Application of DNA barcoding for controlling of the species from Octopus genus

Debenedetti, Francesco; Dalmasso, Alessandra; Bottero, Maria Teresa; Gilli, Maurizio; Gili, Stefano; Tepedino, Valentina; Civera, Tiziana

doi:10.4081/ijfs.2014.4521

Cited by 6 publications

(3 citation statements)

References 17 publications

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“…Application of genomics is highly informative in differentiating individuals and varieties (Singh et al 2014). Identification of percentage identity or similarity from 99-100% with the known ones in the Gen-Bank databases was recorded across the fish species and this demonstrates the effectiveness of this genomics tool in ascertaining individual fish relatedness as previously reported (Debenedetti et al 2014;Bellagamba et al 2015;Abbas et al 2017).…”

Section: Discussionsupporting

confidence: 58%

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Ude

Igwe

Brown

et al. 2020

Conservation Genet Resour

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Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

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Section: Discussionsupporting

confidence: 58%

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Ude

Igwe

Brown

et al. 2020

Conservation Genet Resour

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“…In contrast, O. chierchiae presents a particular morphology among the species evaluated in our study (presence of continuous stripes along mantle, head, and arms and absence of ocelli), while O. bimaculatus is characterized by a pair of ocelli and no stripes; in fact, the high morphological similarity between this species and O. bimaculoides reaches a point where these two species are easily confused (Jereb et al, 2016). Debenedetti et al (2014) detected that the genotypic variability is not correlated with the morphological differences among species of the genus Octopus , which is concordant with what we found in regard to these three species. In addition, O. chierchiae and O bimaculoides are holobenthic octopuses that produce large eggs and hatchlings with direct development (Rodaniche, 1984; Ibarra-García et al, 2018), different from O. bimaculatus , which is merobenthic and produces numerous small eggs that hatch into planktonic paralarvae (Jereb et al, 2016).…”

Section: Discussionsupporting

confidence: 90%

Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses

Díaz‐Santana‐Iturrios

Salinas-Zavala²,

Rodríguez

et al. 2019

PeerJ

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Species of the genus Octopus from the northeastern Pacific are ecologically and economically important; however, their taxonomy is confusing and has not been comprehensively assessed. In this study, we performed a taxonomic evaluation of these species considering the morphological characteristics of the original descriptions, a molecular analysis of partial COI-gene sequences, and a traditional morphometry analysis of nine body measurements. Several interesting findings were obtained with our results: for instance, we updated the diagnoses of some species by including characters such as the number of lamellae per demibranch and the presence of chromatophores in the visceral sac; we deposited partial COI-gene sequences of species that had not been incorporated into the GenBank repository; and according to the morphometric analysis, we confirmed that the lengths of arms I–IV are relevant to discriminate the species under study. The taxa evaluated were morphologically, molecularly and morphometrically well-delimited; however, features such as funnel organ shape and arm length proportions in regard to dorsal mantle length are either not included in the diagnosis of the genus Octopus or overlap with other genera. Hence, this information, combined with the results obtained from the molecular analysis, supports the generic re-assignation of two of the species evaluated.

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“…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%

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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Application of DNA barcoding for controlling of the species from Octopus genus

Cited by 6 publications

References 17 publications

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses

Mitochondrial-Based Phylogenetic Inference of Worldwide Species of Genus Siganus

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