Sains Malaysiana 53(1)(2024): 11-21

http://doi.org/10.17576/jsm-2024-5301-02

The Viability and Potential of Environmental DNA (eDNA) Detection of Freshwater Fish Based on Current Genetic Resources in Malaysia

(Daya Maju dan Potensi Pengesanan DNA Persekitaran Ikan Air Tawar Berdasarkan Sumber Genetik Terkini di Malaysia)

KAVIARASU MUNIAN^1,2, FARAH FARHANA RAMLI¹, NURSYUHADA OTHMAN¹, HIDAYAH HARIS¹, NUR HARTINI SARIYATI¹, NUR AINA AMIRA MAHYUDIN², MOHD FAUDZIR NAJMUDDIN¹, MOHD SHAHFIZ AZMAN² & MUHAMMAD ABU BAKAR ABDUL-LATIFF^1,*

¹Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600 Muar, Johor, Malaysia

²Zoology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), 52019 Kepong, Selangor, Malaysia

Diserahkan: 26 Jun 2022/Diterima: 12 Disember 2023

Abstract

Environmental DNA (eDNA) metabarcoding is a promising tool for regular biological monitoring, especially for freshwater fish, which are facing tremendous threats worldwide. The application of eDNA detection is a dramatic improvement on common methods of biomonitoring as it produces tangible results in a short time with low effort and little expense. However, the accuracy of the technique is largely dependent on the availability of genetic references for the target organisms. In this study, we investigated the availability of genetic resources for freshwater fish in Malaysia in three public depositories, National Center for Biotechnology Information (NCBI), Barcode of Life Data System (BOLD), and Mitochondrial Genome Database of Fish (MitoFish), focusing on seven targeted genes of mitochondrial DNA. We found that only 68.6% of freshwater fish found in Malaysia had information on at least one of the seven targeted genes, with data on Cytochrome C Oxidase Subunit I being most commonly available. Genetic information for threatened and endemic species were underrepresented (33.3%-41.7%), yet fish of commercial value and invasive species were well explored genetically. Although there is still room for improvement to achieve comprehensive and reliable genetic resource information for freshwater fish in Malaysia, the application of eDNA metabarcoding is still highly relevant. This is since the current decline in freshwater fish diversity in Malaysia is alarming and because the technique will assist in the ongoing effort to generate new genetic references for Malaysian freshwater fish.

Keywords: Environmental DNA; Cytochrome b; Cytochrome C Oxidase Subunit I; freshwater fish; metabarcoding and Next-Generation Sequencing (NGS)

Abstrak

Metabarkod DNA persekitaran (eDNA) ialah kaedah yang berpotensi dalam memantau sumber biologi terutamanya dalam pemantauan ikan air tawar terancam di seluruh dunia. Penggunaan teknik eDNA dalam pemantauan sumber biologi merupakan kaedah beteknologi tinggi kerana ia mampu memberikan hasil yang ketara dalam masa yang singkat dengan penggunaan tenaga dan kos yang minimum. Walau bagaimanapun, ketepatan teknik ini sebahagian besarnya bergantung kepada ketersediaan rujukan genetik untuk organisma yang disasar. Dalam penyelidikan ini, kami mengkaji ketersediaan sumber genetik untuk ikan air tawar di Malaysia di tiga depositori awam, iaitu Pusat Maklumat Bioteknologi Kebangsaan, Sistem Data Kehidupan Kod Bar dan Pangkalan Data Genom Mitokondria Ikan dan memfokuskan kepada tujuh gen DNA mitokondria yang terpilih. Hasil keputusan kami menunjukkan hanya 68.6% daripada ikan air tawar yang ditemui di Malaysia mempunyai maklumat tentang sekurang-kurangnya satu daripada tujuh gen yang disasarkan, manakala gen subunit Sitokrom C Oksidase Subunit I merupakan gen yang paling tersedia untuk digunakan. Keputusan kami juga menunjukkan maklumat tentang genetik spesies terancam dan endemik masih kurang dikaji (33.3%-41.7%), tetapi ikan air tawar komersial dan spesies ikan invasif telah dikaji dengan lebih baik dari aspek genetik. Fenomenon penurunan kepelbagaian ikan air tawar di Malaysia yang membimbangkan pada masa kini memberikan kewajaran kepada pelaksanaan aplikasi metabarkod eDNA untuk kajian ikan air tawar. Walaupun masih terdapat ruang penambahbaikan untuk mencapai maklumat sumber genetik yang komprehensif dan boleh dipercayai di Malaysia, aplikasi metabarkod (eDNA) ini wajar diteruskan sebagai sebahagian usaha berterusan para pengkaji dalam menjana rujukan genetik baharu untuk ikan air tawar Malaysia.

Kata kunci: DNA persekitaran; ikan air tawar; metabarkod dan penjujuran generasi hadapan (NGS); sitokrom b; Sitokrom Oksidase Subumit I

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*Pengarang untuk surat-menyurat; email: latiff@uthm.edu.my