Molecular Genetics and Genomics of Marine Fishes

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

Deadline for manuscript submissions: closed (15 November 2025) | Viewed by 2701

Special Issue Editors


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Guest Editor
Fishery College, Zhejiang Ocean University, Zhoushan, China
Interests: marine fish; population genetics; genomics; phylogenetics

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Guest Editor
Fishery College, Zhejiang Ocean University, Zhoushan, China
Interests: population genetics; genomics; phylogenetics; transcriptomics; evolution
Special Issues, Collections and Topics in MDPI journals
Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
Interests: marine fish; population genetics; marine biodiversity; fisheries management
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
Interests: fishery stock enhancement; marine fish diversity; population genetics; adaptive evolution

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Guest Editor
Fishery College, Zhejiang Ocean University, Zhoushan, China
Interests: marine fish; molecular genetics; genomics; adaptive evolution; mitochondrial DNA

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Guest Editor Assistant
Fishery College, Zhejiang Ocean University, Zhoushan, China
Interests: molecular genetics; genomics; ecological adaptation; molecular biology

Special Issue Information

Dear Colleagues,

The living fish species (including bony fish, cartilaginous fish, and jawless fish) encompass the great majority of non-tetrapod vertebrates, and serve as an important clade of highly commercial, ecological, evolutionary, and conservation significance. Marine fishes play crucial ecological roles in marine ecosystems, contributing to high levels of biodiversity; they are also a major source of protein for human populations and support economies and important social structures in many nations. However, overfishing, global warming, and habitat loss contribute drastically to large-scale population declines of marine fish species. It is therefore imperative to understand these species for sound management and conservation of marine fish resources. Genetic and genomic investigations can largely deepen our knowledge on species diversity, adaptation, and evolution, thus facilitating effective fishery management and biodiversity conservation. However, limited genetic and genomic resources of marine fish species have been reported until now, so I am pleased to invite you to contribute to the Special Issue “Molecular Genetics and Genomics of Marine Fishes” in the Fishes journal.

Dr. Shengyong Xu
Prof. Dr. Zhiqiang Han
Dr. Yuan Li
Dr. Binbin Shan
Dr. Tianyan Yang
Guest Editors

Dr. Shaolei Sun
Guest Editor Assistant

Manuscript Submission Information

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Keywords

  • marine fish
  • genome assembly
  • mitochondrial DNA
  • population genetics/genomics
  • phylogenetics/phylogenomics
  • genetic diversity
  • genetic variation
  • adaptive evolution
  • DNA barcoding
  • fisheries management

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Published Papers (3 papers)

