Mitochondrial DNA in the sea urchin Arbacia lixula: evolutionary inferences from nucleotide sequence analysis

From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoids. Furthermore, it underlines the following peculiar features of sea urchin mtDNA: the clustering of tRNAs, the short noncoding regulatory sequence, and the separation by the ND1 and ND2 genes of the two rRNA genes. Comparison with the orthologous sequences from the camarodont species Paracentrotus lividus and Strongylocentrotus purpuratus revealed that (1) echinoids have an extra piece on the amino terminus of the ND5 gene that is probably the remnant of an old leucine tRNA gene; (2) third-position codon nucleotide usage has diverged between A. lixula and the camarodont species to a significant extent, implying different directional mutational pressures; and (3) the stirodont-camarodont divergence occurred twice as long ago as did the P. lividus-S. purpuratus divergence.