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

Abstract

Paralogous sequences of the RPB2 gene are demonstrated in theangiosperm order Gentianales. Two different copies were found by using different PCR primer pairs targeting a regionthat corresponds to exons 22-24 in the Arabidopsis RPB2 gene. One of the copies (RPB2-d) lacks introns in thisregion, whereas the other has introns at locations corresponding to those of green plants previously investigated. When analyzed with other available RPB2 sequences from this region, all 28 RPB2-d sequences obtained from theGentianales and the four sequences from the Lamiales form a monophyletic group, together with a previously publishedtomato cDNA sequence. The substitution patterns, relative rates of change, and nucleotide compositions of the twoparalogous RPB2 exon regions are similar, and none of them shows any signs of being a pseudogene. Althoughmultiple copies of similar, paralogous sequences can confound phylogenetic interpretations, the lack of introns inRPB2-d make a priori homology assessment easy. The phylogenetic utility of RPB2-d within the Gentianales isevaluated in comparison with the chloroplast genes ndhF and rbcL. The hierarchical information in the RPB2-d regionsequenced is more incongruent with that of the plastid genes than the plastid genes are with each other asdetermined by incongruence length difference tests. In contrast to the plastid genes, parsimony-informative third codonpositions of RPB2 have a significantly higher rate of change than first and second positions. Topologically, the treesfrom the three genes are similar, and the differences are usually only weakly supported. In terms of support, RPB2 givesthe highest jackknife support per sequenced nucleotide, whereas ndhF gives the highest Bremer support persequenced nucleotide. The RPB2-d locus has the potential to be a valuable nuclear marker for determination ofphylogenetic relationships within the euasterid I group of plants.