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Journal : Research Journal of Life Science

Cytochrome Oxidase C Subunit I (COI) for Identification and Genetic Variation of Loaches (Nemacheilus fasciatus) Amalia Ayuk Riyadini; Maheno Sri Widodo; Mohamad Fadjar
Research Journal of Life Science Vol 7, No 3 (2020)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.rjls.2020.007.03.4

Abstract

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.
Phytogenetic Relationships of Mystacoleucus marginatus (Valenciennes 1842) based on Cytochrome Oxidase C Subunit I (COI) Gene Fitri Sil Valen; Maheno Sri Widodo; Yuni Kilawati; R. Adharyan Islamy
Research Journal of Life Science Vol 6, No 1 (2019)
Publisher : Lembaga Penelitian dan Pengabdian kepada Masyarakat, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.rjls.2019.006.01.3

Abstract

Mystacoleucus marginatus is a type of freshwater fish that is spread in various countries with tropical climates, one of which is Indonesia. This fish can be found in the Brantas River Basin (DAS), East Java. In its development, identification of fish species needs to be done in detail and more deeply, so that the correct identification results can be obtained. This study aims to identify genetic and phylogenetic characteristics of Mystacoleucus marginatus in the Brantas River Basin based on the Cytochrome Oxidase C Subunit I (COI) gene. Test samples were taken from 11 individuals of Mystacoleucus marginatus in the Brantas watershed, from June to August 2018. The results showed that Mystacoleucus marginatus in the Brantas watershed had 2 Haplotypes with Haplotype (Hd)=0.96 diversity values and nucleotides diversity (Pi)=0.00357. These results indicate that the population in the Brantas watershed is interconnected between one location and another sampling location, this is supported by a phylogenetic topology of DNA barcodes showing a monophyletic clade, as well as a haplotype distribution indicating that the sample area is genetics are not isolated from one another. So that the type of Mystacoleucus marginatus scattered along the Brantas watershed is still in one species, which is indicated by the low level of genetic variation. Genetic identification efforts must be carried out continuously so that appropriate information can be obtained for the diversity of fish species, especially endemic fish.