Advancing DNA Barcoding to Elucidate Elasmobranch Biodiversity in Malaysian Waters (original) (raw)
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Mitochondrial DNA, 2013
Identification of elasmobranchs by conventional taxonomy is difficult due to similarities in morphological characters. Species-specific molecular markers are good choice for identifying species irrespective of it's life stage. Recently, mitochondrial cytochrome c oxidase subunit I (COI) gene got global recognition as a barcode gene to discriminate all animals up-to species level. In this study, mitochondrial COI partial gene was used to develop DNA barcodes for 18 species of elasmobranchs (10 species of sharks and 8 species of rays). The COI barcodes clearly distinguished all the species with high interspecific distance values than intraspecific values. The average interspecific and intraspecific distance values are 8.6% and 0.3% for sharks, respectively and 12.4% and 0.63% for rays, respectively using K2P method. The Neighbor-Joining tree showed distinct clusters shared by the species of same genera. The COI barcodes were also used to estimate allopatric divergences for selected species across broad geographical locations and found that Sphyrna lewini, Aetobatus narinari and Neotrygon kuhlii have cryptic diversity.
Sharks are one of main fisheries commodity that are currently exploited on a large scale because of their high economic value. The identification of sharks has been a difficult one due to the specimen’s similarity in morphology and mostly have had key diagnostic features removed. This study aimed to identify and to review the status of sharks, and also to reconstruct the shark species that were landed at South Java fishing port using molecular approaches. The DNA amplification was using cytochrome oxidase I mitochondrial of locus and 600-700 basepairs. A total of seven species from 59 individuals was identified including Alopias pelagicus, Carcharhinus falciformis, C. sorrah, C. amblyrhynchos, Galeocardo Cuvier, Atelomycterus marmoratus, and Spyrna lewini. The diversity of shark species landed in Muncar during the last 2 years has been decreased. The identified sharks species in this study sites were about 18% of all Indonesian sharks. The result of this study is expected help the Government to manage shark fisheries in Indonesia.
DNA barcoding Indian marine fishes
Molecular Ecology Resources, 2011
DNA barcoding has been adopted as a global bio-identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids representing 79 Genera and 37 Families from the Indian Ocean have been barcoded for the first time using cytochrome c oxidase I gene (COI) of the mtDNA. The species were represented by multiple specimens and a total of 397 sequences were generated. After amplification and sequencing of 707 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two parameter (K2P) distances within species, genera, families, orders were 0.30%, 6.60%, 9.91%, 16.00%, respectively. In addition to barcode-based species identification system, phylogenetic relationships among the species have also been attempted. The neighbour-joining tree revealed distinct clusters in concurrence with the taxonomic status of the species.
Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes
2020
This study attempted to molecular characterization of marine and coastal fishes of Bangladesh based on mitochondrial cytochrome c oxidase subunit I (COI) gene as a marker. A total of 376 mitochondrial COI barcode sequences were obtained from 185 species belonging to 146 genera, 74 families, 20 orders and two classes of fishes. The mean length of the sequences was 652 base pairs. For all the samples, %G was significantly lower compared to the other nucleotides and %GC was significantly lower compared to %AT (p < 0.005). Also, a significantly lowered %GC content was observed in second and third codon position compared to the first codon position in all the samples (1st>2nd>3rd, p-value < 0.005). In Elasmobranchii (Sharks and rays) the average Kimura two parameter (K2P) distances within species, genera, families and orders were 1.2%, 6.07%, 11.08% and 14.68%, respectively and for Actinopterygii, the average K2P distances within species, genera, families and orders were 0.40%, 6.36%, 14.10% and 24.07%, respectively. The mean interspecies distance was 16-fold higher than the mean intraspecies distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species in accordance with their taxonomic position. A total of 21 species were newly recorded in Bangladesh. High efficiency and fidelity in species identification and discrimination were demonstrated in the present study by DNA barcoding, and we concluded that COI sequencing can be used as an authentic identification marker for Bangladesh marine fish species.
Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens
Scientific Data
Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued ...
