Identification of tuna species (Thunnini tribe) by PCR-RFLP analysis of mitochondrial DNA fragments

Xu, Kunhua; Feng, Jia; Ma, Xuting; Wang, Xiao; Zhou, Dan; Dai, Zhiyuan

doi:10.1080/09540105.2015.1086978

Cited by 16 publications

(10 citation statements)

References 33 publications

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“…Damasceno et al (2016) found high bootstrap values for Epinephelidae species tested using the COI marker, indicating that the COI gene is reliable for identifying these species. High bootstrap values were also reported by Xu et al (2016), where several tuna species were examined. As the 650-bp region for the COI barcode may be degraded in highly processed samples, methods such as multiplex PCR and mini-barcoding, which target a shorter fragment of this gene region, are effective in species authentication.…”

Section: Cytochrome C Oxidase I (Coi)mentioning

confidence: 55%

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Singh,

Young,

Hellberg

et al. 2024

Comp Rev Food Sci Food Safe

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Seafood is a prime target for fraudulent activities due to the complexity of its supply chain, high demand, and difficult discrimination among species once morphological characteristics are removed. Instances of seafood fraud are expected to increase due to growing demand. This manuscript reviews the application of DNA‐based methods for commercial fish authentication and identification from 2000 to 2023. It explores (1) the most common types of commercial fish used in assay development, (2) the type of method used, (3) the gene region most often targeted, (4) provides a case study of currently published assays or primer‐probe pairs used for DNA amplification, for specificity, and (5) makes recommendations for ensuring standardized assay‐based reporting for future studies. A total of 313 original assays for the detection and authentication of commercial fish species from 191 primary articles published over the last 23 years were examined. The most explored DNA‐based method was real‐time polymerase chain reaction (qPCR), followed by DNA sequencing. The most targeted gene regions were cytb (cytochrome b) and COI (cytochrome c oxidase 1). Tuna was the most targeted commercial fish species. A case study of published tuna assays (n = 19) targeting the cytb region found that most assays were not species‐specific through in silico testing. This was conducted by examining the primer mismatch for each assay using multiple sequence alignment. Therefore, there is need for more standardized DNA‐based assay reporting in the literature to ensure specificity, reproducibility, and reliability of results. Factors, such as cost, sensitivity, quality of the DNA, and species, should be considered when designing assays.

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Section: Cytochrome C Oxidase I (Coi)mentioning

confidence: 55%

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Singh,

Young,

Hellberg

et al. 2024

Comp Rev Food Sci Food Safe

View full text Add to dashboard Cite

show abstract

“…Being a crucial economic asset among marine fishery resources, tuna (Thunnini) stands out as the most prized and commercially valuable fish globally [1][2][3]. Likewise, the Western and Central Pacific Ocean (WCPO) boasts the world's largest tuna industry, with yearly catches surpassing 2 million metric tons (mt), constituting roughly half of the global tuna harvest [4].…”

Section: Introductionmentioning

confidence: 99%

Environmental Factors Determine Tuna Fishing Vessels’ Behavior in Tonga

Vaihola,

Kininmonth

2023

Fishes

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Comprehending the spatial distribution of human fishing endeavors holds significant importance in the context of monitoring fishery resources and implementing spatial management measures. To gain insights into the spatial arrangement of tuna longline activities within the exclusive economic zones of Tonga and their correlation with the marine environment, this study utilizes data from the Tonga Tuna Longline Fisheries spanning from 2002 to 2018. The data are employed to extract information about the spatial distribution of fishing efforts and coupled with 15 marine environmental variables covering both sea surface and subsurface conditions. This study employs boosted regression trees (BRT) and general additive models (GAM) to establish the non-linear relationships between the distribution of fishing effort and marine environmental factors. Furthermore, it examines and analyzes the ecological niche occupied by tuna longline vessels in high-sea environments. The outcomes of the factor analysis indicate that the most important factors influencing the fishing efforts of tuna longliners are the dissolved oxygen content at the sea surface and latitude. These two factors contribute significantly, accounting for 19.06% and 18.62% of the fishing efforts of vessels, respectively, followed by distance to ports, longitude, and dissolved oxygen at 100 m depth, contributing 10.77%, 7.07%, and 6.30%, respectively. The sea surface chlorophyll, ocean current at 100 m depth, and mixed layer depth contributed the least, 3.63%, 2.13%, and 1.72, respectively. In terms of space and time, tuna longliners are more likely to operate in the 18–22° S latitudinal and 172–178° W longitudinal region, and fishing efforts increased in the months from March to August. The spatial distribution of the fishing efforts modeled for fishing vessels in 2018 is predicted to have good spatial distribution with the actual fishing efforts of these vessels. This research aids in comprehending the environmental impacts resulting from shifts in the spatial distribution of tuna longline vessels, offering valuable insights for the effective management of tuna longline fisheries in Tonga.

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“…In addition, mitochondria remain after processing, which avoids DNA loss, and since mitochondrial DNA is more abundant than nuclear DNA, it is easier to detect [20,21]. Real-time polymerase chain reaction (PCR) [4,5,[22][23][24], multiple PCR [19,21,25,26], loop-mediated isothermal amplification (LAMP) [6], PCR restriction fragment length polymorphism (PCR-RFLP) [7,27], and others have been reported as viable DNA-based PCR techniques for tuna species identification. Real-time PCR assays require an expensive machine and have the disadvantage that it must be done by skilled experimenters.…”

Section: Introductionmentioning

confidence: 99%

Multiplex PCR Assay for Simultaneous Identification of Five Types of Tuna (Katsuwonus pelamis, Thunnus alalonga, T. albacares, T. obesus and T. thynnus)

Lee

Suh

Lee

et al. 2022

Foods

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There is a need to identify the species of similar types of fish, especially those that are commercially sold. Particularly, the price of tuna varies depending on its type, which is difficult to determine as they are sold in cut or processed forms. This study developed a multiplex polymerase chain reaction (PCR) assay to identify the five most common tuna species: bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas. Newly designed species-specific primer sets for these five tuna species were created. Subsequently, the amplicon sizes obtained were 270, 238, 200, 178, and 127 base pairs for bigeye, skipjack, Atlantic bluefin, albacore, and yellowfin tunas, respectively. Each primer’s specificity was further tested using 15 other fish species, and no cross-reactivity was observed. To identify multiple targets in a single reaction, multiplex PCR was optimized to increase its resolution and accuracy. The detection levels of the multiplex PCR assay were confirmed to be 1 pg for all the five tunas. Additionally, it was successfully applied to 32 types of commercial tuna products. Therefore, this multiplex PCR assay could be an efficient identification method for various tuna species.

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Identification of tuna species (Thunnini tribe) by PCR-RFLP analysis of mitochondrial DNA fragments

Cited by 16 publications

References 33 publications

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Twenty‐three years of PCR‐based seafood authentication assay development: What have we learned?

Environmental Factors Determine Tuna Fishing Vessels’ Behavior in Tonga

Multiplex PCR Assay for Simultaneous Identification of Five Types of Tuna (Katsuwonus pelamis, Thunnus alalonga, T. albacares, T. obesus and T. thynnus)

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