The mitochondrial DNA (mtDNA) from the salmon louse,
Lepeophtheirus salmonis, is 15 445 bp. It includes the genes coding for cytochrome
B (Cyt
B), ATPase subunit 6 and 8 (
A6 and
A8), NADH dehydrogenase subunits 1–6 and 4L (
ND1,
ND2,
ND3,
ND4,
ND4L,
ND5 and
ND6), cytochrome
c oxidase subunits I–III (
COI,
COII and
COIII), two rRNA genes (12S rRNA and 16S rRNA) and 22 tRNAs. Two copies of tRNA-Lys are present in the mtDNA of
L. salmonis, while tRNA-Cys was not identified. Both DNA strands contain coding regions in the salmon louse, in contrast to the other copepod characterized
Tigriopus japonicus, but only a few genes overlap. In vertebrates,
ND4 and
ND4L are transcribed as one bicistronic mRNA, and are therefore localized together. The same organization is also found in crustaceans, with the exceptions of
T. japonicus, Neocalanus cristatus and
L. salmonis that deviate from this pattern
. Another exception of the
L. salmonis mtDNA is that
A6 and
A8 do not overlap, but are separated by several genes. The protein-coding genes have a bias towards AT-rich codons.
The mitochondrial gene order in L. salmonis differs significantly from the copepods T. japonicus, Eucalanus bungii, N. cristatus and the other 13 crustaceans previously characterized. Furthermore, the mitochondrial rRNA genes are encoded on opposite strands in L. salmonis. This has not been found in any other arthropods, but has been reported in two starfish species. In a phylogenetic analysis, using an alignment of mitochondrial protein sequences, L. salmonis groups together with T. japonicus, being distant relatives to the other crustaceans.