Genetic Homogenity of Commerson’s Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Markers

Abstract

Commerson’s anchovy (Stolephorus commersonnii) is a small pelagic fish that live in a group and its existence is very abundant in Segara Anakan Cilacap. This anchovy is widely consumed by communities live around Segara Anakan. This leads to a high exploitation rate. Exploited populations generally have low genetic diversity. This study aims to evaluate genetic diversity of commerson’s anchovy population in Segara Anakan Cilacap inferred from PCR-RFLP of the cytochrome c oxidase 1 (CO1) gene. This study was conducted from January to April 2018 and used survey method by applying random sampling. As many as 30 samples of anchovy were taken. Genomic mtDNA was isolated using modified Chelex method. Partial sequences of the COI gene were amplified using a pair forward commercially available primer. The lengths of 650 base pair of the PCR products were digested with four restriction enzymes. The HindIII enzyme produces PCR-RFLP fragment with the size of 416 bp and 234 bp lengths, VspI produces 435 bp and 214 bp, CO1-TaqI produces 556 bp and 94 bp and RsaI produces 319 bp, 183 bp, and 148 bp fragments, respectively. The PCR-RFLP fragments were obtained from all samples but they produced uniform band pattern for all 30 anchovy individuals. These results indicated that the anchovy population in Segara Anakan Cilacap has monomorphic allele for all PCR-RFLP markers. Hence, it can be concluded that genetic homogenity was observed on anchovy population in Segara Anakan Cilacap as inferred from PCR-RFLP COI gene.

Molecular phylogeny of anchovy (Clupeiformes: Clupeidae) from southern waters of Lombok using mitochondrial DNA CO1 gene sequences

“…Some researchers reported the results of this study were a piece longer than the fragment resulting from the previous studies on Indian marine fishes and Taiwan's fishes species (655 bp), groper Epinephelus sp. (526 bp), and anchovy from Indonesia around 650 bp (Lakra et al 2011;Jefri et al 2015;Bingpeng et al 2018;Nuryanto et al 2019;Tapilatu et al 2021;Dwifajri et al 2022). Whereas the other researchers reported the DNA bands size of the anchovy sample obtained was almost the same as those fishes found in the family Labridae (Dailami et al 2018), marine fishes (Bingpeng et al 2018), Rhincodon typus (Toha et al 2020), Thunnus (Kolondam 2020), even in the gastropod group (Saleky et al 2016;Leatemia et al 2018).…”

“…The difference among the PCR products from different species could occur, and it is a common phenomenon even though these fragments amplify using a similar primer pair. For example, several previous studies reported different lengths of the COI gene from divergent fish species (Lakra et al 2011;Kusbiyanto et al 2017;Bingpeng et al 2018;Nuryanto et al 2019). It is due to each species having different specific sequences in its genome.…”