Morphological identity of a taxonomically unassigned cytochrome c oxidase subunit I sequence from stomach contents of juvenile chum salmon determined using polymerase chain reaction

In a previous report, we analyzed the stomach contents of juvenile chum salmon Oncorhynchus keta by morphological observation and also by molecular identification using the mitochondrial cytochrome c oxidase subunit I (COI) region. However, one of the most frequently detected COI sequences could not be assigned to any specific taxon, even at the phylum level. In the present study, we conducted in situ hybridization (ISH) on the stomach contents of juvenile chum salmon using the COI sequence and polymerase chain reaction amplification of a 18S ribosomal RNA gene from the tissue sections where ISH signals were detected. As a result, the organism that was enigmatic at the phylum level was found to be an appendicularian. Moreover, Oikopleura longicauda collected from the bay where the juvenile chum salmon samples were obtained was shown to have the same COI sequences as this taxonomic “orphan” COI sequence from the stomach contents. The present results suggest that the COI sequences previously deposited in public databases for “Oikopleura” are actually derived from taxonomic groups other than appendicularians, and that this may have hampered our understanding of prey richness in the stomach or gut of certain marine animals based on DNA barcoding.