title: Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.
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 on 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 on plant noncoding sequence are considerably rarer than in animal genomes.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Williamson
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Emily B
authors.initials: EB
authors.lastname: Josephs
authors.affiliation: Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada; School for Computer Science, McGill University, Montreal, Quebec, Canada.
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Platts
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
authors.forename: Khaled M
authors.initials: KM
authors.lastname: Hazzouri
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada; Université Lyon 1, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
authors.forename: Annabelle
authors.initials: A
authors.lastname: Haudry
authors.affiliation: Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada; School for Computer Science, McGill University, Montreal, Quebec, Canada.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Blanchette
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Stephen I
authors.initials: SI
authors.lastname: Wright
mesh_terms: D029687:Capsella / Q000235:genetics*; D017124:Conserved Sequence; D019143:Evolution, Molecular; D015870:Gene Expression; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D016366:Open Reading Frames; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions