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RNA-seq following knockdown of a sex determing gene in house fly

ABSTRACT: RNA-seq following knockdown of a sex determing gene in house fly

PROVIDER: PRJNA522995 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8587510.fastq.gz	Fastqsanger.gz
	SRR8587520.fastq.gz	Fastqsanger.gz
	SRR8587511.fastq.gz	Fastqsanger.gz
	SRR8587521.fastq.gz	Fastqsanger.gz
	SRR8587512.fastq.gz	Fastqsanger.gz

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RNA-seq following knockdown of a sex determing gene in house fly

Project description:We injected double-stranded RNA (dsRNA) into house fly embryos to knock down transformer (Md-tra), creating sex-reversed males that do not carry a Y chromosome. We also injected dsRNA trageting GFP as a sham treatment. We used RNA-seq to compare gene expression in the sex-reversed males with genotypic (normal) females (injected with dsRNA targeting GFP) and two types of genotypic (normal) males (injected with dsRNA targeting Md-tra or GFP). The expression profiles of sex-reversed males were similar to normal males. In contrast, about two thousand genes are differentially expressed between sex-reversed males and normal females, a similar magnitude as between normal males and females.

2019-02-19 | GSE126689 | GEO

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Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica

Project description:Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male determining factor, M, on the Y chromosome (Y^M), which is probably the ancestral state. An M factor on the third chromosome (III^M) has reached high frequencies in multiple populations across the world, but the evolutionary forces responsible for the invasion of III^M are not resolved. To test if the III^M chromosome invaded because of sex-specific selection pressures, we used mRNA sequencing to determine if isogenic males that differ only in the presence of the Y^M or III^M chromosome have different gene expression profiles. We find that more genes are differentially expressed between Y^M and III^M males in testis than head, and that genes with male-biased expression are most likely to be differentially expressed between Y^M and III^M males. This suggests that male phenotypes, especially those related to male fertility, are more likely to be affected by the male-determining chromosome, supporting the hypothesis that sex-specific selection acts on alleles linked to the male-determining locus driving evolutionary turnover in the sex determination pathway. We additionally find that III^M males have a "masculinization" gene expression profile, suggesting that the III^M chromosome has accumulated an excess of male-beneficial alleles because of its male-limited transmission.

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intestine of house fly

Project description:Intestinal microbiome of house fly Raw sequence reads

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Project description:fly brm knockdown RNA-seq

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fly brm knockdown MNase-seq

Project description:fly brm knockdown MNase-seq

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Effects of naturally ocurring proto-Y chromosomes on house fly gene expression

Project description:We performed RNA-seq experiments to examine the effects of house fly proto-Y chromosomes on gene expression. Two different Y^M chromosomes were investigated, and two different III^M chromosomes were investigated. One of the Y^M genotypes also was also heterozygous for third chromosomes that do not carry a male-determining locus to evaluate the effect of third chromosomes on gene expression independent of being a proto-Y.

2019-02-19 | GSE126685 | GEO

fly brm knockdown RNA-seq

Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.

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fly brm knockdown MNase-seq

Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted MNase digestion followed by next-generation sequencing (NGS) to analyse the nucleosome profile in both control and Brm knockdown fly larvae.

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Effects of proto-Y chromososomes and temperature on house fly gene expression

Project description:Purpose: House fly has a stable polygenic sex determination system. The male determining factor (Mdmd) is commonly found on the Y chromosome (Y^M) or the third chromosome (III^M). These proto-Y chromosomes are clinally distributed, with Y^M found most commonly in northern latitudes and III^M most commonly found at southern latitudes, hinting at possible genotype-by-temperature interactions that maintain the polymorphism. If this distribution is maintained by temperature-dependent selection pressures, we expect the fitness of III^M and Y^M flies to vary across developmental temperatures. These temperature-dependent effects could be driven by differential gene expression in III^M and Y^M males at different temperatures. Here, we performed RNA-seq experiments to study how genotype-by-temperature interactions affect gene expression in male houseflies carrying different proto-Y chromosomes. Methods: We raised a Y^M strain known as IsoCS and a III^M strain known as CSrab at 18°C and 29°C for two generations. We dissected 5 heads and 15-20 pairs of testes for each of three replicates of each genotype-by-temperature combination. We carried out RNA-seq on these tissues. Results: We identified 247 genes whose expression in testis and 50 genes whose expression in head depends on genotype-by-temperature interactions.

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