DNA barcoding to characterize biodiversity of freshwater fishes of Egypt

Ali, Fawzia S.; Ismail, Mohamed; Aly, Walid

doi:10.1007/s11033-020-05657-3

Cited by 28 publications

(18 citation statements)

References 42 publications

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“…The average percentage of the GC content of the amplified 650 bp mitochondrial COI region in the studied Siganus species was (46.5%). This percentage was comparable to that reported in other fish species (Ward et al 2005;Wang et al 2017;Ali et al 2020). While, a lower GC content was observed for the D-Loop sequences with an average of 30.6% that was nearly agreed with the result of Martins et al (2003).…”

Section: Discussionsupporting

confidence: 89%

“…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).…”

Section: Discussionmentioning

confidence: 88%

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Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

Ali¹,

Mamoon²,

Abbas³

2021

Egypt. J. of Aquatic Biolo. and Fish.

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Genus Siganus encompasses a diverse group of fishes with a broad geographical distribution. Siganus rivulatus and Siganus luridus are the most common species of such group in Egypt. The current study introduced an inclusive framework on the molecular characterization and phylogenetic relationship of Siganus species worldwide. Partial sequence of Cytochrome oxidase 1 gene (COI) and D-loop control region were used to barcode S. rivulatus and S. luridus which have been collected from the Mediterranean Sea and the Red Sea in Egypt. Further, the newly assembled sequences were combined with 56 COI sequences representing another 17 Siganus species and 35 D-loop sequences for eight Siganus species, available at the international databases, to reconstruct the phylogenetic relationship among this group of fishes. The analyses performed in the current study included calculation of GC%, calculation of the genetic distance and reconstruction of the phylogenetic relationship among different siganus species. Based on COI sequences analysis, the average GC% in the studied Siganus species was 46.6%, the genetic distance among Siganus species ranged between 0.004 to 0.166. Based on the D-loop control region analysis, the average GC% was 30.4%, and the genetic distance ranged between 0.048 to 0.346. The COIbased phylogenetic tree clustered the studied species into two major clades. In the first clade, fusiform species inhabiting schools on the inshore reef flats were included. The second clade included deep-bodied species with brightly colored bodies that live on the reef front and those inhabiting the small schools in mangroves, estuaries. In the second clade, S. argentanus, the only species of family Siganidae is known to have a pelagic pre-juvenile stage, was separated into a non-clade group. Whereas, D-loop-based tree grouped S. argentanus in a separate sub-clade with fusiform species. The proper molecular characterization for S. rivulatus, S. luridus and the updated phylogenetic relationship for worldwide Siganus species, provided in the current study, was considered as a primary key for fisheries and aquaculture management for such species.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 88%

Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

Ali¹,

Mamoon²,

Abbas³

2021

Egypt. J. of Aquatic Biolo. and Fish.

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“…DNA barcoding strategies were recruited successfully for different applications in the Middle East, including both plants and animal subjects [26][27][28]. Recently, selected medicinal plant species in Saudi Arabia and the United Arab Emirates were barcoded [29,30].…”

Section: Discussionmentioning

confidence: 99%

DNA Barcoding of Selected Medicinal Plant Species from Jordan Using matK, rbcL, and rpoC1 Genes

Alkaraki

Aldmoor

Lahham

et al. 2021

International Journal of Biology and Biomedical Engineering

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Medicinal plants play an essential role in preventing and treating several diseases. Classical taxonomic tools generally carry out medicinal plant identification and characterization. Unfortunately, conventional methods need well-trained taxonomists and could give a false identity for closely related species. Jordanian flora is rich in a variety of plant species. The phylogeographic architecture of Jordanian medicinal plant samples was not explored yet. This study aims to recruit DNA barcoding using matK, rbcL, and rpoC1 genes to identify different selected medicinal plants species from Jordan. These are Maerua crassifolia, Ziziphus spina-christi, Balanites aegyptiaca, Senna italica, and Moringa peregrina. Plant samples were collected from the Dead Sea area (Jordan), and three DNA barcode regions were amplified, sequenced, and analyzed using different bioinformatic tools. Twelve sequences were obtained and deposited in Genbank . These sequences showed a very good discrimination capacity with sequences retrieved from related species. The phylogenetic analysis illustrated that DNA barcoding could successfully identify the selected medicinal plant species using different chloroplast genes (rbcL, matK, and rpoC1). Further analysis for other plants species is recommended to explore the genetic relationship and the phylogeographic architecture for Jordanian flora.

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“…One of the tools that have been used in fish identification is DNA barcoding. In the last two decades, this molecular method has been employed to identify many fish species globally (Abdullah and Rehbein, 2017;Ali et al, 2020;Bakar et al, 2018;Bamaniya et al, 2016;Bingpeng et al, 2018;Delrieu-Trottin et al, 2019;Duarte et al, 2017;Fadli et al, 2020;Nugroho et al, 2017;Nurilmala et al, 2016;Steinke et al, 2017;Wang et al, 2018;Wibowo et al, 2018) including grouper fish (Alcantara and Yambot, 2016;Basheer et al, 2017;Fadli et al, 2020;Fadli et al, 2021). This method is relatively new in Indonesia, so its use is still limited.…”

Section: Introductionmentioning

confidence: 99%

Grouper DNA barcoding studies in Indonesia: A short review

Razi

Muchlisin

Maulida

et al. 2021

Depik

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Indonesia is recognized as one of the territories that have the highest reef fish biodiversity in the world. One of the commercially valuable fish in this area is the groupers (locally name "kerapu"). At least 76 grouper species have been reported in Indonesian waters, with three species were categorized into "vulnerable", five species "Data Deficient", and 68 species under the "Least Concern" category based on IUCN classification. The increasing exploitations rate had been reported caused the grouper stocks in Indonesia to decrease and threatened extinction. However, only limited scientific data is available regarding the grouper in Indonesia, including their identification. In most fish landing sites across Indonesia, the groupers are morphologically identified and recorded as "kerapu" to replace their scientific species names. Accurate species identification is essential in designing appropriate and sustainable management of fisheries resources. One of the tools that have been used in fish identification is DNA barcoding. In the last two decades, this molecular method has been applied to identify many fish groups globally, including grouper fish. This study reviewed the DNA barcoding approach in grouper identification in Indonesia based on the available literature.Keywords:DNA barcodingGrouperMolecular TaxonomyFisheriesIndonesia

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DNA barcoding to characterize biodiversity of freshwater fishes of Egypt

Cited by 28 publications

References 42 publications

Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

DNA Barcoding of Selected Medicinal Plant Species from Jordan Using matK, rbcL, and rpoC1 Genes

Grouper DNA barcoding studies in Indonesia: A short review

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