Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

  • Piangjai Chalermwong (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Thitipong Panthum (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Pish Wattanadilokcahtkun (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Nattakan Ariyaraphong (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Thanyapat Thong (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Phanitada Srikampa (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Worapong Singchat (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Syed Farhan Ahmad (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Kantika Noito (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Ryan Rasoarahona (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Artem Lisachov (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Hina Ali (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Ekaphan Kraichak (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Narongrit Muangmai (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Satid Chatchaiphan6 (Department of Aquaculture, Faculty of Fisheries, Kasetsart University) ;
  • Kednapat Sriphairoj (Faculty of Natural Resources and Agro-Industry, Kasetsart University) ;
  • Sittichai Hatachote (Faculty of Natural Resources and Agro-Industry, Kasetsart University) ;
  • Aingorn Chaiyes (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Chatchawan Jantasuriyarat (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Visarut Chailertlit (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Warong Suksavate (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Jumaporn Sonongbua (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Witsanu Srimai (Kalasin Fish Hatchery Farm (Betagro)) ;
  • Sunchai Payungporn (Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University) ;
  • Kyudong Han (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Agostinho Antunes (CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto) ;
  • Prapansak Srisapoome (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Akihiko Koga (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Prateep Duengkae (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Yoichi Matsuda (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Uthairat Na-Nakorn (Department of Aquaculture, Faculty of Fisheries, Kasetsart University) ;
  • Kornsorn Srikulnath (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University)
  • Received : 2023.05.09
  • Accepted : 2023.06.23
  • Published : 2023.09.30
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Abstract

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

Keywords

Acknowledgement

The authors are grateful to Chalitra Saysuk (AGB Research Unit, Kasetsart University, Thailand) for helpful discussion. We thank the Center for Agricultural Biotechnology (CAB) at the Kasetsart University Kamphaeng Saen Campus and the NSTDA Supercomputer Center (ThaiSC) for support with server analysis services. We also thank the Faculty of Science for providing research facilities. We also thank the Faculty of Science and the Center for Bio-Medical Engineering Core Facility at Dankook University for providing research facilities. This research was financially supported in part by The National Research Council of Thailand (NRCT) (N42A650233); National Research Council of Thailand : High-Potential Research Team Grant Program (N42A660605) awarded to grant awarded to WSI, SFA, EK, NM, SC, KSR, SH, AC, CJ, VC, WSU, JS, WSR, PS, PD, UN, and KS; a National Science and Technology Development Agency (NSTDA P-19-52238 and JRA-CO-2564-14003-TH) grant awarded to WSI and KS; a Talent Mobility Program under the Office of the Permanent Secretary (OPS) of the Ministry of Higher Education, Science, Research and Innovation (MHESI), Thailand (no. 0224.1/22517) grant awarded to WSI, SFA, and KS; a Higher Education for Industry Consortium (Hi-FI) (6514400949 and 6414400777) grant awarded to PC and NA; a Thailand Science Research and Innovation grant through the Kasetsart University Reinventing University Program 2021 (3/2564) awarded to TP, NA, AL, HA, AA, and KS; the High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency awarded to TP and KS; a Kasetsart University Research and Development Institute grant awarded to WSI, SFA, and KS (FF(S-KU)17.66); and International SciKU Branding (ISB), Faculty of Science, Kasetsart University support awarded to WSI, SFA, and KS.

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