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Research

18 pages, 2640 KB  
Article
Full-Length Transcriptome Characterization and Molecular Analysis of the Longfin Batfish (Platax teira)
by Lingeng Lv, Baosuo Liu, Huayang Guo, Kecheng Zhu, Nan Zhang, Jinhui Sun and Dianchang Zhang
Fishes 2025, 10(11), 575; https://doi.org/10.3390/fishes10110575 - 8 Nov 2025
Viewed by 315
Abstract
Platax teira is a marine fish species with both ornamental and economic value, but it faces challenges in aquaculture due to environmental stress and disease. Genetic research on P. teira has been limited due to the limitations of the partially incomplete reference genome [...] Read more.
Platax teira is a marine fish species with both ornamental and economic value, but it faces challenges in aquaculture due to environmental stress and disease. Genetic research on P. teira has been limited due to the limitations of the partially incomplete reference genome and the lack of a complete transcriptome. In this study, we utilized PacBio SMRT sequencing to generate a full-length transcriptome for P. teira, obtaining 39,770 isoforms, including 32,265 known gene-related transcripts and 4730 novel transcripts from 3455 new genes. All novel genes were annotated, and enrichment analysis revealed significant associations between immune-related pathways, such as cAMP, MAPK, PI3K-Akt, and Wnt. We also identified 14,398 alternative splicing events, 2754 alternative polyadenylation events, 42,250 SSRs, 1569 transcription factors, and 2067 long non-coding RNAs. Additionally, protein–protein interaction (PPI) analysis of immune-related pathways predicted chemokines as key immune factors among novel genes. Domain prediction analysis highlighted the diverse functional potential of immune factors such as NLRC3, tyrosine kinase 2, and A2M in different alternative splicing events. Overall, the characterization of the full-length transcriptome dataset of P. teira lays the foundation for further studies on its genetic analysis and immune regulation. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Marine Fishes)
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20 pages, 4014 KB  
Article
Development of a Multiplex Polymerase Chain Reaction Method for the Simultaneous Identification of Four Species of Genus Lagocephalus (Chordata: Vertebrata)
by Hye Min Lee, Chun Mae Dong, Mi Nan Lee, Eun Soo Noh, Jung-Ha Kang, Jong-Myoung Kim, Gun-Do Kim and Eun-Mi Kim
Fishes 2025, 10(10), 501; https://doi.org/10.3390/fishes10100501 - 7 Oct 2025
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Abstract
Pufferfish are an economically important food in Asia despite the potential risk of tetrodotoxin (TTX) poisoning. To promote food safety by ensuring the correct identification of pufferfish species, we developed common and species-specific primer sets for four Lagocephalus species (Lagocephalus spadiceus, [...] Read more.
Pufferfish are an economically important food in Asia despite the potential risk of tetrodotoxin (TTX) poisoning. To promote food safety by ensuring the correct identification of pufferfish species, we developed common and species-specific primer sets for four Lagocephalus species (Lagocephalus spadiceus, Lagocephalus cheesemanii, Lagocephalus wheeleri, and Lagocephalus inermis) based on analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) in various pufferfish species commonly distributed and/or legally sold in Korea. The common primers were developed based on complete sequence data acquired from GenBank. The total length of fragments amplified by the common primer set was 1280 bp. Then, species-specific multiplex polymerase chain reaction (PCR) amplification was conducted for the four target species, obtaining 980 bp for L. spadiceus, 859 bp for L. cheesemanii, 672 bp for L. wheeleri, and 563 bp for L. inermis. Multiplex PCR is an important tool for the simple, rapid, accurate, and simultaneous identification of target species. The newly developed primer sets will contribute to reducing the occurrence of TTX poisoning and protect consumer rights by eradicating the mislabeling or fraudulent use of pufferfish products. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Marine Fishes)
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14 pages, 2012 KB  
Article
Genetic Diversity and Population Structure of Commercial Eel Conger myriaster (Anguilliformes: Congridae) Along the Coasts of China Based on Complete Mitochondrial Cyt b Sequences
by Peiyi Xiao and Tianyan Yang
Fishes 2025, 10(2), 41; https://doi.org/10.3390/fishes10020041 - 23 Jan 2025
Cited by 1 | Viewed by 1288
Abstract
To better understand the population genetic structure and molecular biological background of Conger myriaster, an economically important marine fish, a total of 217 complete mitochondrial cytochrome b (Cyt b) gene sequences with a length of 1142 bp were obtained to [...] Read more.
To better understand the population genetic structure and molecular biological background of Conger myriaster, an economically important marine fish, a total of 217 complete mitochondrial cytochrome b (Cyt b) gene sequences with a length of 1142 bp were obtained to assess the genetic diversity, population differentiation, and demographic history of seven populations along the coastal waters of China. The analysis of population genetic diversity showed a high level of haplotype diversity and a low level of nucleotide diversity. The analysis of molecular variance (AMOVA) and the genetic differentiation coefficient (FST) showed that most of the variation came from within populations, and the geographic distribution of haplotypes revealed non-significant genetic differentiation among populations. Tracing the population dynamic history, the results of the neutrality test and mismatch analysis suggested that the populations of C. myriaster in coastal China seas had experienced demographic expansion, and the expansion time can be traced back to the middle Pleistocene period. These results provide supplemental information for the sustainable utilization of fishery resources of this species. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Marine Fishes)
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