DNA barcoding of coastal ray-finned fishes in Vietnam

Huang, Wen‐Chien; Chou, Tak-Kei; Nguyen, Van Q.; Chien, Pham Van; Fan, Li; Shao, Kwang‐Tsao; Liao, Te‐Yu

doi:10.1371/journal.pone.0222631

Cited by 52 publications

(46 citation statements)

References 47 publications

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“…DNA barcoding has been successfully identified marine ichthyofauna and provided the wealth of DNA barcode information in many places, such as Australia (Ward et al, 2005), Canada (Hubert et al, 2008;Steinke et al, 2009), India (Lakra et al, 2011), China (Wang et al, 2018;Zhang, 2011;Zhang & Hanner, 2012), Portugal (Costa et al, 2012), Germany (Knebelsberger et al, 2014), Taiwan (Bingpeng et al, 2018;Chang et al, 2017), Vietnam (Thu et al, 2019), and Indonesia (Limmon et al, 2020).…”

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confidence: 99%

Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes

Ahmed

Datta

Saha

et al. 2021

Ecology and Evolution

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Bangladesh has vast coastal and marine resources along its south edge as the Bay of Bengal is situated in the south of Bangladesh.There are a total of 166,000 square km water areas including the Exclusive Economic Zone (EEZ) which is larger than the country's total land area of 147,500 square km. The country is rich not only in terms of its vast water areas but also in terms of biological diversity.The marine fisheries sector plays an important role in the economy of Bangladesh in terms of nutrition, income, employment, and foreign exchange earnings (DoF, 2018). Fish provides about 60% of animal protein in the daily dietary requirement of 160 million people of the country. Marine fisheries alone contribute 654,687 metric tons which is 15.31% of the country's total fish production (DoF, 2018).Nonetheless, description and information of marine fishes of Bangladesh are scattered throughout a wide range of scientific

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mentioning

confidence: 99%

Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes

Ahmed

Datta

Saha

et al. 2021

Ecology and Evolution

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“…COI gene has the characteristics of high evolution rate, obvious interspecific variation, relatively conservative within species, good universality of primers and easy amplification [17]. Therefore, COI gene has been widespread employed as an effective DNA barcode for species classification of varied animal lineages, including bird [18,19], Mosquito [20,21], marine fish [22][23][24], freshwater fish [25][26][27]. DNA barcode based on COI gene can be used to identify marine fish up to 98%, while freshwater fish can be identified with 93% accuracy [28].…”

Section: Genomic Approach Is a New Taxonomic Technique Combining Molementioning

confidence: 99%

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 15, 2021. ; https://doi.org/10.1101/2021.02.15.431244 doi: bioRxiv preprint fundamental premise of fishery biodiversity and fishery resources management, and also an important part of marine biodiversity. As a traditional classification method, morphological identification has successfully described nearly one million species on the earth, which has laid a good foundation for species classification and identification [3,4]. However, routine species classification poses a challenge for fish classification owing to four limitations.…”

Section: Introductionmentioning

confidence: 99%

A deep learning model for fish classification base on DNA barcode

J²,

Yuan

et al. 2021

Preprint

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Fish is one of the most extensive distributed organisms in the world, fish taxonomy is an important part of biodiversity and is also the basis of fishery resources management. However, the morphological characters are so subtle to identify and intact specimens are not available sometimes, making the research and application of morphological method laborious and time-consuming. DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is a valuable molecular tool for species identification and biodiversity studies. In this paper, a novel deep learning classification approach that fuses Elastic Net-Stacked Autoencoder (EN-SAE) with Kernel Density Estimation (KDE), named ESK-model, is proposed bases on DNA barcode. In stage one, ESK-model preprocesses the original data from COI fragments. In stage two, EN-SAE is used to learn the deep features and obtain the outgroup score of each fish. In stage three, KDE is used to select the threshold base on the outgroup scores and classify fish from different families. The effectiveness and superiority of ESK-model have been validated by experiment on three dominant fish families and comparisons with state-of-the-art methods. Those findings confirm that the ESK-model can accurately classify fish from different family base on DNA barcode.

