Analysis of mitogenomes from the family Keratoisididae reveals mitonuclear discordance and the presence of unknown open reading frames

Abstract Historically, evolutionary studies have not been able to resolve relationships within Octocorallia but recent advances in genomic techniques have allowed large numbers of Ultra Conserved Elements and exons, collectively referred to as conserved elements, to be extracted from the nuclear genome. Few studies have compared evolutionary histories generated with these conserved elements and with those inferred from complete mitochondrial genomes. We examined the characteristics of 26 complete mitogenomes and constructed both mitochondrial and nuclear (1418 conserved elements) phylogenies of the family Keratoisididae, a prolific group of exclusively deep-sea corals. Relationships among most keratoisidid groups were well supported by the conserved element phylogeny while many relationships were unresolved from mitogenomic inferences. In addition, some incongruences were observed. The position of keratoisidid groups F1 and I4, and the observed polyphyly of D2 in the nuclear inference phylogeny, provide evidence for mitonuclear discordance within the group. Multiple novel Open Reading Frames (ORFs) of unknown function were found in the mitochondrial genome between cob and nad6. These ORFs ranged in size from 84–537 bp and were present in all examined mitogenomes except those assigned to keratoisidid group A1 which only have a 10 bp gap between coding regions. Further investigation is required to determine whether these ORFs are expressed and, if so, what function they have. The presence of mitonuclear discordance within the family indicates that phylogenies constructed with concatenated mitochondrial and nuclear markers may be inappropriate.