one from the recently colonized species range in Europe. Results: Relatively few genes (<100) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Over 340 genes differed in brain expression between flies from the African and European populations, with the between-population divergence being highly correlated between males and females. The differentially expressed genes include those involved in stress response, olfaction, and detoxification. Expression differences were associated with transposable element insertions at two genes implicated in insecticide resistance (Cyp6g1 and CHKov1). Conclusions: Analysis of the brain transcriptome revealed many genes differing in expression between populations that were not detected in previous studies using whole flies. There was little evidence for sex-specific regulatory adaptation in the brain, as most expression differences between populations were observed in both males and females. The enrichment of genes with sexually dimorphic expression on the X chromosome is consistent with dosage compensation mechanisms affecting sex-biased expression in somatic tissues. mRNA profiles of Drosophila melanogaster brains from adult males and females from a European and an African population (2 biological replicates each)

2012-11-21 | E-GEOD-40907 | biostudies-arrayexpress

Population and sex differences in Drosophila melanogaster brain gene expression

2012-11-21 | GSE40907 | GEO

Malpigian tubules

Project description:modENCODE_submission_5521 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene. Unlike normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Malpighian tubules; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Female; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population ); Tissue: Malpighian tubules; Developmental Stage: cleavage stage; Genotype: TBA; Sex: Unknown; NUMBER OF REPLICATES: 1; EXPERIMENTAL FACTORS: Tissue Malpighian tubules

2012-06-03 | E-GEOD-38439 | biostudies-arrayexpress

Sex-biased transcriptome divergence along a latitudinal gradient

Project description:Although not all sex-dependent gene expression is adaptive, it is likely an important genomic mechanism that allows each sex to independently adapt to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex-differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11,631 genes across eight populations revealed strong sex differences in the frequency, mode, and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population-specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in D. simulans and D. melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.

2017-01-04 | GSE90733 | GEO

Natural variation affecting allele-specific expression in the Malpighian tubules of Drosophila melanogaster

Project description:We used RNA-seq to investigate natural variation in gene expression in the Malpighian tubules of three inbred Drosophila melanogaster strains and their F1 hybrids. One of the strains was from a population in the species’ ancestral range (Zambia), while the other two were from a more recently derived population (Sweden).

2018-08-29 | GSE103645 | GEO

Uncoupling X chromosome number from sex determination separates contribution of sex and X dose to sex-biased gene expression in C. elegans

Project description:The difference in X chromosome copy number creates a potential difference in X chromosomal gene expression between males and females. In many animals, dosage compensation mechanisms equalize X chromosome expression between sexes. Yet, X chromosome is also enriched for sex-biased genes due to differences in the evolutionary history of the X and autosomes. The manner in which dosage compensation and sex-biased gene expression exist on the X chromosome remains an open question. Most studies compare gene expression between two sexes, which combines expression differences due to X chromosome number (dose) and sex. Here, we uncoupled the effects of sex and X dose in C. elegans and determined how each process affects expression of the X chromosome compared to autosomes. We found that in the soma, sex-biased expression on the X chromosome is almost entirely due to sex because the dosage compensation complex (DCC) effectively compensates for the X dose difference between sexes. In the germline where the DCC is not present, X chromosome copy number contributes to hermaphrodite-biased gene expression. These results suggest that X dose contributes to sex-biased gene expression based on the level of dosage compensation in different tissues and developmental stages.

2016-04-06 | GSE77794 | GEO

Uncoupling X chromosome number from sex determination separates contribution of sex and X dose to sex-biased gene expression in C. elegans

2016-04-06 | E-GEOD-77794 | biostudies-arrayexpress

Transcriptome profiles of virgin and mated Callosobruchus maculatus seed beetles

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2016-12-23 | GSE92855 | GEO

Estrogen receptor alpha signaling establishes a sexually dimorphic regulatory node of energy expenditure

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