Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene

Abstract

Abstract. Elvyra R, Solihin DD, Affandi R, Junior MZ, Suhendra M. 2020. Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene. Biodiversitas 21: 3539-3546. The study of molecular characteristics and phylogenetic relationships among silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) is very scarce. Existing data are mostly based on morphological characters. Genetic markers among Kryptopterus, Ompok, and Phalacronotus can be analyzed by exploring the nucleotide and amino acid sequences of the mitochondrial cytochrome b gene region (906 base pairs). This study aims to identify molecular characteristics and phylogenetic relationships of silurid catfishes from the Kampar River based on the cytochrome b gene. This research examined 14 silurids of four species from three genera in the Kampar River of Indonesia. Molecular phylogenetic trees were constructed using the neighbor-joining method. This study revealed that three amino acid sites can be used as specific genetic markers for characterizing Kryptopterus limpok. They are E (glutamic acid) at site 123, V (valine) at site 155, and M (methionine) at site 156. Two amino acid sites can be used as specific genetic markers of Ompok spp., A (alanine) at site 201 for O. hypophthalmus, and S (serine) at site 282 for O. eugeneiatus. Two amino acid sites, I (isoleucine) at site 197 and L (leucine) at site 284, can be used to identify Phalacronotus apogon from the Kampar River, Indonesia. The phylogram results based on genetic distance (p-distance) from nucleotide cytochrome b sequences generally showed that intraspecies of K. limpok, O. eugeneiatus, O. hypophthalmus and P. apogon from the Kampar River formed relationship groups within each species supported by high bootstrap values. Additionally, based on genetic distance, K. limpok data from the Kampar River samples and GenBank formed one relationship group within species of K. limpok with a high bootstrap value. This study proves that cytochrome b gene can be used to identify molecular characteristics and phylogenetic relationships of K. limpok, O. eugeneiatus, O. hypophthalmus, and P. apogon from the Kampar River, Indonesia.

Morphological and molecular characterization of mole crab (Genus: Emerita) in the Cilacap coastlines of Indonesia, with particular focus on genetic diversity of Emerita sp. nov.

“…Amino acid AT was higher than GC in both morphotypes, but the content of A and T was different. The phenomena were also reported in fish (Elvyra et al 2020). The molecular difference observed in this study is in line with morphotypes A and B morphology.…”

“…taxonomy and systematic utilized morphological data during species characterization (Erlank et al 2018;Shu et al 2022). In some animal groups, morphology characteristics are entirely satisfactory (Chan et al 2016;Mauroka et al 2018;Korovchinsky 2019).…”

“…Species identification and population genetic studies were conducted using various molecular markers (Nuryanto et al 2017;Butet et al 2019;Nuryanto et al 2019;Elvyra et al 2020;Riani et al 2021;Setyaningrum et al 2022). The cytochrome c oxidase 1 (COI) gene is a common marker used in species determination (Ko et al 2013;Muchlisin et al 2013;Dahruddin et al 2016;Irmawati et al 2017;Syaifudin et al 2020) and population genetic studies (Song et al 2013;Zhang et al 2014;Fahmi 2015;Nuryanto et al 2019).…”

Molecular characteristics and taxonomic status of morphologically similar barnacles (Amphibalanus) assessed using the cytochrome c oxidase 1 gene

“…Those high nucleotide differences indicate that both barnacle groups are genetically different, which might suggest that they belong to different species. According to Elvyra et al (2020), nucleotide differences among samples might indicate that the samples belong to different species. Similar phenomenon was also reported in fish (Malakar et al 2013)…”

Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

“…Both belong to the family of cyprinidae. Although identifying the species by morphology has several limitations [13], molecular identification techniques have an advantage in rapid and accurate assessment [17]. COI-based on molecular method can identify specimens precisely, reliably, accessible, and at low cost [11].…”