BMC Genomics 2004, 5:69 http://www.biomedcentral.com/1471-2164/5/69 Table 1: CDK-related kinases used in this study. (Continued) T22H22.5 T12H1.1 K16E14.2 F21B7.1 AT4g22940 F8L10.9 F26A9.10 AT4g10010 F14J9.26 F6A14.22 F1M20.1 AAF21469.1 T4P13.34 25405751 15229881 26449318 7488248 15235867 15219169 42572067 30681286 18391043 15221833 25406336 6649591 42570106 AtT22H22.5 AtT12H1.1 AtK16E14.2 AtF21B7.1 At4g22940 AtF8L10.9 AtF26A9.10 At4g10010 AtF14J9.26 AtF6A14.22 AtF1M20.1 AtAAF21469.1 AtT4P13.34 Note: The sequences in bold are the additional sequences from incomplete genomes and uncharacterized CDK9 like-kinases from Arabidopsis and Oryza included in supplemental phylogenetic tree (additional file 1). Arabidopsis followed Joubès et al. (2000) and Vandepoele et al. (2002) [33,34] (Table 1). The catalytic core base, Gly-rich motif and T-loop, required for characterized CDK function, appear to be conserved across all defined and putative kinase sequences analyzed (additional file 2). The 50% majority rule consensus tree of 4,000 likelihood trees, sampled from the posterior probability distribution from Bayesian phylogenetic inference, is shown in Figure 1. This tree provides strong support for grouping a number of previously uncharacterized CDKs, from a vari- ety of organisms, with defined CDKs from animals and yeast. Overall, however, very little support is found for relationships among different CDK orthologous groups. In this unrooted tree the highly diversified cell-cycle kinases defined in humans, CDKs1-6, fall into a large clus- ter with 69% Bayesian support. This grouping includes CDKs from all organisms examined in the study. Among these putative cell-cycle CDKs, some plant and protistan kinases can be assigned with reasonable confidence to specific CDK groups. For example, apparent orthologs of human CDK1 are found in other animals (Drosophila and Caenorhabditis), yeasts, both plants (Arabidopsis and Oryza), Encephalitozoon and Giardia (Fig. 1). Likewise, putative orthologs of CDK5 were identified in all organ- isms examined, except for the two plants (Fig. 1). A number of other sequences, such as TbCrk2 and 3 from Trypanosoma, cluster with cell-cycle kinases but not clearly with any specific CDK family. Significantly, and consist- ent with the results of Liu and Kipreos (2000) [32], CDK5 and PCTAIRE-like kinases from fungi and animals form a strongly supported group, indicating their close relation- ship (Fig. 1). In contrast to cell-cycle kinases, our phylogenetic results failed to identify a clear ortholog of any transcription- related CDKs from two of the complete genomes exam- ined, Trypanosoma brucei and Giardia lamblia. This includes strongly supported clades of presumed orthologs of human CDKs7-11 respectively. A well-defined CDK7 fam- ily is recovered, including sequences from yeasts, the microsporidian, plants, and animals. These are the pri- mary groups that make up the "CTD-clade," in which the RNAP II CTD is invariably conserved (Fig. 2). CDK7 shows an interesting sister relationship to HsCCRK from human and apparent orthologs from Drosophila, Cae- orhabditis and Arabidopsis. In Arabidopsis, four possible CDK7 orthologs were found, as reported previously by Shimotohno and colleagues (2003) [35]; however, AtCdkF (CAK1) is quite divergent from the core CDK7 family and related specifically to HsCCRK in our analyses. PfMRK from Plasmodium, suggested previously to be a CDK7 [36], does not fall within the well-defined CDK7 group, but clusters with another Plasmodium kinase. The a priori hypothesis that PfMRK belongs in the core CDK7 group is strongly rejected with our data set in a likelihood paired-sites test. Likewise, GlCAKlike (gi: 292497120) has been proposed as a CDK7 from Giardia, based on nearest sequence simi- larity to Kin28 in a more limited comparison to CDK sequences from fission yeast [38]. In our expanded analy- ses of CDKs from 11 completed genomes, we find no evi- dence supporting an orthologous relationship to CDK7 for this, or any Giardia sequence. The a priori hypothesis that GlCAKlike belongs in the core CDK7 group also is strongly rejected in a likelihood paired-sites test. A robust CDK8 family is recovered with strong support values in both distance bootstrap and Bayesian inference. Like CDK7, this family includes putative orthologs only from members of the "CTD-clade," specifically yeasts, ani- mals and plants. Although the microsporidian Encepha- litozoon is a member of the RNAP II "CTD clade," TBlastN Page 5 of 13 (page number not for citation purposes)