Molecular identification of three<i>Ompok</i>species using mitochondrial<i>COI</i>gene

Malakar, Abhishek K.; Lakra, W. S.; Goswami, Mukunda; Singh, Mahender; Mishra, Rahasya Mani

doi:10.3109/19401736.2011.643876

Cited by 12 publications

(12 citation statements)

References 25 publications

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“…The concept of DNA barcoding has been empirically supported and used in various studies on different phyla (Hebert et al, 2003;Hebert et al, 2004aHebert et al, , 2004bHogg & Hebert, 2004;Moritz & Cicero, 2004), leading to the development of a standard screening of species diversity that allows taxonomists to accelerate the identification process of fishes (Keskin & Atar, 2013;Lakra et al, 2011;Landi et al, 2014;Ward et al, 2005). Furthermore, since proper identification is crucial for management and trade, this DNAbased barcode provides a simple universal tool for the identification of fish species and products (Lakra et al, 2011;Malakar et al, 2012;Smith et al, 2008). DNA barcoding not only applies for fish species identification, but also for fish product examination (fillets, fins, fragments, canned fish, dried fish, mixtures), conservation of threatened and endangered species, identification of fish eggs and larvae, identification of prey items in stomach contents (Soininen et al, 2009), identification of new species, population structure assessment, phylogenetics and biodiversity assessment.…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

Rabaoui

Yacoubi

Sanna

et al. 2019

Journal of Fish Biology

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We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes– Bayesian PTP (PTP–bPTP) and nucleotide‐divergence‐threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour‐joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.

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Section: Introductionmentioning

confidence: 99%

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

Rabaoui

Yacoubi

Sanna

et al. 2019

Journal of Fish Biology

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“…The current study showed that the partial COI gene sequence of fin clips and muscle tissue can be used as a diagnostic molecular marker for identification and resolution of taxonomic ambiguity of Ompok species [38]. Other study showed that the genes of cytochrome oxidase…”

Section: Introduction *mentioning

confidence: 65%

Molecular Identification and Genetic Characteristics of Genus Mystacoleucus Based on Gene Cytochrome Oxidase C Subunit I (COI) in Sengguruh Dam

Valen

Widodo

Kilawati

2019

JELS

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In general, the process of naming several species of fish including species from the genus Mystacoleucus is still carried out based on morphological characters, which are often found in almost the same morphological characters in different fish species. Therefore, it is necessary to apply a more accurate identification method, which is a DNA-based identification method called DNA barcoding. The purpose of this study was to identify the species of the genus Mystacoleucus on the Sengguruh Dam molecularly based on the Cytochrome Oxidase C Subunit I (COI) gene. A caudal fin was taken on the test fish and preserved in 95% ethanol solution for molecular identification. The results of the identification showed that the sample belonged to the Mystacoleucus marginatus species with Identity values between 99-100% and E-value 0.0. The data obtained showed that from the calculation of genetic distance presented in the form of data matrix and phylogenetic tree reconstruction, there were 2 species that had a far genetic distance from the M. marginatus sample from the Sengguruh Dam namely M. atridorsalis with the furthest genetic distance of 0.1932-0.2595 and M. lepturus with genetic distance between 0.1117-0.1193. However, there is one species that has the closest distance, M. padangensis with genetic distance between 0.0019-0.0038 and identity values up to 99%.

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“…There were between 1 and 12 variable nucleotide sites among the haplotypes, 6 of which differed by transitional substitutions, 3 by transversional changes and 3 insertion/deletions (Table 2). Transitional changes are commonly found in animal mitochondrial genomes compared to tranversional changes (Malakar et al, 2009;Fišer Pečnikar & Buzan, 2013). In addition, 9 variable sites with 2 parsimony informative sites were detected.…”

Section: Resultsmentioning

confidence: 99%

Detection of 16S Mitochondrial Gene Polymorphism on Barb Fish (Barbodes binotatus Valenciennes, 1842) from Lake Lebo Taliwang, West Nusa Tenggara

Arisuryanti

Alfianti

Firdaus

et al. 2020

JFS

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The spotted barb fish (Barbodes binotatus), a tropical cyprinid fish, is one of the abundant fishes in Lake Lebo Taliwang commonly consumed due to high nutrition and utilized as an aquarium trade due to their exotic colour. However, no genetic information related to the intra-population genetic variation of the fish species in Lake Lebo Taliwang. Genetic information of the spotted barb fish can play an important role for the fish conservation. Therefore, the objective of this study was to detect 16S mitochondrial gene polymorphism of the spotted barb fish which can be used to detect their genetic variation. The method used in this study was a PCR method with primers 16Sar and 16Sbr. The data was then analysed using MESQUITE, MEGA, DnaSP and PopART to identify 16S mitochondrial gene polymorphism. This study obtained 610 base pairs after alignment of 16S sequences of all samples. Five haplotypes were detected with 9 variable sites and 2 parsimony informative sites. Haplotype diversity and nucleotide diversity of the spotted barb fish were 1.00 and 0.0066 respectively. In addition, genetic distance among the samples was 0.66. This finding exhibited polymorphism on 16S gene sequence among the fish samples and this data indicated genetic variation of the spotted barb from Lake Lebo Taliwang.

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Molecular identification of threeOmpokspecies using mitochondrialCOIgene

Cited by 12 publications

References 25 publications

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

Molecular Identification and Genetic Characteristics of Genus Mystacoleucus Based on Gene Cytochrome Oxidase C Subunit I (COI) in Sengguruh Dam

Detection of 16S Mitochondrial Gene Polymorphism on Barb Fish (Barbodes binotatus Valenciennes, 1842) from Lake Lebo Taliwang, West Nusa Tenggara

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