• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• Animal Systematics, Evolution and Diversity
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• 제30권2호
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• pp.124-131
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• 2014

The Korean nudibranch faunal study has been conducted since 2011 and five species including Dermatobranchus otome Baba, 1992, Mexichromis festiva (Angas, 1864), Noumea nivalis Baba, 1937, Hoplodoris armata (Baba, 1993), and Okenia hiroi (Baba, 1938) were newly reported with re-descriptions and figures. Also, Noumea purpurea Baba, 1949 was re-described with illustrations because previous records for this species were given without a description. Two congeneric species in the genus Noumea could be distinguished by ground color, dorsal markings, color of the mantle edge and gills, and mantle and dorsal marking. In addition, mitochondrial cytochrome c oxidase subunit I (COI) sequences of five species were provided for further molecular identification study. Consequently, a total of 43 species have been reported for the Korean nudibranch fauna.