Fish DNA Barcoding

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (10 February 2025) | Viewed by 1054

Special Issue Editors


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Guest Editor
Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, China
Interests: fish DNA barcoding; population genomics; phylogeography; conservation genetics; fish resource assessment

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Guest Editor
College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
Interests: fish eggs and larvae; spawning ground protection; DNA barcoding; fishery resource; fishery ecology

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Guest Editor
Department of Biological Sciences, School of Life Sciences, Guizhou Normal University, Guiyang, China
Interests: freshwater fish taxonomy; phylogeny; phylogeography; DNA barcoding; population genetics; speciation

Special Issue Information

Dear Colleagues,

DNA barcoding, using a standardized molecular tag located in the mitochondrial cytochrome c oxidase I gene (COI), has become a dominant approach for the rapid and accurate discrimination of animal species including fish taxa. This technique enables accurate species delimitation and flags the likely existence of morphologically cryptic species. In addition, DNA barcoding also has numerous other applications, such as the identification of fish eggs and larvae, the tracking of exotic invasive species, the enhancement of wildlife protection, and the protection of consumers from market fraud.

The purpose of this Special Issue is to collect manuscripts on the analysis and research of fish DNA barcoding, including but not limited to the following aspects: (1) DNA barcoding reference databases of freshwater and marine fish species; (2) the detection of cryptic diversity; (3) analyzing relationships among closely related species complex; (4) the application of DNA barcoding on fish eggs and larvae; and (5) potential factors that influence the performance of DNA barcoding.

Dr. Weitao Chen
Dr. Gang Hou
Prof. Dr. Renyi Zhang
Guest Editors

Manuscript Submission Information

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Keywords

  • DNA barcoding
  • fish taxa
  • DNA barcoding database
  • cryptic diversity
  • closely related species complex
  • fish diversity
  • fish eggs and larvae

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Published Papers (2 papers)

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Research

24 pages, 2560 KiB  
Article
Comparison of Bioinformatic Pipelines for eDNA Metabarcoding Data Analysis of Fish Populations
by Romulo A. dos Santos and Petr Blabolil
Fishes 2025, 10(5), 214; https://doi.org/10.3390/fishes10050214 - 6 May 2025
Viewed by 313
Abstract
Environmental DNA (eDNA) metabarcoding has gained popularity as a biomonitoring tool, leading to the emergence of various bioinformatic pipelines. However, comparisons are essential to assessing the reliability and similarity of results. In this study, we compared five bioinformatic pipelines (Anacapa, Barque, metaBEAT, MiFish, [...] Read more.
Environmental DNA (eDNA) metabarcoding has gained popularity as a biomonitoring tool, leading to the emergence of various bioinformatic pipelines. However, comparisons are essential to assessing the reliability and similarity of results. In this study, we compared five bioinformatic pipelines (Anacapa, Barque, metaBEAT, MiFish, and SEQme) using samples collected from three reservoirs in the Czech Republic during the autumn and summer seasons. Negative and positive controls were used to monitor potential contamination during sample processing. eDNA was amplified, targeting the 12S fish rRNA gene, sequenced, and analyzed with the selected bioinformatic pipelines. Statistical analyses were applied to assess result similarity, including the number of detected taxa, read count, alpha and beta diversities, and the Mantel test. Our findings showed consistent taxa detection across pipelines, with increased sensitivity compared to traditional methods. Alpha and beta diversities and the Mantel test also exhibited significant similarities between pipelines. Divergences were observed based on the reservoir, season, and their interaction. In conclusion, the choice of bioinformatic pipeline did not significantly affect metabarcoding outcomes or their ecological interpretation. Full article
(This article belongs to the Special Issue Fish DNA Barcoding)
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13 pages, 1277 KiB  
Article
DNA Barcoding of the Genus Discogobio (Teleostei, Cyprinidae) in China
by Hongmei Li, Huan Cheng, Renrong Huang, Zhenya Qiu and Renyi Zhang
Fishes 2025, 10(4), 157; https://doi.org/10.3390/fishes10040157 - 3 Apr 2025
Viewed by 326
Abstract
Discogobio is a genus of small, economically important freshwater fishes that are widely distributed in Southwestern China. The species of the genus are morphologically very similar, which makes their taxonomic identification quite challenging. DNA barcoding technology can identify species at the molecular level, [...] Read more.
Discogobio is a genus of small, economically important freshwater fishes that are widely distributed in Southwestern China. The species of the genus are morphologically very similar, which makes their taxonomic identification quite challenging. DNA barcoding technology can identify species at the molecular level, thus overcoming the limitations of morphological classification. In this study, we collected 16 morphological species of Discogobio from China, analyzed the mitochondrial cytochrome oxidase I subunit (COI) gene sequences of 206 samples, and applied DNA barcoding to identify the species. The COI amplicon was 651 bp in length, and the mean base contents were: (T) 28.83%, (C) 27.63%, (A) 25.97%, (G) 17.57%. The AT content (54.8%) was higher, and the base composition was biased. The intraspecific differences in the genus Discogobio were not significant, and the genetic distances were all less than 2%. The average interspecific genetic distances (3.94%) were about 18.8 times the average intraspecific genetic distances (0.21%), suggesting that there are barcode gaps among the species of the genus Discogobio. Five different species definition methods, Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), Bayesian Poisson Tree Process (bPTP), Generalized Mixed Yule Combination (GMYC), and Refined Single Linkage (RESL), were used to infer molecular operational taxonomic units (MOTU). The number of MOTUs ranged from 9 to 18. Phylogenetic analysis based on COI gene haplotypes showed that most species formed well-evolved branches on the phylogenetic tree, and the clustering among species was obvious without mixing. The results of this study provide reliable DNA barcoding information for species identification within the genus Discogobio, which is of great significance for taxonomic identification. Full article
(This article belongs to the Special Issue Fish DNA Barcoding)
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