Mitochondrial DNA-based species testing of confiscated aquatic wildlife in the Philippines

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 at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.

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“… 11 , 12 ), detect illegally traded wildlife (e.g. 13 ), and confirm the identity of animals sold in markets (e.g. 14 ).…”

Section: Background and Summarymentioning

confidence: 99%

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens

et al. 2023

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“…Gene COI HCO 2198 and LCO 1490 was amplified employing two primers: Forward 5 TAAACTTCAGGGT GACCAAAAAATCA 3 and Reverse 5 GGTCAAATCATA AAGA TATTGG 3 referred to Poniente et al (2022). The amplification conditions were as follows initial denaturation (95C for 5 mins), denaturation (95C for 45 sec with 35 cycles), annealing (60C for 45 sec), extension (72C for 60 sec) and final extension (72C for 5 mins).…”

Section: Pcr Amplificationmentioning

confidence: 99%

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

Utami¹,

Jamil²,

Nidom³

et al. 2023

IJAR

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Background: The genetic diversity information of local cattle and crossbred in South Sulawesi, Indonesia is essential for the establishment of conservation and breeding strategies. This research targeted to evaluate the phylogenetic relationship and genetic diversity of local and crossbred (CB) cattle. Methods: The present research organized at the Animal Laboratory, Professor Nidom Foundation, Surabaya, Indonesia from February to October 2021. The genome was isolated from 20 whole blood samples from seven purebreed belongs to Singosari National Artificial Insemination Center Malang, Indonesia, four crossbred in Gowa and nine crossbred in Sidrap, South Sulawesi, Indonesia. Partial sequences of mtDNA cytochrome oxidase subunit I (COI) gene were amplified employing the polymerase chain reaction technique. Result: This study revealed that a lot of single nucleotide polymorphism (SNP) found in local cattle (Bali and Peranakan Ongole) and CB cattle in Gowa and Sidrap indicated various genetic diversity can be used as a marker candidate and potential to be developed into future research knowing the correlation of the SNP with the growth rate of CB. Thus, this information will be helpful for further strategy in breeding development program.

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Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

Wenne

2023

Genes

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A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

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Mitochondrial DNA-based species testing of confiscated aquatic wildlife in the Philippines

Cited by 3 publications

References 19 publications

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

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