An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

Frentiu, Francesca D.; Adamski, Marcin; McGraw, Elizabeth A.; Blows, Mark W.; Chenoweth, Stephen F.

doi:10.1186/1471-2164-10-40

Cited by 27 publications

(35 citation statements)

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“…serrata (Frentiu et al 2009). The 283 EST sequences that were shorter than 200bp (180bp) and could not be deposited in the TSA are available directly from the authors upon request.…”

Section: Microarray and Experimental Designmentioning

confidence: 99%

“…The sex-specific gene expression data set was produced using a custom species-specific microarray. To develop the microarray, I utilised several expressed sequence tag (EST) libraries (Frentiu et al 2009) that were derived from larval and adult RNA of both sexes and provided an original set of over 100,000 ESTs. I reduced the original set of ESTs to a unique gene set representing 11,631 genes via bioinformatic comparison to the genomes, gene sequences, coding sequences, and transcript sequences of 12 other Drosophila species (McQuilton et al 2012a).…”

Section: Strong Sex Differences Inmentioning

confidence: 99%

“…In order to maximise EST discovery, the samples used for EST sequencing were derived from RNA extracted at multiple life stages (larvae and adults aged 0-4 days) of both sexes (Frentiu et al 2009). The two multi-fasta files (Sanger and Illumina) were combined and then contigs were assembled using the default specifications of Cap3® (Huang and Madan 1999) In addition, all known transposable elements and mitochondrial genes in D. melanogaster (McQuilton et al 2012a) were identified via BLAST and removed from the EST set.…”

Section: Microarray and Experimental Designmentioning

confidence: 99%

“…A custom NimbleGen 12x135K microarray designed from D. serrata expressed sequence tags (ESTs) (Frentiu et al 2009) was used to measure expression of 11,631 ESTs. Probe sequence design and layout of the microarray was performed by Roche-NimbleGen who used my set of 11,666 unique Expressed Sequence Tags (ESTs).…”

Section: Microarray and Experimental Designmentioning

confidence: 99%

“…Five probes per EST were successfully designed for 11,631 ESTs, and each probe was replicated twice per array. The EST set provided to Roche-NimbleGen was constructed from a combination of Sanger (Frentiu et al 2009) and…”

Section: Microarray and Experimental Designmentioning

confidence: 99%

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The evolution of sex-biased gene expression in Drosophila serrata

Allen¹

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Sexual reproduction is an ancient biological process and in most species, has resulted in the evolution of two distinct sexes; females that are typically categorised as producing relatively large and metabolically costly gametes, and males that produce smaller less costly gametes. Such differences between the sexes can result in discordant selection pressures where, for example, males are selected for a fast mating rate, whereas it is beneficial for females to reproduce less often. Because the sexes share a genome, such discordant selection can create an intralocus sexual conflict, where an allele can be simultaneously beneficial in one sex while being detrimental in the other. Ultimately, the resolution of intralocus sexual conflict occurs via the evolution of sexual dimorphism, which allows each sex to approach its individual fitness optimum. A prime mechanism for the evolution of sexual dimorphism is sex-biased gene expression, where males and females express the shared genome differently to produce distinct phenotypes.Sex-biased gene expression (SBGE) appears to be a common feature of dioecious species and during my PhD candidature, I studied the following aspects of the evolution of SBGE in the Australian vinegar fly Drosophila serrata. 1) A deficit of male-biased X-linked genes has been observed in several other species. I assessed the possibility that such a nonrandom distribution of sex-biased genes in D. serrata is a by-product of dosage compensation rather than selection. I found that both selection and dosage compensation likely play a part. 2) While the rapid evolution of male-biased genes is a strikingly consistent pattern of divergence between species, I asked whether the same patterns occur for divergence among populations within species spanning a latitudinal gradient. I found that the patterns are indeed reflective, and I also discovered that many more genes diverged in males than females. Because a lot of the malespecific divergence did not clinally vary with latitude, as might be expected of spatially variable natural selection, I hypothesised that male-driven divergence might be in response to stronger sexual selection on males, which may occur on a population-specific scale. 3) While comparisons of protein coding sequence between species indicate that positive selection is a possible explanation for the rapid evolution of male-biased genes, I found support for several other explanations in relation to the evolution of gene expression of male-biased genes in D.

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“…serrata (Frentiu et al 2009). The 283 EST sequences that were shorter than 200bp (180bp) and could not be deposited in the TSA are available directly from the authors upon request.…”

Section: Microarray and Experimental Designmentioning

confidence: 99%

Section: Strong Sex Differences Inmentioning

confidence: 99%

Section: Microarray and Experimental Designmentioning

confidence: 99%

Section: Microarray and Experimental Designmentioning

confidence: 99%

Section: Microarray and Experimental Designmentioning

confidence: 99%

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The evolution of sex-biased gene expression in Drosophila serrata

Allen¹

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Expression screening and annotation of Sepiella maindroni ink sac cDNA library

Wei-wei

Chu

et al. 2012

J Genet

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The Phenome-Wide Distribution of Genetic Variance

Blows¹,

Allen²,

Chenoweth³

et al. 2015

The American Naturalist

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JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. abstract: A general observation emerging from estimates of additive genetic variance in sets of functionally or developmentally related traits is that much of the genetic variance is restricted to few trait combinations as a consequence of genetic covariance among traits. While this biased distribution of genetic variance among functionally related traits is now well documented, how it translates to the broader phenome and therefore any trait combination under selection in a given environment is unknown. We show that 8,750 gene expression traits measured in adult male Drosophila serrata exhibit widespread genetic covariance among random sets of five traits, implying that pleiotropy is common. Ultimately, to understand the phenome-wide distribution of genetic variance, very large additive genetic variancecovariance matrices (G) are required to be estimated. We draw upon recent advances in matrix theory for completing high-dimensional matrices to estimate the 8,750-trait G and show that large numbers of gene expression traits genetically covary as a consequence of a single genetic factor. Using gene ontology term enrichment analysis, we show that the major axis of genetic variance among expression traits successfully identified genetic covariance among genes involved in multiple modes of transcriptional regulation. Our approach provides a practical empirical framework for the genetic analysis of highdimensional phenome-wide trait sets and for the investigation of the extent of high-dimensional genetic constraint.

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An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

Cited by 27 publications

References 82 publications

The evolution of sex-biased gene expression in Drosophila serrata

The evolution of sex-biased gene expression in Drosophila serrata

Expression screening and annotation of Sepiella maindroni ink sac cDNA library

The Phenome-Wide Distribution of Genetic Variance

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