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Special Issue "Genetic Identification of Fishes"

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (5 July 2023) | Viewed by 2777

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Special Issue Editors

Dr. Ravindra Kumar

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Guest Editor

Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
Interests: fishes; genetics; biotechnology; conservation biology

Dr. Ayyathurai Kathirvelpandian
E-Mail Website
Guest Editor

PMFGR Centre, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Post Box No. 1603, Ernakulam North P.O., Kochi 682 018, Kerala, India
Interests: taxonomy; DNA barcoding; mitochondrial DNA; genetic identification; genetic stock structure

Dr. Murali S Kumar
E-Mail Website
Guest Editor

Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
Interests: bioinformatics; fish cell lines; genomics

Special Issue Information

Dear Colleagues,

Fish are one of the most diverse taxon groups with rich variation in distribution. Accurate and timely species identification is vital to assess their distribution, genetic diversity, evaluate species for aquaculture and ornamental fishery, and to plan their sustainable management and conservation strategies. Traditionally, morphometric and meristic studies alone were applied for deciphering information at species level. With the advent of cutting-edge biotechnological tools and NGS data generation as well as analysis, species identification has become an integrated science.

In the Special Issue, we look at original articles and critical reviews covering various aspects of fish genetics, such as integrative taxonomy, sex determination systems, cytogenetics, stock characterization, genome sequencing, aquatic biodiversity and conservation, molecular phylogeny and evolution, etc. We look forward to your contribution. The publications arising in this Special Issue on the genetic identification of fish species will provide much impetus for the research programs in the field of fish taxonomy. To improve our knowledge, contributions from experts in the field are invited.

Dr. Ravindra Kumar
Dr. Ayyathurai Kathirvelpandian
Dr. Murali S Kumar
Guest Editors

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Keywords

cytogenetics
DNA barcoding
fish systematics
mitochondrial/nuclear genes
phylogenetics, whole genome

Published Papers (3 papers)

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Research

Open AccessArticle

A Comprehensive Analysis of Triplophysa labiata (Kessler, 1874) Mitogenome and Its Phylogenetic Implications within the Triplophysa Genus

and

Genes 2023, 14(7), 1356; https://doi.org/10.3390/genes14071356 - 27 Jun 2023

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Abstract

In order to resolve the long-standing controversy surrounding the relationships within the Triplophysa genus, we conducted an extensive analysis of the complete mitogenome of Triplophysa labiata using DNBSEQ short reads. Additionally, we reconstructed the phylogeny of the Nemacheilidae family using mitogenome data. By comparing all available mitogenomes within the Triplophysa genus, we gained valuable insights into its evolutionary history. Our findings revealed that the mitogenome sequence of T. labiata is circular, spanning a length of 16,573 bp. It encompasses 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (D-loop). Among the PCGs, the start codon ATG was commonly observed, except in cox1, while the stop codons TAA/TAG/T were found in all PCGs. Furthermore, purifying selection was evident across all PCGs. Utilizing maximum likelihood (ML) methods, we employed the 13 PCGs and the concatenated nucleotide sequences of 30 Triplophysa mitogenomes to infer the phylogeny. Our results strongly supported the division of the Triplophysa genus into four primary clades. Notably, our study provides the first evidence of the close relationship between T. labiata and T. dorsalis. These findings serve as a significant foundation for future investigations into the mitogenomics and phylogeny of Nemacheilidae fishes, paving the way for further advancements in this field of research. Full article

(This article belongs to the Special Issue Genetic Identification of Fishes)

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Open AccessArticle

High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market

Evanthia Chatzoglou

Nefeli Tsaousi

Apostolos P. Apostolidis

Athanasios Exadactylos

Raphael Sandaltzopoulos

Ioannis A. Giantsis

Georgios A. Gkafas

Emmanouil E. Malandrakis

Joanne Sarantopoulou

Maria Tokamani

George Triantaphyllidis

and

Helen Miliou

Genes 2023, 14(6), 1255; https://doi.org/10.3390/genes14061255 - 12 Jun 2023

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Abstract

The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring. Full article

(This article belongs to the Special Issue Genetic Identification of Fishes)

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Open AccessArticle

Development of Multiplex PCR and Melt–Curve Analysis for the Molecular Identification of Four Species of the Mullidae Family, Available in the Market

Ioannis A. Giantsis

Maria Tokamani

George Triantaphyllidis

Stella Tzatzani

Emmanuella Chatzinikolaou

Athanasios Toros

Anastasia Bouchorikou

Athanasios Exadactylos

Raphael Sandaltzopoulos

and

Apostolos P. Apostolidis

Genes 2023, 14(5), 960; https://doi.org/10.3390/genes14050960 - 23 Apr 2023

Viewed by 798

Abstract

The authentication of food products and the verification of their identity are of major importance for consumers. Food fraud through mislabeling is an illegal practice consisting of the substitution of an expensive food product by a relatively cheaper one, misleading false labelling of their origin and adulteration in processed or frozen products. This issue is particularly of high importance concerning fish and seafood, which are easily adulterated primarily due to difficult morphological identification. Fish species of the Mullidae family are considered among the most high-valued seafood products traded in Greece and Eastern Mediterranean in general, in terms of the price and demand. Specifically, the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus) are both indigenous in the Aegean (FAO Division 37.3.1) and the Ionian (FAO Division 37.2.2) Seas, with high levels of consumers’ preferences. However, they could be easily adulterated or misidentified by the invasive Aegean Sea Lessepsian migrator goldband goatfish (Upeneus moluccensis) as well as by the imported West African goatfish (Pseudupeneus prayensis). Keeping this in mind, we designed two novel, time-saving and easy-to-apply multiplex PCR assays and one multiple Melt–Curve analysis real-time PCR for the identification of these four species. These methodologies are based on species-specific primers targeting single nucleotide polymorphisms (SNPs) detected via sequencing analysis of the mitochondrial cytochrome C oxidase subunit I (CO1) and of the cytochrome b (CYTB) genes in newly collected individuals, with additional comparison with congeneric and conspecific haplotypes obtained from the GenBank database. Both methodologies, targeting CO1 or CYTB, utilize one common and four diagnostic primers, producing amplicons of different length that are easily and reliably separated on agarose gel electrophoresis, yielding a single clear band of diagnostic size for each species or a certain Melt–Curve profile. The applicability of this cost-effective and fast methodology was tested in 328 collected specimens, including 10 cooked samples obtained from restaurants. In the vast majority (327 out of the 328) of the specimens tested, one single band was produced, in agreement with the expected products with a single exception a M. barbatus sample that was identified as M. surmuletus, the identity of which was confirmed using sequencing, indicating erroneous morphological identification. The developed methodologies are expected to contribute to the detection of commercial fraud in fish authentication. Full article

(This article belongs to the Special Issue Genetic Identification of Fishes)

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