Studies on the Origin, Evolution, Genetic Diversity and Adaptive Evolution of Fish

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

Deadline for manuscript submissions: closed (20 January 2025) | Viewed by 893

Special Issue Editor


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Guest Editor
Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
Interests: aquatic animals; genetic diversity; adaptive evolution; genomics; transcriptomics; multiomics; functional genes

Special Issue Information

Dear Colleagues,

The study of the genomics and evolution of fish aims to foster a deep understanding of the genetic information, genomic structure and evolutionary process of fish in order to reveal their adaptation and evolutionary mechanisms in different environments. The journal of Genes has been published since 2010 and contains many articles related to genomics and evolution. This Special Issue’s current research topics of interest encourage original research papers, reviews or other recognized article types on subjects ranging from freshwater fish to seawater fish, including but not limited to the following: (1) Genome structure and function: studying the composition, structure and function of fish genomes, including features of gene localization, genome size, gene family, gene expression regulation, etc. (2) Evolutionary history and phylogeny: exploring the evolutionary history, kinship and phylogenetic relationships of different fish species and revealing the evolutionary relationships among fish species by comparing their genome sequences and genetic variation. (3) Environmental adaptive evolution: studying the adaptation and evolutionary processes of fish under different environmental conditions, including their adaptive evolution due to environmental factors such as temperature, ammonia nitrogen, dissolved oxygen, heavy metals and organic pollutants in the water. (4) Population genetics: the genetic structure, gene flow and genetic diversity of fish populations are studied through population genetics to reveal the patterns of population evolution and genetic variation. (5) Transcriptomics and functional genomics: undertaking the study of the overall composition and regulation of transcripts (mRNA) in fish genomes; the study of gene regulatory networks, signaling pathways or new genes and functional genes in fish under different physiological states and environmental conditions; the study of functional genes, regulatory elements and functional regions in fish genomes and the exploration of their roles and regulatory mechanisms in biological processes.

Dr. Xin Zhang
Guest Editor

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Keywords

  • aquatic animals
  • genetic diversity
  • adaptive evolution
  • genomics
  • transcriptomics
  • multiomics
  • functional genes

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Published Papers (1 paper)

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Research

14 pages, 1958 KiB  
Article
Complete Mitochondrial Genome of King Threadfin, Polydactylus macrochir (Günther, 1867): Genome Characterization and Phylogenetic Analysis
by Jiufu Wen
Genes 2025, 16(1), 88; https://doi.org/10.3390/genes16010088 - 15 Jan 2025
Viewed by 429
Abstract
Background: Polydactylus macrochir (Günther; 1867) is a member of the family Polynemidae. The placement of Polynemidae among teleosts has varied over the years. Methods: Therefore, in this study, we sequenced the complete mitochondrial genome of P. macrochir, analyzed the characterization of the [...] Read more.
Background: Polydactylus macrochir (Günther; 1867) is a member of the family Polynemidae. The placement of Polynemidae among teleosts has varied over the years. Methods: Therefore, in this study, we sequenced the complete mitochondrial genome of P. macrochir, analyzed the characterization of the mitochondrial genome, and investigated the phylogenetic relationships of Polynemidae. Results: The length of the P. macrochir mitogenome was 16,738 bp, with a typical order. Nucleotide composition analysis showed that the P. macrochir mitogenome was AT-biased (54.15%), and the PCGs tended to use A and C rather than T and G at the third codon. All the PCGs started with the regular codon ATG, except for cox1, which started with GTG. The termination codon varied across the PCGs. It was shown that the ka/ks ratios of all the PCGs were less than one. Phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, indicated that eight threadfins formed a well-supported monophyletic cluster. Polynemidae and Sphyraenidae clustered together as a monophyletic group. According to TimeTree analyses, the most recent common ancestor (MRCA) of Polynemidae was traced back to about 52.81 million years ago (MYA), while six species within Polynemidae diverged from 11.70 MYA to 20.05 MYA. Conclusions: The present study provides valuable mitochondrial information for the classification of P. macrochir and new insights into the phylogenetic relationships of Polynemidae. Full article
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