DNA Barcoding of Ichthyoplankton and Juvenile Fishes of a Tropical River in Malaysia

  • B. Akbar John
  • Hassan I. Sheikh
  • K. C. A. Jalal
  • B. Y. Kamaruzzaman
  • H. Sanower
  • M. Nur Hanisah
  • M. H. Rahman
  • M. Rozihan


Taxonomic identification of early larval stages of fishes using conventional morphological keys is extremely laborious due to the overlapping characters shared between genetically closer species. Especially, species-level differentiation during their ontological development is challenging due to paucity of information on their diagnostic features. In the present study, we aimed to use universal DNA barcoding technology to identify ichthyoplankton and juvenile fishes of a tropical river (Kuantan River in Pahang) in Malaysia. This sampling station was chosen in order to check the distribution of juvenile and fish ichthyoplankton samples after the recent massive flood encountered in East Peninsular Malaysia during 2014. We adopted mitochondrial cytochrome oxidase C subunit 1 gene sequencing to identify fish samples. A total of 28 species from 15 families and 5 orders were identified successfully to the species level from the total of 58 DNA barcodes. Unlike the previous report, the most dominant fishes in this study belong to the Cyprinidae family followed by Toxotidae, Ambassidae, and Eleotridae. We admit that the modified bubu light trap method adopted for larval collection in this study has its limitation to attract larvae which had negative phototactic behavior (i.e., Ariidae fishes). Phylogenetic and BLAST analysis showed accuracy of species identification with high bootstrap and percentage similarity value, respectively. Results in this study confirmed the efficiency of universal DNA barcode technology in species-level delimitation of morphologically cryptic species identification. The data presented in this study is valuable for analyzing post-flood effect on fish distribution in tropical river and implementing plans for future fishery resource management in Kuantan River, Pahang, Malaysia.


DNA barcoding COX1 gene Fish larvae Ichthyoplankton Kuantan River 



The research work was sponsored under special flood Fundamental Research Grant Scheme (FRGS), Ministry of Science and Technology, Malaysia.


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • B. Akbar John
    • 1
  • Hassan I. Sheikh
    • 2
  • K. C. A. Jalal
    • 1
  • B. Y. Kamaruzzaman
    • 2
  • H. Sanower
    • 2
  • M. Nur Hanisah
    • 2
  • M. H. Rahman
    • 2
  • M. Rozihan
    • 3
  1. 1.INOCEM Research Station (IRS), Kulliyyah of ScienceInternational Islamic University Malaysia (IIUM)KuantanMalaysia
  2. 2.Department of Biotechnology, Kulliyyah of ScienceInternational Islamic University Malaysia (IIUM)KuantanMalaysia
  3. 3.Department of AquacultureUniversity Putra Malaysia (UPM)SelangorMalaysia

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