Caution and Curation for Complete Mitochondrial Genome from Next-Generation Sequencing: A Case Study from Dermatobranchus otome (Gastropoda, Nudibranchia)

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.