Chalermwong Piangjai, Panthum Thitipong, Wattanadilokcahtkun Pish, Ariyaraphong Nattakan, Thong Thanyapat, Srikampa Phanitada, Singchat Worapong, Ahmad Syed Farhan, Noito Kantika, Rasoarahona Ryan, Lisachov Artem, Ali Hina, Kraichak Ekaphan, Muangmai Narongrit, Chatchaiphan Satid, Sriphairoj Kednapat, Hatachote Sittichai, Chaiyes Aingorn, Jantasuriyarat Chatchawan, Chailertlit Visarut, Suksavate Warong, Sonongbua Jumaporn, Srimai Witsanu, Payungporn Sunchai, Han Kyudong, Antunes Agostinho, Srisapoome Prapansak, Koga Akihiko, Duengkae Prateep, Matsuda Yoichi, Na-Nakorn Uthairat, Srikulnath Kornsorn
Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
Genomics Inform. 2023 Sep;21(3):e39. doi: 10.5808/gi.23038. Epub 2023 Sep 27.
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.
在不评估可靠性和有效性的情况下进行DNA条形码分析会导致物种鉴定的分类错误，这会对它们的保护和水产养殖业造成干扰。尽管DNA条形码有助于物种的分子鉴定和系统发育分析，但其在胡子鲶科鲶鱼谱系中的可用性仍不确定。在本研究中，开发并验证了用于胡子鲶科鲶鱼的DNA条形码分析方法。对37种胡子鲶科鲶鱼的线粒体细胞色素c氧化酶I（COI）、细胞色素b（Cytb）基因和D环序列的2970个条形码序列进行了分析。COI、Cytb和D环序列的种内最近邻距离最高分别为85.47%、98.03%和89.10%。这表明Cytb基因最适合用于鉴定胡子鲶科鲶鱼，并且可以作为DNA条形码分析的标准区域。在Cytb数据集中观察到种间和种内序列分歧之间存在正向条形码间隙，但在COI和D环数据集中未观察到。种内变异通常小于4.4%，而种间变异一般大于66.9%。然而，在步行鲶中检测到一个物种复合体，并且在北非鲶中观察到显著的种内序列分歧。这些发现表明需要专注于开发一个DNA条形码系统，以正确分类胡子鲶科鲶鱼，并验证其对更广泛的胡子鲶科鲶鱼的有效性。通过丰富目标物种及其属的多个序列的数据库，可以更准确地进行物种鉴定，并促进对该物种的生物多样性评估。
