DNA barcoding of fish species reveals low rate of package mislabeling in Qatar

Chen, Kuei-Chiu; Zakaria, Dalia; Altarawneh, Heba N.; Andrews, Gabriala; Ganesan, Gowrii Saswathy; John, Karen Maria; Khan, Sarah; Ladumor, Heta

doi:10.1139/gen-2018-0101

Cited by 13 publications

(5 citation statements)

References 23 publications

(28 reference statements)

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“…The mitochondrial DNA (mtDNA) sequence has compact gene arrangement, short coalescence time, rapid evolutionary rate, and maternal inheritance, allowing scientists to use them for phylogenetic analyses, population genetics, and taxonomic studies [ 2 ]. Currently, mtDNA sequences (both partial and complete) are used extensively as molecular markers for species identification [ 3 , 4 , 5 , 6 , 7 , 8 ]. However, incomplete mitochondrial gene sequences have limited the ability to identify complex genetic evolutionary relationships in many fish lineages [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Li¹,

et al. 2020

IJMS

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Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

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Section: Introductionmentioning

confidence: 99%

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Li¹,

et al. 2020

IJMS

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“…DNA barcoding is simple, accurate, and fast, and is therefore the most effective method for species identification 19 , 20 . Sequences with high success rates of amplification and sequencing, high variability among species but low nucleotide variation within species (less than 2%) are considered to be excellent DNA markers 21 .…”

Section: Discussionmentioning

confidence: 99%

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae)

Mao¹,

Zou²,

Sun

et al. 2023

Sci Rep

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Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species’ chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.

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“…Identifikasi dengan DNA Barcoding dapat dilakukan dalam mengidentifikasi spesies dengan tingkat akurasi yang tinggi, dan dapat menjawab tantangan dalam identifikasi secara cepat dan akurat, tetapi hal tersebut juga bergantung pada database yang baik dan lengkap (Bingpeng et al, 2018;. DNA Barcoding digunakan dalam mengungkap kesalahan pelabelan jenis ikan pada beberapa supermarket di Qatar (Chen et al, 2019), hal yang sama juga terjadi di Vietnam (Ha et al, 2018). Identifikasi melalui DNA Barcoding makanan laut juga dilakukan di Brasil Selatan (Carvalho et al, 2015).…”

Section: Pendahuluanunclassified

Identifikasi dan Analisis Filogenetik Ikan Ekonomis Penting Oreochromis sp. dengan Pendekatan DNA Barcoding

Sianturi

Dailami²,

Saleky³

2021

B : JIB

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Species identification is one of the most basic and important factors in fisheries management. Oreochromis sp., such as tilapia (Oreochromis mosambicus) and tilapia (Oreochromis niloticus) are introduced species of fish originating from outside Merauke which are now the dominant fish and are commonly found in inland waters of Merauke. The purpose of this study was to identify the economically important fish species Oreochromis sp. which landed at Merauke Traditional Market with DNA Barcoding approach. DNA amplification with the COI gene resulted in a DNA sequence length of 655 bp with the identification result being Tilapia (Oreochromis niloticus). Based on the phylogenetic tree data and genetic distance, the DNA sequences of the samples formed the same clade as the Oreochromis niloticus sequences from GeneBank with 0% genetic distance and it was estimated that these species came from the same parents. Identification with DNA Barcoding makes it easy to identify species quickly and accurately.

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DNA barcoding of fish species reveals low rate of package mislabeling in Qatar

Cited by 13 publications

References 23 publications

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae)

Identifikasi dan Analisis Filogenetik Ikan Ekonomis Penting Oreochromis sp. dengan Pendekatan DNA Barcoding

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