Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Nur Asiah,Muhamad Kadapi,Junianto Junianto,Melta Rini Fahmi,Ayi Yustiati,Zainal A Muchlisin,Sukendi Sukendi

doi:10.12688/f1000research.17319.1

Nur Asiah, Muhamad Kadapi + Show 5 more

Open Access

https://doi.org/10.12688/f1000research.17319.1

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Abstract

Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Highlights

Kelabau are ancient fish belonging to genus Osteochilus of family Cyprinidae
In Sumatra Island in Indonesia, the fish is commonly found in the Siak, Kampar and Rokan rivers in Riau Province[3,4]
Morphological identification The morphological traits of all kelabau used in this study matched those of O. melanopleurus

Summary

Introduction

Kelabau are ancient fish belonging to genus Osteochilus of family Cyprinidae. The species is distributed throughout Thailand, Vietnam, Peninsular Malaysia, Borneo and Sumatra[1,2]. In Sumatra Island in Indonesia, the fish is commonly found in the Siak, Kampar and Rokan rivers in Riau Province[3,4]. A study was needed to identify the species using morphological and molecular methods to determine these types in the Siak, Rokan and Kampar rivers. MtDNA CO1 is selected as a target in DNA barcoding because it is a highly conserved site This method has advantages over the morphological identification approach in that it is fast, reliable and it can be used for all types of samples because it uses a single gene along with mutations in the nucleotides to acknowledge the taxonomic features of each species[16]. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were edited and aligned using MEGA v

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