BMC Genomics 2004, 5:69 http://www.biomedcentral.com/1471-2164/5/69 FHiygpuortehe2sis of RNA polymerase II evolution inferred from phylogenetic analyses of RPB1 sequences conserved regions A-H Hypothesis of RNA polymerase II evolution inferred from phylogenetic analyses of RPB1 sequences conserved regions A-H. The tree displayed, after Stiller and Cook [60] had the highest likelihood of all trees sampled from the posterior probability dis- tribution in 106 generations of Bayesian inference. Organisms with genomes included in this study are in larger/bold font, and whether each of the three primary CTD kinases (CDKs7,8,9) are present in this genome, as inferred from global phylogenetic analyses and distributions of CDK kinases (see Fig. 1), are indicated next to the name. Names in blue indicate the presence of repeated heptads at the RPB1 C-terminus, which includes several from protistan organisms that do not conform to the con- sensus sequence or known structural requirements of the canonical CTD [60]; names in red have no tandem-heptapeptide structure whatsoever. The node supporting a "CTD-clade," in which the consensus sequence and repetitive structure of the CTD are invariably conserved, occurred in 98% of the 8000 trees sampled from the Bayesian posterior probability distribution. See references 31 and 60 for a more complete phylogenetic treatment of the origin and conservation of the CTD. searches of the complete genome of Encephalitozoon found six CDKs but none show a phylogenetic affinity to CDK8. A CDK9 grouping also is supported as monophyletic with representative CDKs from yeasts, Encephalitozoon, ani- mals, plants and Plasmodium. This group is divided into two well-defined sub-clades. One of them consists of BUR1 from yeast along with CDK9 orthologs from ani- mals; the other contains CTK1 from yeast, CDC2L5 and CrkRS from human, and apparent orthologs from Dro- sophila and Caenorhabditis, both plants, and Plasmodium. A putative CDK9 also is found in Encephalitozoon, but falls at the base of the larger CDK9 grouping and does not asso- ciate clearly with either subgroup (Fig. 1). Plants also con- tain a large number of putative CDKs that show strong phylogenetic affinity to CDK9 (additional file 1). These kinases appear to represent a plant-specific amplification of CDK9, although their functions have not been deter- mined experimentally. Human CDK10 and CDK11 group with apparent orthologs from other animals, plants, fission yeast, and Page 7 of 13 (page number not for citation purposes)