Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes.

Partial sequences of the mitochondrial genomes were determined for two calanoid copepods, Eucalanus bungii [9530 bp (base pairs)] and Neocalanus cristatus (7965 bp), using an approach that employs a long polymerase chain reaction (PCR) technique and primer walking. In contrast to Tigriopus japonicus (Harpacticoida), in which the complete mitochondrial genome has been determined, genes are encoded on both strands of the genome. In spite of the close relationship between E. bungii and N. cristatus, the gene orders of these calanoid copepods differed greatly from each other. From the sequence we obtained, new copepod-specific versatile primers were designed for the cytochrome c oxidase I (COI) gene (1200 bp). These primer pairs, as well as the previously designed primer pairs for the small ribosomal RNA (srRNA) gene (500 bp), were applied for 20 species representing four orders of both calanoid and non-calanoid copepods and amplification of sequences from at least one species from each order was successful.