The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Seq
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The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Sequences on the GenBank Database Sapto Andriyono 1,2
&
Md. Jobaidul Alam 1 & Hyun-Woo Kim 1,3
Received: 4 July 2019 / Revised: 12 January 2020 / # Springer Nature Switzerland AG 2020
Abstract The molecular approach provides an alternative method of easy identification of marine finfish, quickly and has high accuracy. This study represents the molecular identification based on the 12S rRNA and 16S rRNA partial region (12S–16S rRNA PR) then confirm by Cytochrome C Oxidase I (COI) of commercial marine fish of Jawa and Bali, Indonesia. We examined 169 samples and identified 78 new 12S–16S rRNA PR sequences confirmed by the COI region representing 136 genera, 50 families, and 12 orders. Carangids were dominated and followed by Lutjanids, Scombrids, and Serranids. We highlight the importance of implementing molecular identification of marine resources for complementing biodiversity assessment in Indonesian marine ecosystems. This study represents the first step toward the environment DNA (e-DNA) analysis in Java and Bali marine ecosystem using the 12S–16S rRNA PR. Keywords Species identification . Molecular . Partial region . Marine fish
Introduction The DNA barcoding, the currently accepted methods for the identification of terrestrial and aquatic animals and plants has attracted much attention and numerous advantages. The accuracy of DNA-base identification is near-100% indicating this method able to prove in the identification of specimens under different environmental conditions (Meyer and Paulay 2005). Identification based on DNA barcode has been agreed globally with various advantages possessed is very simple and uses a universal tool that includes all the animals both in the fresh samples and or processed products (Pepe et al. 2007; Giusti et al. 2017). This barcoding system uses sequences that have a diversity in the single region of mitochondrial DNA * Sapto Andriyono [email protected] 1
Interdisciplinary Program of Biomedical, Mechanical, and Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea
2
Departmen of Marine Science, Fisheries and Marine Faculty, UNAIR C Campus Jl. Mulyorejo Surabaya 60115. Universitas Airlangga, Surabaya, East Java 60115, Indonesia
3
Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
Cytochrome c Subunit I gene (COI) and deposited to the Genbank database as central bioinformatics. Scientists have demonstrated their effectiveness in conducting DNA barcoding in freshwater fish and deep-sea fish (Ward et al. 2005; Lakra et al. 2011). Besides the COI region, the other region for barcoding is 12S and 16S rRNA (Cawthorn et al. 2012), cytochrome b (Sevilla et al. 2007), NADH-5 (Johnson and O’Brien 1997) and control region (Mitchell and Hellberg 2016). The 12S–16S rRNA partial region (12S–16S rRNA PR) is located from small subunit to large subunit of ribosomal RNA and has potentially
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