Discovery of paralogous nuclear gene sequences coding for the second-largest subunit of RNA polymerase II (RPB2) and their phylogenetic utility in gentianales of the asterids

Paralogous sequences of the RPB2 gene are demonstrated in the angiosperm or der Gentianales. Two different copies were found by using different PCR pri mer pairs targeting a region that corresponds to exons 22-24 in the Arabido psis RPB2 gene. One of the copies (RPB2-d) lacks introns in this region, wh ereas the other has introns at locations corresponding to those of green pl ants previously investigated. When analyzed with other available RPB2 seque nces from this region, all 28 RPB2-d sequences obtained from the Gentianale s and the four sequences from the Lamiales form a monophyletic group, toget her with a previously published tomato cDNA sequence. The substitution patt erns, relative rates of change, and nucleotide compositions of the two para logous RPB2 exon regions are similar, and none of them shows any signs of b eing a pseudogene. Although multiple copies of similar, paralogous sequence s can confound phylogenetic interpretations, the lack of introns in RPB2-d make a priori homology assessment easy. The phylogenetic utility of RPB2-d within the Gentianales is evaluated in comparison with the chloroplast gene s ndhF and rbcL. The hierarchical information in the RPB2-d region sequence d is more incongruent with that of the plastid genes than the plastid genes are with each other as determined by incongruence length difference tests. In contrast to the plastid genes, parsimony-informative third codon positi ons of RPB2 have a significantly higher rate of change than first and secon d positions. Topologically, the trees from the three genes are similar, and thc:differences are usually only weakly supported. In terms of support, RP B2 gives the highest jackknife support per sequenced nucleotide, whereas nd hF gives the highest Bremer support per sequenced nucleotide. The RPB2-d lo cus has the potential to be a valuable nuclear marker for determination of phylogenetic relationships within the euasterid I group of plants.