117 research outputs found

    Identification of internal reference genes for gene expression normalization between the two sexes in dioecious white Campion.

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    Quantitative real time (qRT)-PCR is a precise and efficient method for studying gene expression changes between two states of interest, and is frequently used for validating interesting gene expression patterns in candidate genes initially identified in genome-wide expression analyses, such as RNA-seq experiments. For an adequate normalisation of qRT-PCR data, it is essential to have reference genes available whose expression intensities are constant among the different states of interest. In this study we present and validate a catalogue of traditional and newly identified reference genes that were selected from RNA-seq data from multiple individuals from the dioecious plant Silene latifolia with the aim of studying gene expression differences between the two sexes in both reproductive and vegetative tissues. The catalogue contains more than 15 reference genes with both stable expression intensities and a range of expression intensities in flower buds and leaf tissues. These reference genes were used to normalize expression differences between reproductive and vegetative tissues in eight candidate genes with sex-biased expression. Our results suggest a trend towards a reduced sex-bias in sex-linked gene expression in vegetative tissues. In this study, we report on the systematic identification and validation of internal reference genes for adequate normalization of qRT-PCR-based analyses of gene expression differences between the two sexes in S. latifolia. We also show how RNA-seq data can be used efficiently to identify suitable reference genes in a wide diversity of species

    Supplementary material from "Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia?"

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    Supplementary Figure S1. Summary of the estimated expression intensities in contigs with detectable sex biases in expression in S. latifolia males and females due to changes that are mainly in females or males). The changes in each sex, relative to the expression in the hermaphrodite, are indicated using the same notation as in Figure 1, and panels A to D correspond with the panels with the same letters in Figure 2, which shows results for changes specific to females or males; as in that figure, differences significant with P < 0.05, after adjusting for multiple testing ( Benjamini and Hochberg 1995) using multiple Wilcoxon tests are indicated by different letters in the figure.The evolution of separate sexes may involve changed expression of many genes, as each sex adapts to its new state. Evidence is accumulating for sex differences in expression even in organisms that have recently evolved separate sexes from hermaphrodite or monoecious (cosexual) ancestors, such as some dioecious flowering plants. We describe evidence that a dioecious plant species with recently evolved dioecy, Silene latifolia, has undergone adaptive changes that improve functioning in females, in addition to changes that are probably pleiotropic effects of male-sterility. The results suggest pervasive adaptations as soon as males and females evolve from their cosexual ancestor.Zemp, Niklaus; Widmer, Alex; Charlesworth, Deborah (2018): Supplementary material from "Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia?". The Royal Society. Collection. https://doi.org/10.6084/m9.figshare.c.4158059.v

    Supplementary data from "Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia?"

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    Assembly: GCA_900095335.1 trinity_orf_cap3 assembly for Silene latifolia. Genome assembly: FMHP01000000 Silene latifolia, WGS project FMHP01000000 data. Experiment (32): ERX1495856 Illumina HiSeq 2000 paired end sequencing. Study (2): ERP015793 & PRJEB14171Evolution of sex-biased gene expression in a dioecious plant.The evolution of separate sexes may involve changed expression of many genes, as each sex adapts to its new state. Evidence is accumulating for sex differences in expression even in organisms that have recently evolved separate sexes from hermaphrodite or monoecious (cosexual) ancestors, such as some dioecious flowering plants. We describe evidence that a dioecious plant species with recently evolved dioecy, Silene latifolia, has undergone adaptive changes that improve functioning in females, in addition to changes that are probably pleiotropic effects of male sterility. The results suggest pervasive adaptations as soon as males and females evolve from their cosexual ancestor.Zemp, Niklaus; Widmer, Alex; Charlesworth, Deborah (2018): Supplementary data from "Has adaptation occurred in males and females since separate sexes evolved in the plant Silene latifolia?". The Royal Society. Collection. Data are available in the European Nucleotide Archive (ENA accession no. PRJEB14171

    Supplementary Figure S1 from Has adaptation occurred in males and females since separate sexes evolved in the plant <i>Silene latifolia</i>?

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    Summary of the estimated expression intensities in contigs with detectable sex biases in expression in S. latifolia males and females due to changes that are mainly in females or males). The changes in each sex, relative to the expression in the hermaphrodite, are indicated using the same notation as in Figure 1, and panels A to D correspond with the panels with the same letters in Figure 2, which shows results for changes specific to females or males; as in that figure, differences significant with P < 0.05, after adjusting for multiple testing (Benjamini and Hochberg 1995) using multiple Wilcoxon tests are indicated by different letters in the figure

    3. The 8-Queens Problem and an Approach to Its Solution

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    is a digitized copy derived from an ACM copyrighted work. It is not guaranteed to be an accurate copy of the author&apos;s original work
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