Feb 10, 2014

Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora

BioRxiv : the Preprint Server for Biology
Robert J WilliamsonStephen I Wright

Abstract

The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects we show that selection is strong in coding regions, but weak in most noncoding regions with the exception of 5’ and 3’ untranslated regions (UTRs). However, estimates of selection in noncoding regions conserved across the Brassicaceae family show strong signals of selection. Additionally, we see reductions in neutral diversity around functional substitutions in both coding and conserved noncoding regions, indicating recent selective sweeps at these sites. Finally, using expression data from leaf tissue we show that genes that are more highly expressed experience stronger negative selection but comparable levels of positive selection to lowly expressed genes. Author Summary Selection will have consequences for genomic variation, but it is unclear how much the genomic effects of selection vary across plant genomes, particularly in noncoding regions. To determine the strength and extent of selective signatures across the gen...Continue Reading

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Mentioned in this Paper

Patterns
Untranslated Regions
Genome
Genes
Alfalfa (Dietary)
Site
Brassicaceae
Capsella grandiflora
Species
Analysis

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