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“…DNA barcoding telah terbukti berhasil mengidentifikasi berbagai individu hingga tingkat spesies (Dahruddin et al, 2016;Thu et al, 2019). Penelitian dari Madduppa et al (2017), misalnya telah mengidentifikasi 7 teripang di Kepulauan Seribu, Madduppa et al (2016) berhasil mengidentifikasi 5 ikan pari yang didapatkan dari Pelabuhanratu, Lampung dan Muara Saban, dan mendapatkan catatan baru munculnya spesies kakap (Lutjanus ophuysenii) di Korea.…”

Section: Terdapat Setidaknya 6 Spesies Dari Familiunclassified

IDENTIFIKASI IKAN LIDAH Cynoglossus arel (Bloch & Schneider, 1801) BERDASARKAN MORFOMETRIK DAN DNA BARCODING YANG DIPERDAGANGKAN DI TEMPAT PELELANGAN IKAN MUARA ANGKE

Alina¹,

Madduppa

2020

BAWAL Widya Riset Perikanan Tangkap

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Ikan lidah merupakan ikan ekonomis penting yang menjadi salah satu komoditas yang diperdagangkan di Tempat Pelelangan Ikan (TPI) Muara Angke. Ikan lidah memiliki keunikan karena metamorfosis mereka, kebiasaan membenamkan diri dalam substrat dan sirip pektoralnya yang terdegradasi sedangkan sirip lainnya saling bertemu. Terdapat enam spesies ikan lidah dari famili Cynoglossidae yang dapat ditemukan di Indonesia, sedangkan penelitian terkait identifikasi ikan lidah masih terbatas. Penelitian ini bertujuan untuk mengidentifikasi dan memastikan spesies ikan lidah yang diperdagangkan di TPI Muara Angke berdasarkan pengukuran morfometrik dan DNA Barcoding menggunakan sekuen COI. Hasil analisis morfologi menggunakan literatur menunjukkan bahwa ikan lidah sampel memiliki kemiripan karakteristik morfologi dengan Cynoglossus lingua dan Cynoglossus arel yang kemudian diyakini sebagai C. arel berdasarkan ciri diagnostiknya. Berdasarkan analisis DNA barcoding diperoleh spesies Cynoglossus cf. arel dengan identifikasi kesamaan 100% yang tercantum dalam GenBank. Dari hasil analisis morfologi dan DNA barcoding menunjukkan bahwa ikan lidah yang diperdagangkan di TPI Muara Angke merupakan ikan dari famili Cynoglossidae, genus Cynoglossus, spesies Cynoglossus arel.Tongue Fish Identification Traded in Muara Angke Fish Auction Based on Morphometric and DNA Barcoding Using COI Sequences. Tongue fish is an important economical fish which is one of the commodities traded at Muara Angke Fish Auction. Tongue fish are unique because of their metamorphosis, their habit of immersing themselves in the substrate, and their pectoral fins degraded while the other three fins are confluent. There are six species of tongue fish from the Cynoglossidae family that can be found in Indonesia, whereas the study about tongue fish identifications are limited. The present study aims to identify and clarify the species of tongue fish traded at Muara Angke Fish Auction based on morphometric measurements and DNA Barcoding using the COI sequence. The results of the morphological analysis using the literature showed that the tongue fish samples had similar morphological characteristics with Cynoglossus lingua and Cynoglossus arel which were then believed to be C. arel based on their diagnostic characteristics. DNA barcoding analysis of tongue fish sample shows Cynoglossus cf. arel with 100% similarity identification listed in GenBank. From the results of morphological analysis and DNA barcoding showed that the tongue fish traded at TPI Muara Angke are fish from the family Cynoglossidae, genus Cynoglossus, species of Cynoglossus arel.

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DNA barcoding of coastal ray-finned fishes in Vietnam

Cited by 52 publications

References 47 publications

Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes

Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes

A deep learning model for fish classification base on DNA barcode

IDENTIFIKASI IKAN LIDAH Cynoglossus arel (Bloch & Schneider, 1801) BERDASARKAN MORFOMETRIK DAN DNA BARCODING YANG DIPERDAGANGKAN DI TEMPAT PELELANGAN IKAN MUARA ANGKE

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