Evolution of a RNA Polymerase Gene Family in Silene (Caryophyllaceae)—Incomplete Concerted Evolution and Topological Congruence Among Paralogues

Abstract

Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 species from the tribe Sileneae (Caryophyllaceae). We used a low stringency nested polymerase chain reaction (PCR) approach to overcome the difficulties of constructing specific primers for amplification of the low copy nuclear DNA regions. Maximum parsimony analyses resulted in largely congruent phylogenetic trees for all regions. We tested overall model congruence in a likelihood context using the software PLATO and found that ITSs, RPA2, and RPB2 deviated from the maximum likelihood model for the combined data. The topology parameter was then isolated and topological congruence assessed by nonparametric bootstrapping. No strong topological incongruence was found. The analysis of the combined data sets resolves previously poorly known major relationships within Sileneae. Two paralogues of RPD2 were found, and several independent losses and incomplete concerted evolution were inferred. The among-site rate variation was significantly lower in the RNA polymerase introns than in the rps16 intron and ITSs, a property that is attractive in phylogenetic analyses.

A New Lineage‐Based Tribal Classification of the Family Caryophyllaceae

“…Our matK analysis identified a paraphyletic Silene with Lychnis nested within it, which is consistent with results of other studies, including Oxelman and Lidén (1995;ITS and 5.8S), Oxelman et al (1997;rps16), Erixon and Oxelman (2008), and Rautenberg et al (2008;SIX1 and YI). Our combined analysis showed that Silene and Lychnis were sister to each other, consistent with findings of Popp and Oxelman (2004; RNA polymerase gene family, ITS, and rps16), Oxelman et al (2001;ITS and rps16), and Fior et al (2006); this may be due to the more limited sampling in those analyses. However, independent data indicate that the incongruence between these molecular phylogenies may be due to a reticulate history (Delichère et al 1999;Frajman et al 2007).…”

“…& Schltdl. : Soltis et al 1996; Scleranthus: Smissen et al 2003;Schiedea: Wagner et al 2005; Arenaria L. and Moehringia L.: Fior and Karis 2007; Polycarpon L.: Kool et al 2007; Silene: Popp and Oxelman 2001) and are beginning to provide an understanding of the complexities of the family. Finally, a recent study by Brockington et al (2009) has advanced our understanding of the order Caryophyllales and the placement of the Caryophyllaceae.…”

Phylogenetic utility of the AP3/DEF K-domain and its molecular evolution in Impatiens (Balsaminaceae)

“…The use of large multigene family members for molecular phylogenetics is often considered to be problematic as paralogues loci could be mistaken for orthologues loci (Popp and Oxelman, 2004). Although AP3/DEF-like genes form a well-supported clade within angiosperms, several studies illustrated the occurrence of numerous duplication events at every taxonomic level within this AP3/DEF lineage (e.g., Di Stilio et al, 2005;Geuten et al, 2006;Kramer et al, 1998Kramer et al, , 2003Stellari et al, 2004;Zahn et al, 2005).…”

The arctic mouse-ear in Scotland – and why it is not arctic

“…To obtain sequences of the low-copy number gene RPB2, degenerated primers and a low-stringency nested PCR approach were used (Brysting et al 2007). Four primers were used in four different combinations to amplify all four genes of the RNA polymerase second largest subunit family (RNAP10F, RNAP11R, RNAP10FF and RNAP11bR; Popp and Oxelman 2004). The pooled and diluted PCR products of these four reactions were used as template in a second PCR run with subunit specific primers for the RPB2 region (B2F and B2R; Popp and Oxelman 2004).…”

“…Four primers were used in four different combinations to amplify all four genes of the RNA polymerase second largest subunit family (RNAP10F, RNAP11R, RNAP10FF and RNAP11bR; Popp and Oxelman 2004). The pooled and diluted PCR products of these four reactions were used as template in a second PCR run with subunit specific primers for the RPB2 region (B2F and B2R; Popp and Oxelman 2004). All PCR runs were performed under the following thermal cycling conditions: initial denaturation at 95 ºC for 5 min followed by 35 cycles (30 sec denaturation at 95 ºC, 1 min annealing at 55 ºC, and 2 min extension at 72 ºC) and a final extension for 2 min at 72 ºC.…”