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A novel dataset for identifying sex-biased genes in Drosophila.

ABSTRACT: Phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. To accurately identify genes differentially expressed between males and females in Drosophila, we sequenced the testis and ovary transcriptomes of D. yakuba, D. pseudoobscura, and D. ananassae and used them to identify sex-biased genes in the latter two species. We highlight the increased sensitivity and improved power of sex-biased gene detection methods when using our testis/ovary data versus male and female whole body transcriptome data. We thus provide a resource specifically designed to accurately identify and characterize sex-biased genes across Drosophila. This dataset is available through NCBI GEO accession GSE52058.

SUBMITTER: VanKuren NW

PROVIDER: S-EPMC4091448 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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A novel dataset for identifying sex-biased genes in Drosophila.

VanKuren Nicholas W NW Vibranovski Maria D MD

Journal of genomics 20140310

Phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. To accurately identify genes differentially expressed between males and females in Drosophila, we sequenced the testis and ovary transcriptomes of D. yakuba, D. pseudoobscura, and D. ananassae and used them to identify sex-biased genes in the latter two species. We highlight the increased sensitivity and i ...[more]

PMID: 25031657

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Project description:BackgroundGenes with sex-biased expression often show rapid molecular evolution between species. Previous population genetic and comparative genomic studies of Drosophila melanogaster and D. simulans revealed that male-biased genes have especially high rates of adaptive evolution. To test if this is also the case for other lineages within the melanogaster group, we investigated gene expression in D. ananassae, a species that occurs in structured populations in tropical and subtropical regions. We used custom-made microarrays and published microarray data to characterize the sex-biased expression of 129 D. ananassae genes whose D. melanogaster orthologs had been classified previously as male-biased, female-biased, or unbiased in their expression and had been studied extensively at the population-genetic level. For 43 of these genes we surveyed DNA sequence polymorphism in a natural population of D. ananassae and determined divergence to the sister species D. atripex and D. phaeopleura.ResultsSex-biased expression is generally conserved between D. melanogaster and D. ananassae, with the majority of genes exhibiting the same bias in the two species. However, about one-third of the genes have either gained or lost sex-biased expression in one of the species and a small proportion of genes (approximately 4%) have changed bias from one sex to the other. The male-biased genes of D. ananassae show evidence of positive selection acting at the protein level. However, the signal of adaptive protein evolution for male-biased genes is not as strong in D. ananassae as it is in D. melanogaster and is limited to genes with conserved male-biased expression in both species. Within D. ananassae, a significant signal of adaptive evolution is also detected for female-biased and unbiased genes.ConclusionsOur findings extend previous observations of widespread adaptive protein evolution to an independent Drosophila lineage, the D. ananassae subgroup. However, the rate of adaptive evolution is not greater for male-biased genes than for female-biased or unbiased genes, which suggests that there are differences in sex-biased gene evolution between the two lineages.

Dataset Information

A novel dataset for identifying sex-biased genes in Drosophila.

Publications

A novel dataset for identifying sex-biased genes in Drosophila.

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