Determination of the complete nucleotide sequence and haplotypes in the D-loop region of the mitochondrial genome in the Oriental white stork, Ciconia boyciana

The complete nucleotide sequence of the mitochondrial genome of the Orienta l white stork, Ciconia boyciana, has been determined from captive storks by a novel method incorporating Long PCR and shotgun sequencing. 13 protein-c oding genes, two ribosomal RNA genes and 22 transfer RNA genes were identif ied as in other vertebrate mitochondrial genomes. The position and directio n of the NADH6 and tRNA-Glu genes were the same as previously reported for avian mitochondrial genomes. A 71 bp direct repeat and long CAAA repeat seq uences were found at the 3' end of the D-loop region, together with SCB-1, SCB-2, SCB-3, and three TAS sequences. Direct sequencing of the PCR fragmen ts in the D-loop region in 26 captive Oriental white storks originating fro m Japan, China, and Russia revealed nucleotide differences at 18 sites alon g 1,248 bp, and a total of nine haplotypes have been identified. It was fou nd that one pair of individuals in the Japanese captive breeding program we re of the same haplotype, suggesting that they were caught from the same ne st. The pair has since been dissolved in consideration of the possibility o f inbreeding depression.