Phylogenetic of Marble Goby (Oxyeleotris marmorata Blkr.) in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene

Abstract

Marble goby (Oxyeleotris marmorata) in Indonesia, spread across Sumatra, Kalimantan and Papua. The purpose of this study was to utilize a sequence of mitochondrial DNA Cytochrome Oxidase Subunit I gene, to analyze the phylogenetic tree and genetic distance between cultured and captured populations. This research was conducted on March-August 2020. The methods used in barcoding species were DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of the COI mtDNA gene. The domesticated samples (n=3) were collected from Gandus Fish Seed Center (GFSC), while the wild samples (n=3) were captured from the Musi River in Beruge Village, Babat Toman District, both in Musi Banyuasin Regency. The sequenced COI mtDNA gene fragments were obtained from the PCR method. Three samples performed good PCR results, while the other three didn’t amplify properly. After the editing process, the COI gene sequencing produced a nucleotide length of 610 bp. Based on the BLAST (Basic Local Alignment Search Tool), domesticated marble goby (OMD2, OMD3) was in the same cluster with marble goby from the Musi River (OMS3). The genetic distance indicated that two specimens of domesticated marble goby were 100% identical, while the wild (OMS3) indicated a genetic distance of 0.0066 to domesticated species.

Molecular phylogenetic analysis of commercially important Asian monsoon scallop, Amusium pleuronectes (Linnaeus 1758) from Indonesia

“…So that the phylogenetic constructs obtained indicate a genetic distance with nucleotide changes 2 times in every 100 bp. DNA barcoding technology has been utilized and validated for many aquatic species with detected more variation among congeneric species than among conspecific individual (Ward et al, 2005;Syaifudin et al, 2021). Therefore, it can effectively use to distinguish a complex of morphologically distinct species in the Indo-Pacific (Last et al, 2005;Khansa et al, 2023).…”

“…DNA barcoding combined with a molecular phylogenetic tree is a system designed for precise and accurate identification of a species using a short and standardized gene region (Hebert et al, 2003). Research on DNA Barcode and phylogenetic tree has been carried out on marine organism like fish (Khansa et al, 2023;Nursalim et al, 2022;Syaifudin et al, 2021), shellfish (Beden and Karahan, 2020;Praipue et al, 2021), crustacean (Irwani et al, 2020;Vella and Vella, 2022; ) and coral reef (Wijayanti et al, 2017a;Wijayanti et al, 2018). The most promising benefit of DNA barcoding and phylogenetic tree for species authentication lies in the ability to identify early stages that cannot be done by using morphological descriptions and inter species connections.…”

Molecular analysis of the blood cockle, Tegillarca granosa (Linnaeus 1758) from Indonesia

“…The resulting phylogenetic structures show a genetic distance with nucleotide alterations occurring twice every 100 base pairs (bp). Many aquatic species have been studied using DNA barcoding technology, which has shown to identify greater variation between congeneric species than between conspecific individuals [21] [22]. The Indo-Pacific region may so efficiently use it to differentiate a complex of physically dissimilar species [6] [28].…”