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Background  Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges.    Results  We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families:  Agelas oroides  (Agelasidae, Agelasida) , Cymbaxinella   p   verrucosa  (Hymerhabdiidae, Agelasida) and  Axinella polypoides  (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals’ mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of  C. verrucosa.  Phylogenetic analysis indicates that the Group II introns present in  C. verrucosa  are related to red algae (Rhodophyta) introns.    Conclusions  The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-015-0556-1) contains supplementary material, which is available to authorized users.

Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida