Discrimination between closely related Pacific oyster species (Crassostrea) via mitochondrial DNA sequences coding for large subunit rRNA.

Mitochondrial DNA sequence variation was characterized for the large subunit rRNA-coding gene (16SrDNA) in two closely related Pacific oyster species (Crassostrea gigas and C. sikamea) and an out group, the Olympia oyster (Ostrea lurida). Although each species was shown to have a single, fixed haplotype for the DNA sequence under study, 7 nucleotide differences were found between C. gigas and C. sikamea, and these two species differed from the O. lurida haplotype at 62 and 60 nucleotide sites, respectively. Nucleotide differences for the two Crassostrea species showed a notable transition bias (85.7%) in contrast to the marginal transversion bias (54.5%) in nucleotide differences between Crassostrea haplotypes and the more distantly related O. lurida. Conservation of primary sequence in all three oyster species as well as other published 16SrDNA sequences was noted for regions with apparent functional significance. We developed DNA sequence-specific discrimination techniques and employed sequence-specific PCR primers, dot-blot hybridization, and restriction digests as alternate techniques for rapid diagnosis of Crassostrea oyster larvae.