Here we present the complete mitochondrial genome of the common fouling barnacle, Amphibalanus amphitrite (Sessilia: Balanidae). Refer to pancrustacean mitochondrial ground pattern, seven conserved genes blocks are found in A. amphitrite mitochondrial genome. On the other hand, translocations of at least six tRNAs (trnA, trnE/trnS2, trnP/trnT, trnK, trnQ and trnC) are identified and translocation and inversion occurred simultaneously in one tRNAs (trnY). Comparison among the acorn barnacle mitogenomes reveals inversion of a six-gene block (trnP-nd4L-nd4-trnH-nd5-trnF) between A. amphitrite and Megabalanus. Volcano (Balanidae), suggesting non-conserved gene order even at intrafamilial level. The three species share three conserved genes blocks, of which the two are derived from the pancrustacean ground pattern and represent synapomorphies of acorn barnacles. In sum, large-scale gene rearrangements are observed in A. amphitrite mitochondrial genome as compared to the pancrustacean ground pattern and other barnacle species.
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