We present the discovery of microRNAs (miRNAs) in the calcisponges Sycon and Leucosolenia (phylum Calcarea), and potential miRNAs in the homoscleromorph Oscarella carmela (Phylum Homoscleromorpha), expanding the complement of poriferan miRNAs previously known only from the siliceous sponges (demosponges and hexactinellids). Comparison of these miRNAs with those previously described from silicisponges and eumetazoans reveals that these newly described miRNAs are novel, with each metazoan lineage (Silicea, Calcarea, Homoscleromorpha, and Eumetazoa) characterized by a unique and non-overlapping repertoire of miRNAs (or potential miRNAs as in the case of the homoscleromorphs). Because each group is characterized by a unique repertoire of miRNAs, miRNAs cannot be used to help resolve the contentious issue of sponge mono- versus paraphyly. Further, because all sponges are characterized by a similar repertoire of tissue types and body plan organisation, we hypothesize that the lack of conserved miRNAs amongst the three primary sponge lineages is evidence that cellular differentiation and cell type specificity in sponges are not dependent upon conserved miRNAs, contrary to many known cases in eumetazoans. Finally, we suggest that miRNAs evolved multiple times independently not only among eukaryotes, but even within animals, independently evolved miRNAs representing molecular exaptations of RNAi machinery into pre-existing gene regulatory networks. The role(s) miRNAs play though in sponge biology and evolution remains an open question.
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