Evaluation of the 5' end of the 16S rRNA gene as a DNA barcode marker for the Cephalopoda

The present study seeks to incorporate a highly variable DNA barcode marker, additional to the standard regions of the cytochrome oxidase I gene and the 3' end of the 16S large ribosomal subunit (16S rRNA), for a more effective species-level identification among cephalopods. Thus, we evaluated whether the 5' end region of the 16S rRNA gene can be suitable as a DNA barcode marker among these taxa. Using a novel primer set, 28 different species were evaluated based on the pairwise intra- and interspecific distance and neighbor-joining (NJ) analysis. Except for Enteroctopus dofleini, we were able to obtain the sequences for the remaining species which formed highly supported clusters in the NJ tree. Divergence at the interspecific level may indicate high genetic variation of the region being proposed as compared to the standard of 16S rRNA. In addition, two well-supported clades and high levels of divergence within Sthenoteuthis oualaniensis, Loliolus japonica and Sepia pharaonis suggest the occurrence of cryptic species. This study confirms the efficiency of the 5' end region of the 16S rRNA gene as a DNA barcode marker which can be used along with the standard DNA markers in future studies.