DNA barcoding to identify fish species

WHAT crosses your mind when you see fish? Ulam (viand)? Pet? “Finding Nemo”, perhaps?

The thought would probably depend on your pre-established association with the idea of what a fish is and what it is supposed to be. My recent experience with fishes turned the tide on how I came to view them.

Up until that point, I never really took fish seriously. What did I know about fish except that they looked great when put on a plate?

On December 1-6, 2019, the University of the Philippines Mindanao Coral Reef Resiliency and Ecology Studies (CRREST) Laboratory hosted a training-workshop on laboratory techniques for fish barcoding at the UP Mindanao CRREST lab.

According to the project leader, Dr. Cleto L. Nañola Jr., the workshop was conceptualized and was made possible to serve as training for the faculty and staff of the Mindanao State University-Tawi-Tawi College of Technology and Oceanography (MSU-TCTO) on DNA barcoding protocols for marine fishes. MSU-TCTO is one of the partner institutions of UP Mindanao on the DNA barcoding project funded by the DOST-PCAARRD.

DNA barcoding and its many uses

DNA barcoding, simply put, is used to accurately identify a species by utilizing the short DNA sequence of a sample species.

With more than 30,000 species of fish in existence around the world, there is great value to them in terms of biodiversity and economy and as food source, according to Bingpeng Xing (1). Barcoding has been used in researches all over the world to identify fish species.

The Philippines is one of the world’s mega-biodiverse countries, but there is still a lot of things we need to learn about our country’s rich biodiversity. This is where DNA barcoding enters the picture.

Aside from species identification, DNA barcoding is used to help in conducting biodiversity assessments, resolving taxonomic resolution, detecting seafood fraud, tracking illegal wildlife trade, developing new methods to further improve species resolution, and adding new information to the existing reference database.

In the Philippines, DNA barcoding was used in a study by Sarmiento et.al (2), to address seafood fraud involving fishballs, some of which didn’t actually contain fish. The study’s results showed that some samples contained meat from pig and chicken. The results from this study encourages us to be more vigilant when it comes to food quality and control.

DNA barcoding has also been used in the Philippines to track illegal trade of regulated and protected aquatic species such as juvenile eels and manta rays, which are either sold live or as dried or processed products. (3)

Different Perspectives

I was lucky enough to be one of the participants, along with five other participants: Yennyriza Abduraup (training assistant, Office of Continuing Education and Extension Services), Kimtang Joy H. Mohammad (science research assistant, Office of Research), Marilyn J. Enojario (training assistant, OCEANes), Nurhima H. Jammang (faculty, College of Arts and Sciences), and Wahaymin H. Jamil (Instructor I, College of Fisheries), from MSU-TCTO.

During the workshop-training, we were engaged in both field and laboratory activities, such as collecting fish samples through conducting market surveys, doing hands-on fish morphometrics, photography, and tissue extraction, and performing actual laboratory work to extract the collected fish samples’ DNA for barcoding. We were instructed on molecular laboratory techniques for tissue analysis, DNA extraction, Agarose Gel Electrophoresis (AGE), and Cytochrome Oxidase I Amplification (COI) via Polymerase Chain Reaction (PCR).

The activities served as a primer for knowledge establishment and to allow the participants to have first-hand understanding and experience of fish barcoding processes. For processes like fish morphometrics or the measuring of a fish’s dimension (e.g. length, depth), photography, and tissue extraction, we used simple tools like rulers, a weighing scale, and cameras to extract information from the fish, such as its measurements and photos for archiving purposes.

This made me realize that the absence of highly technical equipment and even geography are not hindrances if we want to use science to address the questions that we have, the results of which may eventually be added to the existing body of scientific knowledge.

At the end of the activity, we were able to gain new knowledge as well as new insights on fish barcoding. Jammang remarked that the time and effort she spent during the activity were well worth it because of the detailed and hands-on approach. Enojario chimed in with her appreciation for the availability of the workshop materials.

Jamil was pleased with the workshop, citing that aside from the capable facilitators, his expectations for the activity were met. He added that he found fish morphometrics and photography to be the most interesting part of the workshop given that he can replicate the steps and can apply it in the future to his class. Enojario also appreciated how the study and the methods used can be replicated at MSU-TCTO.

The outlier’s experience

In a group of individuals who are in the field of science or research, I was the perpetual fish out of water. What did I know of laboratory processes, or even scientific names for that matter? I couldn’t even differentiate one fish from another.

But the experience gave me a newfound appreciation for the sciences, especially the painstaking work that goes into research. After all, what we have now and what we know are all results of years of hard work, painstaking attention to detail, and an insatiable thirst to shed a light on the world’s mysteries that are still waiting to be discovered and understood.

We would like to acknowledge the support of the DOST-Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRD), DNA Barcoding of Selected Marine Fishes in Davao and Sulu Archipelago (MINDA), the DNA Barcoding and Genetic Diversity of Selected Marine Fishes along the North Bifurcation of the North Equatorial Current (NEC), and the CHED DARE TO-Bio-economic Assessment and Modeling of Reef Fisheries in Davao Gulf for Sustainable Harvest (BEAM) projects for this activity.


1 Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W (2018) DNA barcoding for identification of fish species in the Taiwan Strait. PLoS ONE 13(6): e0198109. https://doi.org/10.1371/journal.pone.0198109

2 Sarmiento K, Pereda J, Ventolero M, Santos, M (2018) Not fish in fish balls: fraud in some processed seafood products detected by using DNA barcoding. Philippine Science Letters Vol.11 No. 01, pp.30-36.

3 Asis A, Lacsamana J, Santos M (2014) Illegal trade of regulated and protected aquatic species in the Philippines detected by DNA barcoding. Mitochondrial DNA, Early Online 1-8. doi: 10.3109/19401736.2014.913138.


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