Complete Mitochondrial Genomes of Endangered Japanese Birds

Abstract

Nucleotide sequences of mitochondrial DNA (mtDNA) are highly suitable for phylogenetic analyses of animals and are therefore extensively used as a standard phylogenetic method. Today, complete mitochondrial genomes have been revealed because the cost of sequencing has decreased due to technical advances in molecular biology. While complete mitochondrial genomes from many avian samples are registered in the DDBJ, EMBL, andGenBank data banks, not all avian species are registered. It is important to gather mtDNA nucleotide sequence data, which are useful for assessing genetic diversity, establishing conservation-management units, detecting threatened cryptic species, and selecting more suitable lineages for reintroduction. We collected samples of birds designated endangered by the Japanese Government and determined their complete mitochondrial genomes. Because the DNA extracted from the samples was degraded and fragmented, we designed 16 primer sets to amplify the shorter fragments. Polymerase chain reaction (PCR) with LA Taq and these primer sets resulted in 16 fragments of the mtDNA coding region (12S rRNA to cytochrome b), of which we determined the sequences. We designed two additional external PCR primers on both ends of the determined coding region and amplified the region by long PCR. Our method provided the complete mitochondrial genomes of 51 samples, across which two types of gene orders were found from cytochrome b to 12S rRNA. Differences in these gene orders could be effective genetic markers for phylogeny. The samples were derived from 49 species included in 27 families and 12 orders. Of them, 46 species/subspecies are threatened in Japan. Our data will contribute to avian phylogeny and conservation biology.