The largest subunit of RNA polymerase II as a molecular marker for inferring land plant phylogeny.

Abstract

This is an initial study using the gene encoding the largest subunit of RNA polymerase II (RPB1) to elucidate evolutionary relationships among ten land plants. This is the first study to use a single nuclear protein-coding gene to examine seed plant evolution. Results show RPB1 to contain no base compositional bias and to evolve at a conservative rate that is similar in most species studied here. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve all relationships among the seed plants in this study. Maximum parsimony, neighbor-joining and maximum likelihood analyses all generate identical tree topologies with similar support values at each node. The angiosperms are a monophyletic clade comprised of Nymphaea as the most basal angiosperm, followed by Magnolia, then Arabidopsis and a monophyletic monocot clade containing maize and Oryza . The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycad and Zamia clade. These findings concur with recent studies that refute the Anthophyte theory and place Nymphaea near the root of the angiosperm tree. The RPB1 sequence shows great promise to resolve the phylogenetic relationships among plants.