Conclusions Our analyses of the APC C and its main targets showed that this complex system was very likely present in LECA and has been conserved, to a few exceptions, all along the diversification of the eukaryotic such information domain. This study provided first insights into the mechanisms responsible of the control of the cell cycle in LECA, sug gesting that it was tightly regulated like in present day eukaryotes. Finally we showed that the components of the APC C and its main targets can be good phyloge netic markers to complement those used so far. Indeed, the latter have proven not to be sufficient to fully resolve the phylogeny of eukaryotes, making neces sary to identify new complementary markers. This will certainly be a difficult task that will require many ana lyses but we think that the phylogenomic study of con served cellular systems is a promising approach to tackle this issue.

Methods Dataset assembly We used the 37 APC C components and main targets identified in four opisthokont species, the plant A. thaliana and the kinetoplastid T. brucei to survey public sequence databases. We identified homologues of these proteins using BLASTp and PSI BLAST in a sub set of complete or ongoing genomes representative of eukaryotic diversity available at the NCBI.

To increase the taxonomic sampling, homologues of Mono siga brevicollis, Salpingoeca rosetta, Lottia gigantea, Nematostella vectensis, Helobdella robusta, Daphnia pulex, Capsaspora owczarzaki, Batrachochytrium den drobatidis, Spizellomyces punctatus, Thecamonas trahens, Naegleria gruberi, Phaeodactylum tricornutum, Aureococcus anophagefferens, Ostreococcus lucimarinus, Physcomitrella patens, Chlorella vulgaris, Micromonas pusilla, Selaginella moellendorffii and Emiliania huxleyi were retrieved using the BLASTp and tBLASTn pro grams from the JGI, the Broad Institute and the TBestDB database In addi tion, homologues of two representatives of Rhodophyta were retrieved from the Galdieria sulphuraria genome project galdieria blast. cgi and the Cyanidioschyzon merolae genome project blast blast. html BLAST outputs were examined by eye to identify homo logues of each protein to avoid applying an arbitrary cutoff on e value or score. To ensure an exhaustive sampling of homologues, we performed additional searches using as seeds homologues that were identified at previous steps. The absence of any homologue in a given lineage was systematically verified by hand using tBLASTn searches on the nucleotide sequences of the corresponding complete genomes. For each protein, the homologous Entinostat sequences were gathered in a dataset and aligned with MAFFT 6. 833.