Phylogenetic distribution of POLN, POLQ, and HELQ genes in eukaryotes.
Genomic DNA sequence databases for the indicated model organisms, accessed from the NCBI Genome portal, were searched using Blastp for each genus, and then individually verified by alignment. For illustrative purposes, the occurrence of each gene was mapped onto the phylogenetic distribution of the universal stress protein (USP) genes . The presence of POLN in the indicated organism is shown by a light blue colored bar, of POLQ by a light green bar and HELQ by a light orange bar. All identifications were cross-checked and confirmed by accessing Gene Tree view in Ensembl and Ensembl Metazoa (metazoa.ensembl.org). POLN genes were distinguished from pol I / polA type homologs frequently present in genomes and plastids of other organisms. Criteria included: 1. The presence of complete sequences for all six conserved polymerase motifs (S1 Fig), with key catalytic residues intact. 2. All three sequence inserts present in POLN as described (see S1 Fig in ref ). 3. In motif 4 encoding the core of the O-helix, a conserved (K/R)xxY in POLN orthologs, in contrast to (A/T)xxF in pol I orthologs (c.f. Fig 1 in ref ). POLQ gene distribution indicates presence in the last eukaryotic common ancestor (LECA). In some lineages, shown with grey rectangles, POLQ is annotated as split apart into two domains (helicase-like and polymerase like). POLQ has been lost in the fungal branch. HELQ genes are part of a wider family of helicase genes, with paralogs ASCC3 and SNRNP200. The ancestor of this family may have arisen by lateral gene transfer from archaea, as similar Hel308 genes are present in both crenarchaea and euryarchaea. HELQ, shown here, itself arose in a common metazoan ancestor. HELQ genes are absent in several lineages (white rectangles). The relative sister group positions of the Ctenophora and the Porifera with respect to Bilateria are under discussion  and are shown illustratively here.