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PLoS Genet. 2014 Sep 25;10(9):e1004622. doi: 10.1371/journal.pgen.1004622. eCollection 2014 Sep.

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

Author information

1
Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
2
Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada; School for Computer Science, McGill University, Montreal, Quebec, Canada.
3
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.
4
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.
5
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.

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.

PMID:
25255320
PMCID:
PMC4178662
DOI:
10.1371/journal.pgen.1004622
[Indexed for MEDLINE]
Free PMC Article

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