%0 Journal Article %A Robert J. Williamson %A Emily B. Josephs %A Adrian E. Platts %A Khaled M. Hazzouri %A Annabelle Haudry %A Mathieu Blanchette %A Stephen I. Wright %T Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora %D 2014 %R 10.1101/002428 %J bioRxiv %P 002428 %X 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. Overall, we observe widespread positive and negative selection in coding and regulatory regions, but our results also suggest that both positive and negative selection in plant noncoding sequence are considerably rarer than in animal genomes.Author Summary Selection affects patterns of 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 genome, we sequenced and analyzed genomes from 13 Capsella grandiflora individuals. C. grandiflora is well-suited for this task because it has experienced a large, stable effective population size, so we expect that selection signatures will not be overly distorted by demographic effects. Our analysis shows that positive and negative selection acting on new mutations have broadly shaped patterns of genomic diversity in coding regions but not in most noncoding regions. However, when we focus only on noncoding regions that show evidence of constraint across species, we see evidence for strong positive and negative selection. In addition, we find that genes with high expression experience stronger negative selection than genes with low expression, but the extent of positive selection appears to be equivalent across expression categories. %U https://www.biorxiv.org/content/biorxiv/early/2014/06/09/002428.full.pdf