Predicting Plastid Marker Variation: Can Complete Plastid Genomes from Closely Related Species Help?

Abstract

Rapidly evolving non-coding plastid regions (NCPs) are currently widely used in evolutionary biology especially in plant systematic studies where NCPs have become one of the most commonly used tools in clarifying species relationships. Currently, the generally small amount of sequence variation provided by NCPs compared to nuclear regions makes plastid phylogeny reconstruction challenging at the species-level, especially so in species rich clades such as Solanum with c. 1,200 species. Previous studies have established that the set of most highly variable NCPs vary between major plant families, and here we explore whether this variation extends beyond family level to genera and major clades within genera. Using full plastome data, we identify the most highly variable plastid markers in the Potato clade of Solanum. We then compare sequence variation between the Potato and the closely related Morelloid clade. Results show that whilst a narrow set of NCPs show consistently high variation, levels of sequence variation in most NCPs differ greatly between the two closely related clades. The high variation detected between closely related groups implies that repeated screening studies will be needed for individual projects despite the potential availability of results from closely related taxa, and indicates a narrower applicability of family-specific screening studies than previously thought.

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

“…A few NC‐cpDNA regions stand out as being the most likely to contain high levels of variability at the inter‐ and intraspecific levels, even though this study (Figs. 2–4) and a body of literature (Mort et al, 2007; Shaw et al, 2007; Särkinen and George, 2013) reinforces the observation that there is no universally best NC‐cpDNA. That said, screening what are known to be, on average, the fastest evolving regions is a good starting point for molecular investigations of new groups (Cires et al, 2012; Fior et al, 2013).…”

Efficient Identification of the Forest Tree Species in Aceraceae Using DNA Barcodes

“…The non-coding spacer trn S- trn G provided more interspecific distance (0.0268) than the two coding fragments ( rbc L and mat K), but trn S- trn G provided lower species discrimination (33.3%). However, the debate regarding the use of non-coding regions in DNA barcoding is ongoing due to unreliable alignment of sequences with very high variation (Särkinen and George, 2013). In addition, some authors suggest that indel regions of non-coding DNA sequences provide important phylogenetic information and species discrimination power for some of the group, e.g., Taxus (Liu et al, 2011).…”

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

“…Many of the top 10 markers listed with less than 900 bp have been occasionally used in phylogenetic studies across disparate plant lineages with variable resolution, but never in cacti. The clpP gene is usually employed with its introns Lam et al 2016), and the psbB-clpP intergenic spacer has been increasingly reported as useful marker (Loera et al 2012;Särkinen and George 2013;Prince 2015). The intergenic spacer ycf4-cemA has been used for phylogenetic studies in Asteraceae and Poaceae genera Ekenas et al 2007) and the rps2 gene in Orobanchaceae and…”