The use of large ribosomal subunit RNA in evolutionary research of crown protists

In this study, ten LSU rRNA (large subunit rRNA) sequences from crown protist taxa of which no sequences had previously been known, were determined. These taxa include four heterokont algae (Ochromonas danica, Nannochloropsis salina, Tribonema aequale, Skeletonema pseudocostatum), two heterokont fungi (Phytophthora megasperma, Hyphochytrium catenoides), one chytridiomycete (Blastocladiella emersonii), two rhodophytes (Palmaria palmata, Gracilaria verrucosa), and one cryptomonad nucleomorph (Guillardia theta). Phylogenetic trees were constructed on the basis of LSU rRNA, and a combination of SSU (small subunit) and LSU rRNA sequences. It was concluded that these data generally do not resolve the relationships between the crown taxa any better than SSU rRNA sequences do. On the contrary, stramenopile phylogenies were resolved with more confidence on the basis of LSU rRNA data. Also the secondary structure of the SSU and LSU rRNA was scanned in order to identify characteristics that could point to evolutionary relationships, but these could not be found. LSU rRNA proved to be a useful asset for studying crown protist phylogeny, but whether determining complete LSU rRNA sequences is worthwhile primarily depends on the problem to be examined, since LSU rRNA is not always a better molecular clock than SSU rRNA, in spite of its length.