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Background  The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effects on cells by interacting with cell surface chemokine receptors. In the European rabbit and in rodents such as mouse, rat and guinea pig,  CCL16  was identified as a pseudogene, while in the thirteen-lined ground squirrel it appears to be potentially functional. To gain insight into the evolution of this gene in the superorder Glires (rodents and lagomorphs), we amplified the  CCL16  gene from eleven Leporidae and seven Ochotonidae species.    Results  We compared our sequences with  CCL16  sequences of twelve rodent species retrieved from public databases. The data show that for all leporid species studied  CCL16  is a pseudogene. This is primarily due to mutations at the canonical Cys Cys motif, creating either premature stop codons, or disrupting amino acid replacements. In the Mexican cottontail,  CCL16  is pseudogenized due to a frameshift deletion. Additionally, in the exon 1 (signal peptide), there are frameshift deletions present in all leporids studied. In contrast, in  Ochotona  species,  CCL16  is potentially functional, except for an allele in Hoffmann’s pika. In rodents,  CCL16  is functional in a number of species, but patterns of pseudogenization similar to those observed in lagomorphs also exist.    Conclusions  Our results suggest that while functional in the Glires ancestor,  CCL16  underwent pseudogenization in some species. This process occurred stochastically or in specific lineages at different moments in the evolution of Glires. These observations suggest that the  CCL16  had different evolutionary constrains in the Glires group that could be associated with the CCL16 biological function.    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1390-7) contains supplementary material, which is available to authorized users.

Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern