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

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

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Capsella / genetics*
  • Conserved Sequence*
  • Evolution, Molecular
  • Gene Expression
  • Genome, Plant
  • Genome-Wide Association Study
  • Open Reading Frames*
  • Polymorphism, Genetic
  • Selection, Genetic*
  • Untranslated Regions*

Substances

  • Untranslated Regions

Grant support

This work was supported by grants from Genome Canada, and Genome Quebec (to Thomas Bureau, Mathieu Blanchette, Alan Moses, Anuar Nasseem, John Stinchcombe, Daniel Schoen, Paul Harrison, and Stephen Wright) and a NSF Graduate Research Fellowship to EBJ (DGE-1048376). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.