Comparative Molecular Identification of Genus Dicentrarchus Using Mitochondrial Genes and Internal Transcribed Spacer Region

Abstract

DNA barcoding is one of the powerful DNA-based identification tools that are used for accurate identification of a species. Despite several DNA barcodes were used, the accuracy and suitability of these barcodes depend on speciesspecific variations.The current study was conducted to compare the efficiency of two mitochondrial genes to the nuclear Internal Transcribed Spacer (ITS) region in the molecular identification of genus Dicentrarchus. A total of 80 fish samples for Dicentrarchus labrax and Dicentrarchus punctatus were randomly collected from two different locations in Egypt; Alexandria and Bardawil Lagoon. All samples were morphologically characterized. For species barcoding, the ITS region was firstly employed to carry out the PCR amplifications. Additionally, two mitochondrial genes; cytochrome b (Cyt b) and cytochrome oxidase subunit I (COI) were also used for species barcoding. To evaluate the efficiency of each marker, three different approaches were used. Firstly, phylogenetic relationship was constructed between the collected samples and a reference species using each genetic marker. Secondly, Automated Barcode Gap Discovery (ABGD) method was used for each marker in order to assign the samples into presumed species without priori species assumption. Lastly, the Poisson Tree Processes (PTP) model was used which relies on Bayesian support values to delimit species on the input tree. The two species of genus Dicentrarchus exhibited nearly similar ITS sequences, leading to an ambiguous identification of the two species. However, the two mitochondrial COI and Cyt b genes were able to accurately distinguish between the two species. The three approaches, phylogeny, ABGD and PTP presented consistent results. Overall, COI and Cyt b outperformed ITS in assigning species accurately. Mitochondrial barcodes could provide a leading guide for fish species identification. ITS should be abandoned in favor of COI and Cyt b as primary DNA barcode markers for fish species in general and Dicentrarchus genus, in particular.

Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

“…DNA barcoding has been widely used for delineating species boundaries, discriminating closely related species of fish (Hajibabaei et al 2007a). Similarity or percentage identity ranged from 99-100% with the identified species in the GenBank databases that was commonly recorded among the fish species and demonstrated the potency of such genomic technique in confirming individual fish similarity (Debenedetti et al 2014;Bellagamba et al 2015;Abbas et al 2017;Ali et al 2019a;Ali et al 2020;Ibrahim et al 2020). On the nucleotide level, the sequence alignment detected considerable polymorphism at different consensus positions in 28 fish species, the differences had been widely verified (Persis et al 2009).…”

Freshwater fish diversity from Siberut Island, a small island in the western part of Sumatra, Indonesia

“…Many studies have reported that a lack of database species (DNA barcodes) can influence the accuracy of species identification (Deichmann et al 2017). DNA barcoding has effectively differentiated organisms up to the species level (Lakra et al 2016;van der Walt et al 2017;Bingpeng et al 2018;Ali et al 2019).…”

Novel Comprehensive Molecular and Ecological Study Introducing Coastal Mud Shrimp (Solenocera Crassicornis) Recorded at the Gulf of Suez, Egypt

“…DNA barcoding applies universal primers to amplify a targeted genomic region. The efficiency of this method depends on the diverse nature of the targeted region among species [22,23]. In crustaceans, targeting the region of the cytochrome oxidase subunit I (COI) mitochondrial gene using the primer pairs described by Folmer et al [24] was the most efficient.…”