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.

Impact of demography on linked selection in two outcrossing Brassicaceae species

“…The general observation of reduced purifying selection associated with smaller effective population size has been found also in other plant species, for example in Populus, Helianthus and Lactuca (Strasburg et al, 2011;Wang, Street, Scofield, & Ingvarsson, 2016). We hence suggest that demographic history is likely the ultimate cause of these observed patterns al- in C. grandiflora (Slotte et al, 2010(Slotte et al, , 2013Williamson et al, 2014) and A. lyrata Gossmann et al, 2010) and support generally stronger efficacy of selection in C. grandiflora. In plants, the strongest correlates were mating system and longevity, with selfing and long-lived species having weaker purifying selection in comparison with outcrossing annual species.…”

“…Indeed, many studies have suggested some degree of selection also in intergenic regions, especially close to genes (Andolfatto, 2005;Williamson et al, 2014;Woerner et al, 2018) although the strongest selection is usually found in coding regions. In addition, if mapping rate in the intergenic regions is low due to high divergence, this could cause frequent allelic dropout and hamper diversity estimation in these regions.…”

Genome-wide nucleotide diversity and associations with geography, ploidy level and glucosinolate profiles in Aethionema arabicum (Brassicaceae)

“…The PCOA analysis was done with the 'bigmemory' and 'ape' packages in R v 3.2.1 (Paradis et al 2004;R Core Team 2014;Kane et al 2013). With the exception of the network trees, all figures were made in R v 3.2.1 with the 'ggplot2' package (Wickham 2009) and combined with Inkscape and GIMP.…”

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

“…mammals (Lindblad-Toh et al, 2005;Miller et al, 2007;Siepel et al, 2005), fish (Braasch et al, 2016;Jones et al, 2012;Lowe et al, 2011) and crucifer plants (Haudry et al, 2013;Williamson et al, 2014). In the best-studied organisms such as human, the detection of conserved elements (CEs) has recently been performed at increasingly fine-scale resolutions Rosenbloom et al, 2015).…”