Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus.

Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10(-6) of total RNA. Transcripts restricted to the 3' end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated the likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species. With both methods, an age of more than 30 million years is suggested.