The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus

We determined the complete 14,985-nt sequence of the mitochondrial DNA of t he horseshoe crab Limulus polyphemus (Arthropoda: Xiphosura). This mtDNA en codes the 13 protein, 2 rRNA, and 22 tRNA genes typical for metazoans. The arrangement of these genes and about half of the sequence was reported prev iously; however, the sequence contained a large number of errors, which are corrected here. The two strands of Limulus mtDNA have significantly differ ent nucleotide compositions. The strand encoding most mitochondrial protein s has 1.25 times as many A's as T's and 2.33 times as many C's as G's. This nucleotide bias correlates with the biases in amino acid content and synon ymous codon usage in proteins encoded by different strands and with the num ber of non-Watson-Crick base pairs in the stem regions of encoded tRNAs. Th e sizes of most mitochondrial protein genes in Limulus are either identical to or slightly smaller than those of their Drosophila counterparts. The us age of the initiation and termination codons in these genes seems to follow patterns that are conserved among most arthropod and some other metazoan m itochondrial genomes. The noncoding region of Limulus mtDNA contains a pote ntial stem-loop structure, and we found a similar structure in the noncodin g region of the published mtDNA of the prostriate tick Ixodes hexagonus. A simulation study was designed to evaluate the significance of these seconda ry structures; it revealed that they are statistically significant. No sign ificant, comparable structure can be identified for the metastriate ticks R hipicephalus sanguineus and Boophilus microplus. The latter two animals als o share a mitochondrial gene rearrangement and an unusual structure of mt-t RNA(C) that is exactly the same association of changes as previously report ed for a group of lizards. This suggests that the changes observed are not independent and that the stem-loop structure found in the noncoding regions of Limulus and Ixodes mtDNA may play the same role as that between trnN an d trnC in vertebrates, i.e., the role of lagging strand origin of replicati on.