DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the Indo- West Pacific oceans based on COI and 16S rRNA genes

Wu, Renxie; Zhang, Hao-Ran; Liu, Jing; Niu, Su‐Fang; Xiao, Yao; Chen, Yongxia

doi:10.1007/s00343-018-7214-6

Cited by 17 publications

(12 citation statements)

References 49 publications

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“…Sequencing target was the cytochrome c oxidase subunit I (COI) gene due to DNA barcoding based on a fragment of the COI gene in the mitochondrial genome is widely applied in species identification and biodiversity studies (Bingpeng et al, 2018). The COI gene is recommended as the standard barcoding marker for most animals (Renxie et al, 2018). Based on COI barcoding, high rates of species-level identification are well documented in many animal species, for instance, 95.27% for numerous northwestern pacific mollusks (Sun et al, 2016) and 98% for marine fishes (Ward, 2009).…”

Section: Molecular Analysismentioning

confidence: 99%

Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia

Olii

Sahami

Hamzah

et al. 2019

OnLine Journal of Biological Sciences

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Data of the species scientific name is required to study biodiversity and conservation of local fish species. Nike and hundala are the local names for fish found in Gorontalo whose scientific names are unknown and recognized by local people as two different species of fish. This study aims to identify the genetic and species of nike and hundala fish. Nike and hundala specimens were collected using a fish net from the estuary of Gorontalo Bay and Bone River, Gorontalo, Indonesia in April 2018. Molecular analysis of fish over sequencing methods shows that nike and hundala at Gorontalo waters are alleged as Sicyopterus longifilis.

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Section: Molecular Analysismentioning

confidence: 99%

Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia

Olii

Sahami

Hamzah

et al. 2019

OnLine Journal of Biological Sciences

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“…Additionally, mitochondrial DNA (mtDNA) markers can be used in biodiversity research for monitoring and for studying the molecular phylogeny [15,16,17]. In particular, mtDNA cytochrome c oxidase subunit 1 (CO1) and 16S ribosomal RNA (16S rRNA) genes are widely used in sh taxonomy and phylogenetics since these genes are extremely conserved and as they help identify and differentiate closely related species [9,13,18,19,20,21,22,23]. Therefore, genetic molecular marker-based species identi cation can be applied to accurately identify closely related sh species, in cases where traditional morphological classi cation methods lead to ambiguities.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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 rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the western Paci c Ocean, respectively. This is the rst study to report new records of the genera Bassozetus and Synaphobranchus from the western Paci c Ocean based on mitochondrial DNA markers.

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“…DNA barcoding based on the mitochondrial 16S rRNA gene is a good alternative method to identify the species of sh products when morphological characteristic identi cation is di cult to obtain [15][16].…”

Section: Introductionmentioning

confidence: 99%

Molecular Identification of Commercial Fish Maws using mtDNA 16S rRNA Nucleotide Sequences

Zhang¹,

Deng²,

Li³

et al. 2020

Preprint

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Background: Fish maws (dried swim bladders of fish) have long been used as a medicinal material and valuable tonic food which are very popular in Southeast Asia. It is difficult to identify the original species of fish maws sold on the market due to a lack of taxonomic characteristics. The present study aims to investigate the origin of commercial fish maws using DNA sequencing based on a partial sequence of the mtDNA 16S rRNA gene.Methods: Mitochondrial genomic DNA was extracted from a total of 44 individual fish maw samples collected from different markets by a QIAamp® DNA Mini Kit. The fragments of the 16S rRNA gene were amplified by PCR and bidirectionally sequenced using an ABI 3730 genetic analyser. Sequence assembly was performed with DNASTAR SeqMan software, and the resulting sequence was compared with reference sequences in GenBank using BLAST. Interspecific divergence and intraspecific variation were calculated by the Kimura 2-parameter model. Sample sequences were clustered in MEGA 6 using a neighbour-joining tree.Results: Forty-two of 44 fish maw samples were sequenced successfully. Fourteen taxa matched known fish species in the DNA sequence database, and 10 of them were supported by high homogeneity (99-100%). According to the results, 88% of the total samples belonged to family Sciaenidae. The clustering and genetic distance results, including in-group divergence and out-group divergence, indicated conﬁdence in species identiﬁcations. Moreover, there was no strict correspondence between the commercial names provided by traders and the origin of the fish maws. This study also found a probable correlation between the molecular characteristics and morphological features of fish maws from croakers and non-croakers.Conclusion: In this study, DNA sequencing based on mtDNA 16S rRNA was carried out successfully to identify the origin of ~95% of the samples. This result indicated that 16S rRNA is a suitable barcode for identifying fish maws. The identification results allowed us to learn more about the fish species available in the fish maw market in Guangdong-Hongkong-Macao Great Bay. In addition, the association between trade category and species found in this study provides both consumers and merchants with an important reference for identifying the origin of fish maws.

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DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the Indo- West Pacific oceans based on COI and 16S rRNA genes

Cited by 17 publications

References 49 publications

Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia

Molecular Approach to Identify Gobioid Fishes, “Nike” and “Hundala” (Local Name), from Gorontalo Waters, Indonesia

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

Molecular Identification of Commercial Fish Maws using mtDNA 16S rRNA Nucleotide Sequences

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