Polymorphism in nucleotide sequence of mitochondrial intergenic region in scleractinian coral (Galaxea fascicularis)

A region of 826 bp that is unlikely to code for a protein, ribosomal RNA, or transfer RNA was identified between the cytochtome b and NADH-ubiquinone oxidoreductase chain 2 loci in the mitochondrial DNA of the scleractinian reef coral Galaxea fascicularis. Nucleotide sequences were determined in a part (625 bp) of this intergenic region in 95 individuals collected at 9 sites in the Ryukyu Archipelago in southwestern Japan. A total of 8 haplotypes were found, and a deletion of 290 bp was found in 3 of them. Significant differences were found in frequencies of the haplotypes at 3 sampling sites. The presence or absence of the deletion was highly correlated with the hard or soft morphotype. The deletion was found in the majority of hard-type colonies, but in a small fraction of soft-type individuals.