A case study for application of DNA barcoding in identifying species and genetic diversity of fish from the Suez city market, Egypt

Abstract

The Red Sea is one of the key areas of biodiversity in the world. It is a hotspot for speciation and biological invasions. In the current work, a pilot, random sampling trial was carried out to characterize some species in the landings reaching the fish market in Suez city, which is one of the largest fish markets in the Northern Red Sea. Samples of different fish species were subjected to the standard procedures of DNA barcoding, applying the sequencing of the cytochrome oxidase subunit 1 mitochondrial gene (COI). DNA barcoding could successfully identify all the targeted fishes to the species-level (>98%). The results exhibited a taxonomically-versatile commercial trends in this market, being the collected species belonging to 7 different fish families and 3 orders. These species were Coris aygula, Papilloculiceps longiceps, Priacanthus sagittarious, Gerres longirostris, Alepes djedaba, Psettodes erumei Cheilinus trilobatus, Calotomus viridescens, and Pardachirus marmoratus. Haplotype diversities in the first six species were moderate. However, their nucleotide diversities were low. This may have resulted from fishing from bottlenecked populations, or from areas that do not hinder the genetic flow. Also, possible cryptic speciation could be detected in P. sagittarius, P. erumei and G. longirostris. Applying the DNA barcoding for species identification in Suez city fish market could then detect various aspects of fish species diversity. More works using the applied analyses can be strongly recommended to aid proper conservation and management of economic fisheries in the Red Sea.

Molecular barcoding of marine ornamental fish from the southern coast of West Java validates conventional identification

“…We determined the taxonomic status of each morphotype based on the sequence identity or similarity value of 95%. The present study chose that value based on a consideration that species could have other sequences divergences within species [6] and geographic locality between the current samples and the references species [17] available in the barcode library (GenBank and Boldsystems). The Kimura 2-parameter genetic distance of 0.05 was selected as additional data for species-level identification.…”

“…The assignment to the species level is defined according to the barcoding gap used in species determination is 5% genetic divergence, which means 95% genetic similarity between query samples with conspecific references. Several studies reported that 95% could be used for species-level barcoding [17,[22][23]. The use of 3% to 5% genetic divergences must be added by other data [31], including geographic localities [32].…”

“…Combining both molecular and conventional identification for WJM5, we finally decided that WJM5 was referred to as L. decussatus. The argument was that samples of single species collected from different localities could have a relatively low genetic identity and high genetic distance to their conspecific references in barcode libraries [6,17,[21][22][23][31][32].…”

“…Other researchers used a minimum of 98% sequence homology as species threshold. However, low genetic homology (below 95%) was observed when the reference species came from different localities [17], while other studies used 99% homology for species determination [18]. At the same time, many studies also reported that intraspecific genetic distances in fish were wildly variable among species ranging from 0.0 to higher than 0.05 [19,20,21,22,23].…”

Status, Trends, and Potentials of Turtle Conservation in Bali: A Mini Review

“…A research conducted by Abdalwahhab et al, (2020) revealed that DNA Barcoding was successfully carried out to identify 7 different fish families and 3 orders, by applying the sequencing of the cytochrome oxidase subunit 1 mitochondrial gene (COI) in the Northern Red Sea. This study revealed a 98% success of species identification implementing DNA Barcoding.…”