The evolution of land plants inferred using domains D-F of the largest subunit of RNA polymerase II.

The aim of this project has been to develop the use of the nucleotide and amino acid sequences of the largest subunit of RNA polymerase II (RPB1) to study the evolutionary relationships of diverse land plants. 1.3 kb of this gene, which includes 900bp of coding sequence corresponding to regions D-F of the protein, have been cloned and sequenced from genomic DNA of seven plant species, one from each of seven divisions. 900 bp of cDNA sequence of regions D-F of RPB1 from Zea mays revealed identity with the genomic sequence. Phylogenetic analysis of these nucleotide and corresponding amino acid sequences by parsimony, neighbor-joining and maximum likelihood methods revealed inconsistent results. The maximum-likelihood method presented the best resolved trees. It is unlikely that the inconsistencies are the result of compositional biases, multiple substitutions, or unequal substitution rates. Analysis of amino acid sequences of regions D-F and F-H of RPB1 in animals, plants and fungi showed that animals are more closely related to plants than to fungi, contrary to recent literature. In comparing regions D-F of the largest subunits of RNA polymerases I, II and III (RPA1, RPB1 and RPC1) of all eukaryotes, though, the evolutionary relationships of the major eukaryotic kingdoms were not resolved but RPA1 was found to be more closely related to RPB1 than to RPC1. Since analyses in the literature of longer RPB1 sequences from fewer taxa did clearly resolve relationships of major eukaryotic lineages, this study shows that region D-F of this gene is too short to be informative. Due to the conserved nature of this partial sequence, it appears that a longer sequence from this gene with more synapomorphic sites is required to better assess the evolutionary relationships of plants