Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences

Abstract

To study the inter- and infrafamilial phylogenetic relationships in the order Caryophyllales sensu lato (s.l.), ∼930 base pairs of the matK plastid gene have been sequenced and analyzed for 127 taxa. In addition, these sequences have been combined with the rbcL plastid gene for 53 taxa and with the rbcL and atpB plastid genes as well as the nuclear 18S rDNA for 26 taxa to provide increased support for deeper branches. The red pigments of Corbichonia, Lophiocarpus, and Sarcobatus have been tested and shown to belong to the betacyanin class of compounds. Most taxa of the order are clearly grouped into two main clades (i.e., "core" and "noncore" Caryophyllales) which are, in turn, divided into well-defined subunits. Phytolaccaceae and Molluginaceae are polyphyletic, and Portulacaceae are paraphyletic, whereas Agdestidaceae, Barbeuiaceae, Petiveriaceae, and Sarcobataceae should be given familial recognition. Two additional lineages are potentially appropriate to be elevated to the family level in the future: the genera Lophiocarpus and Corbichonia form a well-supported clade on the basis of molecular and chemical evidence, and Limeum appears to be separated from other Molluginaceae based on both molecular and ultrastructural data.

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

“…The matK gene region was sequenced using the primers -19F, and trnK-2R, 390F and 1326R of Cuénoud et al (2002). All sequencing was performed by Invitrogen Biotech Co. Ltd. (Shanghai, China) using a ABI-3730XL DNA sequencer.…”

Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales

“…Simmondsiaceae are supported as sister to the core Caryophyllales (Cuénoud et al 2002), with Physenaceae and Asteropeiaceae forming a strongly supported sister group (combined matK/rbcL analysis; Cuénoud et al 2002). Rhabdodendraceae have been associated with Simmondsiaceae as sister to the core Caryophyllales or as sister to both core and noncore Caryophyllales but with little support for either position (matK analysis; Cuénoud et al 2002).…”

“…The carnivorous clade plus Polygonaceae/Plumbaginaceae was further expanded to include Ancistrocladaceae, Dioncophyllaceae, Frankeniaceae, and Tamaricaceae (Fay et al 1997). Numerous analyses have recognized this expanded clade, which is variously termed the noncore Caryophyllales (Cuénoud et al 2002;APG II 2003), Caryophyllales II (Hilu et al 2003), and Polygonales (Judd et al 1999), as sister to Caryophyllales sensu stricto (Soltis et al 1999.…”

DNA barcoding plants in biodiversity hot spots: Progress and outstanding questions

“…This gene has a reputation for being one of the more difficult chloroplast regions to routinely amplify and sequence across divergent lineages, so the success rate reported by Lahaye et al is notable. They used primers described by Cuenoud et al (2002) targeting a region up to approximately 900 bp in length in the middle of the gene (forward:…”