Cytochrome C Oxidase Subunit 1 Gene (COI) for Identification and Genetic Variation of Loaches ( Nemacheilus fasciatus )

Nemacheilus fasciatus is an Indonesian freshwater fish species that can be found in river waters on Java. This fish has a morphological similarity between species. This study aims to identify species of samples found and know their genetic kinship. This study used the Cytochrome Oxidase subunit I (COI) gene as a molecular marker, and then the results were analyzed using MEGA X software. The genetic structure and phylogeny of N. fasciatus sequences were combined with outgroup species from GenBank and analyzed using Maximum Likehood (ML), Pairwise Genetic Distance and Bootstrapping Phylogeny Model of Kimura 2 Parameters. The results showed that the primary pairs of LCO1490 and HCO2198 used to amplify the sample N. fasciatus with COI as a marker. The nucleotide frequencies of these loaches are A=26.5%, T=23.8%, C=19.9% and G=29.9%. The estimated Transition/Transversion bias (R) is 0.60. The number of haplotype diversity (Hd) was 0.972, and nucleotide (Pi) diversity was 0.05115. The kinship of N. fasciatus compared to the outgroup is closer to N. pallidus than N. chrysolaimos . Research needs to be conducted with a larger sample size for the genetic diversity of N. fasciatus in Indonesia.

[1]  R. A. Islamy,et al.  Identification and Physiological Characteristics of Potential Indigenous Bacteria as Bio-Remediation Agent in the Wastewater of Sugar Factory , 2021 .

[2]  R. A. Islamy,et al.  Checklist of mangrove snails (Mollusca: Gastropoda) in South Coast of Pamekasan, Madura Island, East Java, Indonesia , 2020, Biodiversitas Journal of Biological Diversity.

[3]  M. Widodo,et al.  New records of alligator gar, Atractosteus spatula (Actinopterygii: Lepisosteiformes: Lepisosteidae) from Bali and Java, Indonesia , 2020, Acta Ichthyologica et Piscatoria.

[4]  D. Burks.  DNA Structure , 2020, Definitions.

[5]  M. Fadjar,et al.  Short communication: First record of Arapaima gigas (Schinz, 1822) (Teleostei: Osteoglossomorpha), in the Brantas River, Sidoarjo, East Java, Indonesia , 2019 .

[6]  Y. Kilawati,et al.  The Antigenotoxic Activity of Brown Seaweed (Sargassum sp.) Extract Against Total Erythrocyte and Micronuclei of Tilapia Oreochromis niloticus Exposed by Methomyl-Base Pesticide , 2019, The Journal of Experimental Life Sciences.

[7]  Y. Kilawati,et al.  Phytogenetic Relationships of Mystacoleucus marginatus (Valenciennes 1842) based on Cytochrome Oxidase C Subunit I (COI) Gene , 2019, Research Journal of Life Science.

[8]  M. Musa,et al.  Short Communication: Species composition and density of mangrove forest in Kedawang Village, Pasuruan, East Java, Indonesia , 2019, Biodiversitas Journal of Biological Diversity.

[9]  U. Yanuhar,et al.  Assessing the Genotoxic Potentials of Methomyl-based Pesticide in Tilapia (Oreochromis niloticus) Using Micronucleus Assay , 2017 .

[10]  H. Esmaeili,et al.  A new loach of the genus Oxynoemacheilus from the Tigris River drainage and its phylogenetic relationships among the nemacheilid fishes (Teleostei: Nemacheilidae) in the Middle East based on mtDNA COI sequences , 2016 .

[11]  D. V. Muley,et al.  Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae). , 2016, Comptes rendus biologies.

[12]  W. S. Lakra,et al.  Intra- Specific Morphometric and Genetic Comparisons in Hillstream Loach, Nemacheilus montana (McClelland 1838) from Western Himalaya, India , 2016 .

[13]  R. Hadiaty,et al.  Taxonomic study of the genus Nemacheilus (Teleostei: Nemacheilidae) in Indonesia , 2014 .

[14]  P. Munday,et al.  High Genetic Diversity in Geographically Remote Populations of Endemic and Widespread Coral Reef Angelfishes (genus: Centropyge) , 2013 .

[15]  Martin I. Taylor,et al.  DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes) , 2012, PloS one.

[16]  Kevin L Tang,et al.  Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). , 2011, Molecular phylogenetics and evolution.

[17]  Damon P. Little,et al.  Choosing and Using a Plant DNA Barcode , 2011, PloS one.

[18]  N. Barton,et al.  Mutation and the evolution of recombination , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[19]  J. Rozas.  DNA sequence polymorphism analysis using DnaSP. , 2009, Methods in molecular biology.

[20]  B. Lyon,et al.  Improving the reliability of molecular sexing of birds using a W‐specific marker , 2008, Molecular ecology resources.

[21]  Xavier Messeguer,et al.  DnaSP, DNA polymorphism analyses by the coalescent and other methods , 2003, Bioinform..

[22]  P. Hebert,et al.  Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[23]  J. G. Burleigh,et al.  Investigating Evolutionary Questions Using Online Molecular Databases , 2001 .

[24]  A. Eyre-Walker.  Fundamentals of Molecular Evolution (2nd edn) , 2000, Heredity.

[25]  M. Kottelat,et al.  Freshwater Fishes of Western Indonesia and Sulawesi , 1993 .

[26]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[27]  Freshwater Fishes , 1942, Nature.