Williamson Robert J, Josephs Emily B, Platts Adrian E, Hazzouri Khaled M, Haudry Annabelle, Blanchette Mathieu, Wright Stephen I
Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada; School for Computer Science, McGill University, Montreal, Quebec, Canada.
PLoS Genet. 2014 Sep 25;10(9):e1004622. doi: 10.1371/journal.pgen.1004622. eCollection 2014 Sep.
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.
正向选择和负向选择在植物基因组不同部分的变化程度仍知之甚少。在此，我们对13个大花荠苨个体的全基因组进行测序，并量化全基因组的选择量。利用适合度效应分布的估计值，我们发现选择在编码区很强，但在大多数非编码区较弱，5'和3'非翻译区（UTR）除外。然而，对十字花科家族保守的非编码区的选择估计显示出强烈的选择信号。此外，我们在编码区和保守非编码区的功能替代周围观察到中性多样性的降低，表明这些位点最近发生了选择性清除。最后，利用叶片组织的表达数据，我们表明表达水平较高的基因经历更强的负向选择，但与低表达基因的正向选择水平相当。总体而言，我们在编码区和调控区观察到广泛的正向和负向选择，但我们的结果也表明，植物非编码序列上的正向和负向选择都比动物基因组中少见得多。
