Feasibility of melting fingerprint obtained from ISSR-HRM curves for marine mammal species identification

Abstract

Currently, species identification of stranded marine mammals mostly relies on morphological features, which has inherent challenges. The use of genetic information for marine mammal species identification remains limited, therefore, new approaches that can contribute to a better monitoring of stranded species are needed. In that context, the ISSR-HRM method we have proposed offers a new approach for marine mammal species identification. Consequently, new approaches need to be developed to identify individuals at the species level. Eight primers of the ISSR markers were chosen for HRM analysis resulting in ranges of accuracy of 56.78–75.50% and 52.14–75.93% in terms of precision, while a degree of sensitivity of more than 80% was recorded when each single primer was used. The ISSR-HRM primer combinations revealed a success rate of 100% in terms of discrimination for all marine mammals included in this study. Furthermore, ISSR-HRM analysis was successfully employed in determining marine mammal discrimination among varying marine mammal species. Thus, ISSR-HRM analysis could serve as an effective alternative tool in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and success rate. It would also offer field practice to veterinarians, biologists and other field-related people a greater degree of ease with which they could interpret results when effectively classifying stranded marine mammals. However, further studies with more samples and with a broader geographical scope will be required involving distinct populations to account for the high degree of intraspecific variability in cetaceans and to demonstrate the range of applications of this approach.

First Stranding Event of a Common Minke Whale (Balaenoptera acutorostrata Lacépède, 1804) Reported in the Gulf of Thailand

“…The D-loop of this sample was amplified from the extracted DNA using PCR primers: forward, 5 -CAT ATT ACA ACG GTC TTG TAA ACC-3 ; and reverse, 5 -GTC ATA AGT CCA TCG AGA TGT C-3 [31] as the universal primers. This pair of primers has the ability to amplify the tRNA-Pro gene to the middle of D-loop, as shown for other cetacean species [32][33][34]. PCR reactions were conducted in 25 µL reaction volumes using Platinum Taq DNA polymerase (Invitrogen) consisting of 1× reaction buffer, 2 mM MgCl 2 , 0.4 mg/mL bovine serum albumin, 0.25 mM dNTPs, 0.4 µM of both forward and reverse primers, and 2 µL of the DNA sample (10 ng/µL).…”

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

“…Several accurate and widely used techniques can be applied to identify cetacean species, such as morphology, fingerprinting, and DNA barcoding [60,61]. However, it remains challenging to investigate the genetic diversity of cetaceans, due to the difficulty of obtaining accurate samples, especially for species threatened with extinction.…”

Genetic Diversity and Maternal Lineage of Indo-Pacific Bottlenose Dolphin (Tursiops aduncus) in the Andaman Sea of Thailand

“…One pair of PCR primers designed for dugongs-forward (5 -CATATTACAACGGT CTTGTAAACC-3 ) and reverse (5 -GTCATAAGTCCATCGAGATGTC-3 ) [26]-was used to amplify the mitochondrial DNA control region of T. aduncus as the universal primers. This pair of primers has the ability to amplify the tRNA-Pro gene to the middle of the control region (D-loop), as shown for many other cetacean species [27][28][29]. PCR reactions were conducted in 25 µL reaction volumes consisting of 1X reaction buffer, 2 mM MgCl2, 0.4 mg/mL bovine serum albumin, 0.25 mM dNTPs, 0.4 µM of both forward and reverse primers, 5 U/µL platinum Taq DNA polymerase (Invitrogen), and 10 ng/µL of the DNA sample.…”