The largest subunit of RNA polymerase II (rpb1) as a phylogenetic marker of seed plant species

Abstract

The phylogeny of land plants, especially angiosperms, has been perplexing scientists for more than 125 years. The aim of this study was to help elucidate unanswered phylogenetic issues using rpb1 genes from twenty-six land plant species (8 gymnosperm species, 17 angiosperm species and Psilotum, a fernally, as the outgroup). The sixteen rpb1 genes which were sequenced in this study had very similar lengths and contained no base compositional bias. Synonymous substitutions of rpb1 sequences were saturated when compared to the outgroup. The third codon positions of these genes contained misleading phylogenetic information. The topology of trees based on first and second codon positions were in line with that of protein trees. Both angiosperms and gymnosperms were monophyletic. Amborella was found at the base of the angiosperm tree, followed by Nymphae, then Illicium. These data rejected the anthophyte hypothesis, weakly supported the gnepine hypothesis, but did not resolve the interrelationship among eumagnoliids and eudicots. rpb1 genes were combined with the 18S ribosomal RNA gene and chloroplast atpB and rbcL genes to obtain more robust phylogenies. This combined data set produced a topology similar to that of the first and second positions of rpb1 genes except that they better resolved the interrelationship among eumagnoliids and eudicots. We conclude that our rpb1 sequences evolve too slowly to provide enough phylogenetic information to fully resolve the phylogeny of seed plants and that other gene sequences will need to be added to these data sets to obtain a well-resolved phylogenetic tree of seed plants.