New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Kim, Hanjun; Han, Jeonghoon; Kim, Byung‐Jik; Lee, Kyun-Woo; Hyeong, Kiseong; Choi, Young-Ung

doi:10.1007/s11033-021-06559-8

Mol Biol Rep

2021

DOI: 10.1007/s11033-021-06559-8

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New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Hanjun Kim

Jeonghoon Han

Byung‐Jik Kim

et al.

Abstract: Two deep-sea eels collected from the western Paci c Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae. To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal RNA (16S rRNA)). Through molecular phylogenetic analysis based on mtDNA CO1 and 16S rRN… Show more

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Cited by 4 publications

References 28 publications

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Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Arisuryanti,

Hutasuhut,

Koentjana

et al. 2023

Genetika

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Rockskipper belongs to the species-rich family of Blenniidae (Combtooth blenny) and is known for its cryptic and species complexes presence. Identifying cryptic species based solely on morphological features is challenging due to their similar morphological characteristics. As a result, molecular genetic techniques based on two partial mtDNA genes, COI and 16S rRNA, were employed to identify fish accurately. This study aimed to evaluate the effectiveness of COI and 16S rRNA gene for the identification of Rockskipper fish and investigate the genetic relationship between species of Rockskipper from Porok Beach. The result revealed that the thirteen Rockskipper samples from Porok Beach that belong to six species (E. vermiculatus, E. striatus, I. lineatus, I. dussumieri, I. edentulus, and B. caudolineata) with more than 99% similarity. In contrast, the 16S analysis identified five species. A Bayesian phylogenetic tree demonstrated that six species of Rockskipper from Porok Beach are genetically distinct and separated into two clusters. We also found that two samples (RS-9 and RS-10) form a monophyletic group with B. caudolineata with maximum bootstrap (NJ and ML: 100%) and posterior probability (1.00). We hypothesized that B. caudolineata is a species complex with at least two lineages: one was genetically closer to RS-8, and another was more closely related to RS-9 and RS-10. Both the COI and 16S rRNA genes were found to be capable of delineating species and revealing genetic variation among Rockskipper samples in this study. However, our findings demonstrated that the COI gene is a more accurate and reliable marker for identifying Rockskipper species from Porok Beach, Gunungkidul, Yogyakarta, Indonesia.

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Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Arisuryanti,

Hutasuhut,

Koentjana

et al. 2023

Genetika

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New Record of the Grey Cutthroat, Synaphobranchus affinis (Anguilliformes: Synaphobranchidae) from the East Mariana Basin, Western Pacific Ocean

Han

Kim

et al. 2022

JMSE

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Two deep-sea eels collected from the East Mariana Basin in the western Pacific Ocean are described in this study. Based on their morphological features, two eel specimens were assumed to belong to the Gray cutthroat eel family, Synaphobranchidae. Mitochondrial DNA (mtDNA) genes have been widely used as genetic markers to identify fish species. To accurately identify the species of the two eel specimens, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes from the two eel specimens. The sequences from the specimens were 100% identical. The molecular phylogenetic tree confirmed that the two eel specimens were closely related to Synaphobranchus affinis with a bootstrap value of 100%. This is the first study to report new records of S. affinis from the East Mariana Basin in the western Pacific Ocean.

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Complete Mitochondrial DNA Genomes of Deep-Sea Eels Synaphobranchus brevidorsalis and S. affinis and New Record of S. brevidorsalis from the East Mariana Basin

Han

Kim

Lee

et al. 2023

JMSE

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In this study, we document the first recorded range extension of the genus Synaphobranchus from the East Mariana Basin in the Western Pacific Ocean. We sequenced the complete mitochondrial (mt) genome of two deep-sea eels (Synaphobranchus brevidorsalis and S. affinis) collected in the East Mariana Basin in the Western Pacific Ocean. The complete mt genomes of S. brevidorsalis and S. affinis were 16,686 bp and 16,677 bp in length, respectively, and consisted of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Molecular phylogenetic analysis of the two deep-sea eel species was performed, based on the mt cytochrome c oxidase subunit I (COI) gene using the maximum likelihood method. The molecular phylogenetic tree demonstrated that S. brevidorsalis and S. affinis were congeneric species of S. brevidorsalis and S. affinis reported in previous studies with bootstrap values of 100% and 100%, respectively. This is the first report on the complete mt genomes of S. brevidorsalis and S. affinis collected in the East Mariana Basin in the Western Pacific Ocean. Overall, our study highlights the potential of molecular approaches in identifying species diversity and distribution in the Western Pacific Ocean.

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New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Cited by 4 publications

References 28 publications

Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

Molecular species identification of Rockskipper (Pisces: Blenniidae) from Porok Beach (Yogyakarta, Indonesia) based on 16S rRNA and COI genes

New Record of the Grey Cutthroat, Synaphobranchus affinis (Anguilliformes: Synaphobranchidae) from the East Mariana Basin, Western Pacific Ocean

Complete Mitochondrial DNA Genomes of Deep-Sea Eels Synaphobranchus brevidorsalis and S. affinis and New Record of S. brevidorsalis from the East Mariana Basin

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