DNA barcoding analysis of larval fishes in Peninsular Malaysia
Journal of Environmental Biology, 2020
To identify fish larvae to species level by DNA barcoding method using the mitochondrial Cytochrome c Oxidase I (COI) gene. The lack of species identification work on fish larvae in Peninsular Malaysia has warrant this study to be conducted. Identification of fish larvae species from mangrove areas of Pendas Johor, Matang Perak, Pekan Pahang and Setiu Terengganu was conducted. Samples were collected from April 2015 to September 2015 using a bongo net, towed at a depth of about 0.5 m from the surface for 5 min against the tidal flow. From the total of 354 fish larvae collected, a representative of 177 fish larvae was selected and sequenced using COI gene. Results from BLAST and BOLDSYSTEM search showed all sequences had high percentage identity index and similarity (90% to 100%). Fish larvae were identified through phylogenetics analysis showing monophyletic status between query sequences with reference sequences obtained from own collection and GenBank. The Sillago vittata and Sillago sihama sequences was found to be in separate clusters despite their similar genus. A few strong match of specimens from different genus was found with high bootstrap value (n>90%) through Neighbour-Joining (NJ) and Maximumlikelihood (ML) analysis e.g the Paramugil parmatus with Liza melinoptera (NJ =100%, ML = 99%) and Pseudogobius oligactis with Eugnathogobius oligactis (NJ = 92%, ML 94%). Identification of fish larvae were best conducted with the aid of molecular method, DNA barcoding in particular rather than comparative taxonomical studies alone that able to identify fish larvae sample to genus level at best. DNA barcoding, Fish larvae, Mangroves, Peninsular Malaysia, Phylogenetic Cytochrome c Oxidase I (COI) gene, DNA barcoding analysis of larval fishes in Peninsular Malaysia
DNA barcoding Indian marine fishes: DNA BARCODING
Molecular Ecology Resources, 2010
DNA barcoding has been adopted as a global bio-identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids representing 79 Genera and 37 Families from the Indian Ocean have been barcoded for the first time using cytochrome c oxidase I gene (COI) of the mtDNA. The species were represented by multiple specimens and a total of 397 sequences were generated. After amplification and sequencing of 707 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two parameter (K2P) distances within species, genera, families, orders were 0.30%, 6.60%, 9.91%, 16.00%, respectively. In addition to barcode-based species identification system, phylogenetic relationships among the species have also been attempted. The neighbour-joining tree revealed distinct clusters in concurrence with the taxonomic status of the species.
Molecular diversity of freshwater fishes of Bangladesh assessed by DNA barcoding
Bangladesh Journal of Zoology, 2020
This study represents the comprehensive molecular identification of freshwater fishes of Bangladesh based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome. A total of 315 mitochondrial COI barcode sequences were obtained from 153 species,114 genera, 49 families and 16 orders of fishes. The mean length of the sequences was 652 base pairs. For all the samples, %G was significantly lower compared to the other nucleotides and %GC was lower compared to %AT (p-value ˂ 0.05). Also, a significantly lower %GC content was observed in second and third codon position compared to the first one in all the samples (1st>2nd>3rd, p-value˂ 0.05). The average K2P distances within species, genera, families and orders were 0.38%, 7.02%, 12.75% and 18.68%, respectively. The mean interspecific distance was 18-fold higher than the mean intraspecific distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species according to t...
DNA barcoding of threatened fishes of Bangladesh
2021
The ichthyofaunal diversity of Bangladesh is declining dramatically due to various anthropogenic factors. For authentic identification at species level, approximately 655 bp of the mitochondrial cytochrome c oxidase subunit I (COI) gene of 29 threatened fish species were amplified and a barcode dataset was generated. Among these species, 7% were categorized as Critically Endangered (CR), whereas 55% and 38% were categorized as Endangered (EN) and Vulnerable (VU), respectively. K2P genetic distances were evaluated and found to be increasing with higher taxonomic rank—1.01% to 13.09% within species and 17.42% to 41.57% between species with a DNA barcode gap of 4.33%. The average %GC content of the fish species was 44.7 ± 0.49. On the other hand, the %GC values for the 6 orders—Cypriniformes, Siluriformes, Synbranchiformes, Syngnathiformes, Perciformes and Osteoglossiformes were 44.8 ± 0.81, 45.6 ± 0.61, 44.8 ± 0.85, 47 ± 0.99, 46.3 ± 0.89, 47 ± 0.90, respectively. The %GC content was ...
DNA barcoding of nomei fish ( Synodontidae : Harpadon sp . ) in Tarakan Island , Indonesia
2017
Nomei or “lembe-lembe”, a local name for fishes of the family Synodontidae, is an economically important fish in the city. The lack of detailed and precise reports of this fish has caused extinction status of nomei species in its distribution range in Tarakan. These were sequenced for the 618-bp region of the mitochondrial cytochrome c oxidase sub unit I gene (COI). The aim of this research was to evaluate the genetic variation and phylogenetic comparison among nomei fish in Tarakan Island, Indonesia. The results of alignment showed 12 substitutions of nucleotides bases, which consisted of 12 transitions with no transversions, insertions and deletions. The phylogenetic tree resulting Neighbour Joining (NJ), Maximum Parsimony (MP) analysis and network analysis showed that Nomei fish from Amal and Juata samples were clustered in one group. Divergent sequence of nomei fish from Amal and Juata (average 0.354±0.008) in comparison of Harpadon nehereus. This novel of Nomei barcode will hel...