Development of fish diversity studies by next-generation mitogenome sequencing: From Sanger method to massively parallel method

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Whole mitochondrial genome (mitogenome) sequences are extremely useful for resolving phylogenies of animals including fishes. This study aims to establish efficient procedures to obtain mitogenome data from many samples including degraded ones by using "next-generation" massively parallel sequencing technologies. For samples in good condition, long-PCR amplification/purification and parallel tagged sequencing successfully provided mitogenome data from many samples simultaneously, suggesting that this is a rather easier method for such samples. For degraded samples, many segments from mitogenome were successfully captured by using the capture-on-beads method with double indexing. Thus, we conclude that efficient procedures have been established to have large mitogenome data from many samples including degraded ones by using next-generation sequencing technologies.