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Background  Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of  Riox1  and  Riox2  genes and their encoded proteins across eukaryotic taxa.    Results  In this study, we have analysed  Riox1  and  Riox2  orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the  Riox2  gene, although in the early phylum Cnidaria both genes,  Riox1  and  Riox2,  are present and expressed.  Riox1  is an intronless single-exon-gene in several species, including humans. In contrast to  Riox2 ,  Riox1  is ubiquitously present throughout the animal kingdom suggesting that  Riox1  is the phylogenetically older gene from which  Riox2  has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique  N -terminal extension domain. Immunofluorescence analyses in Hela cells and in  Hydra vulgaris  identified a nucleolar localisation signal within the extended  N -terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2.    Conclusions  Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for  Hydra , point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of  Riox1 / Riox2  gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1215-0) contains supplementary material, which is available to authorized users.

Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution