A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

“…Within angiosperms, most plastid genomes are highly conserved in sequence and structure (Jansen et al 2007;Wicke et al 2011), but multiple independent lineages have experienced accelerated rates of aa substitution in similar subsets of nonphotosynthetic genes (Jansen et al 2007;Erixon and Oxelman 2008;Greiner et al 2008b;Guisinger et al 2008Guisinger et al , 2010Guisinger et al , 2011Straub et al 2011;Sloan et al 2012aSloan et al , 2014aBarnard-Kubow et al 2014;Weng et al 2014;Dugas et al 2015;Williams et al 2015;Zhang et al 2016). Several mechanisms have been hypothesized to explain these repeated accelerations including positive selection, reduced effective population size (N e ), altered DNA repair, changes in gene expression, and pseudogenization following gene transfer to the nucleus (see above citations).…”

“…In many cases of extreme plastid genome evolution, accelerations have disproportionately affected nonsynonymous sites, resulting in elevated ratios of nonsynonymous to synonymous substitution rates (d N /d S ) (e.g., Erixon and Oxelman 2008;Guisinger et al 2008;Barnard-Kubow et al 2014;Sloan et al 2014a), which indicates that changes in selection are likely involved. In addition, recent studies showed correlated increases in d N /d S between nuclear-and plastidencoded subunits in ribosomal (Sloan et al 2014b;Weng et al 2016) and RNA polymerase complexes (Zhang et al 2015), providing further evidence for changes in selection pressures.…”

“…In most angiosperms, the sequences of the clpP1 and accD genes are generally conserved, but they are among the plastid-encoded genes that exhibit elevated rates of sequence evolution in multiple independent lineages. The clpP1 gene, in particular, exhibits recent and dramatically increased rates of nonsynonymous substitutions and indels (e.g., Erixon and Oxelman 2008;Sloan et al 2014a).…”

“…The angiosperm tribe Sileneae (Caryophyllaceae) has emerged as model for studying organelle genomes under divergent rates of sequence evolution (Mower et al 2007;Erixon and Oxelman 2008;Sloan et al 2012aSloan et al ,b, 2014a. This group contains multiple lineages with phylogenetically independent accelerations in rates of plastid genome evolution (Sloan et al 2012a(Sloan et al , 2014a.…”

“…This group contains multiple lineages with phylogenetically independent accelerations in rates of plastid genome evolution (Sloan et al 2012a(Sloan et al , 2014a. In contrast, closely related Sileneae lineages have largely maintained low ancestral rates of evolution.…”