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Animals
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Omics in Economic Aquatic Animals
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Omics in Economic Aquatic Animals

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Welfare".

Deadline for manuscript submissions: 1 November 2025 | Viewed by 9299

Special Issue Editor

Dr. Changxu Tian

E-Mail Website
Guest Editor
Fisheries College, Guangdong Ocean University, Zhanjiang 524091, China
Interests: fish; omics; breeding; genetics; environmental stressors; sex determination; reproductive biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquatic animals provide a large amount of food biomass and high-quality nutrients, making it necessary to conduct genetic improvement research on more aquatic animals. Omics research (genomics, transcriptomics, proteomics, and metabolomics) has focused on various aquaculture research areas, targeting different aspects, including physiology and endocrinology, genetic breeding, nutrition, environmental stress response, disease, and health management. These technologies are increasingly used to study economic aquatic animals. We are particularly interested in integrating a wide range of omics data to carefully analyze and interpret the genetic mechanisms of important economic traits in economic aquatic animals. The scope of this Special Issue of Animals covers the latest advances in the study of omics in economic aquatic animals. Submissions may include original reports, reviews, perspectives, and methodology articles.

Dr. Changxu Tian
Guest Editor

Manuscript Submission Information

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Keywords

  • aquatic animals
  • economic traits
  • omics
  • next-generation sequencing

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Published Papers (7 papers)

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Research

15 pages, 1870 KiB  
Article
Transcriptome Analyses Reveal the Molecular Response of Juvenile Greater Amberjack (Seriola dumerili) to Marine Heatwaves
by Yali Tian, Liancheng Li, Hongzhao Long, Dongying Zhang, Chen Wang, Ruijuan Hao, Hang Li, Xiaoying Ru, Qiuxia Deng, Qin Hu, Yang Huang and Chunhua Zhu
Animals 2025, 15(13), 1871; https://doi.org/10.3390/ani15131871 - 24 Jun 2025
Viewed by 410
Abstract
Marine heatwaves (MHWs) have recently become more frequent, intense, and prolonged, posing significant threats to marine life and fisheries. In this study, transcriptomic analysis was employed to investigate the genes and pathways in Seriola dumerili that respond to MHW-induced stress at 28 °C [...] Read more.
Marine heatwaves (MHWs) have recently become more frequent, intense, and prolonged, posing significant threats to marine life and fisheries. In this study, transcriptomic analysis was employed to investigate the genes and pathways in Seriola dumerili that respond to MHW-induced stress at 28 °C (T28) and 32 °C (T32), using 24 °C (T24) as the control. Transcriptome sequencing revealed that 17 differentially expressed genes (DEGs) belonging to the heat shock protein (HSP) families—HSP30, HSP40, HSP70, and HSP90—were significantly upregulated under short-lasting MHW stress in the T24-4d vs. T32-4d comparison. Additionally, genes related to oxidative stress (e.g., protein disulfide isomerase family A member 6 [pdia6]), immune responses (e.g., interferon regulatory factor 5 [irf5]), and energy metabolism (e.g., hexokinase-1 [hk1]) were also identified. Enrichment analysis of DEGs in the T24-4d vs. T32-4d group revealed that S. dumerili exhibited adaptive responses to MHWs through the upregulation of HSPs and the activation of antioxidant, energy metabolism, and immune response pathways. However, in the T24-13d vs. T32-13d group, DEGs associated with these pathways were either not significantly expressed or were downregulated. These findings indicate that S. dumerili is unable to sustain its adaptive responses under repeated, intense MHW exposure, resulting in the disorder of its antioxidant defense system, immune suppression, and metabolic dysfunction. This study provides valuable insights into the molecular responses of S. dumerili to MHWs and supports the selection for thermal resistance in this species. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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25 pages, 3875 KiB  
Article
Characteristics and Functions of Different Intestinal Segments in Juvenile Greater Amberjack (Seriola dumerili)
by Kunfeng Zhu, Mouyan Jiang, Mengyao Yan, Yang Huang, Tonglin Yang and Chunhua Zhu
Animals 2025, 15(11), 1672; https://doi.org/10.3390/ani15111672 - 5 Jun 2025
Viewed by 509
Abstract
The greater amberjack (Seriola dumerili), a key species in marine aquaculture, relies heavily on its intestine for nutrient absorption and immune function. However, the structural and functional specialization of its intestinal segments remains poorly understood. In this study, we divided the [...] Read more.
The greater amberjack (Seriola dumerili), a key species in marine aquaculture, relies heavily on its intestine for nutrient absorption and immune function. However, the structural and functional specialization of its intestinal segments remains poorly understood. In this study, we divided the intestine of S. dumerili into foregut, midgut, and hindgut, and conducted a multi-omics analysis integrating histological staining (H&E/AB-PAS), digestive enzyme assays, transcriptome sequencing, and 16S rRNA microbiota profiling to characterize structural, functional, molecular, and microbial differences across intestinal segments. Histological examinations revealed that brush border microvillus length, muscle layer thickness, and folding height were significantly greater in the foregut and hindgut compared to the midgut, while mucus and goblet cell density was higher in the foregut and midgut. Digestive enzyme assays showed that lipase activity peaked in the foregut, α-amylase in the midgut, and protease in the midgut and hindgut. Alkaline phosphatase (AKP) and acid phosphatase (ACP) activities were highest in the foregut and midgut. Immune-related enzyme activities (SOD (Superoxide dismutase), GSH-Px (Glutathione peroxidase), T-AOC (Total Antioxidant Capacity)) were elevated and MDA levels were lower in the midgut, indicating its role as the primary immune site. Transcriptome analysis identified segment-specific expression of nutrient transporters, such as slc6a19b (hindgut, protein), apoa1b (foregut, lipid), and slc37a4 (midgut, carbohydrate). Microbiome analysis revealed Ruminococcus dominance in the foregut (lipid digestion) and Prevotella, Bifidobacterium, and Lactobacillus enrichment in the midgut (carbohydrate metabolism and immunity). These findings highlight functional zonation in S. dumerili: the foregut specializes in lipid digestion, the midgut in carbohydrate metabolism and immunity, and the hindgut in protein digestion. This study provides foundational insights for optimizing aquaculture practices and advancing research in nutrition, immunology, and disease modeling in S. dumerili. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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20 pages, 4388 KiB  
Article
Comparative Transcriptomics and Intestinal Microbiome Analysis Provide Insights into the Semi-Terrestrial Adaptation of Helice tientsinensis
by Zhengfei Wang, Lijie Cui, Xinyu Wang, Chenchen Shen, Yan Wang, Weijie Jiang and Yue Gu
Animals 2025, 15(9), 1244; https://doi.org/10.3390/ani15091244 - 28 Apr 2025
Viewed by 463
Abstract
Helice tientsinensis, a Grapsidae family member, can adapt to terrestrial and semi-terrestrial environments. This study used transcriptomic and microbiome analyses to explore its adaptation mechanisms. Transcriptome analysis showed gene changes related to cytoskeleton–motor, water–osmotic pressure, and energy metabolism. For example, DST was [...] Read more.
Helice tientsinensis, a Grapsidae family member, can adapt to terrestrial and semi-terrestrial environments. This study used transcriptomic and microbiome analyses to explore its adaptation mechanisms. Transcriptome analysis showed gene changes related to cytoskeleton–motor, water–osmotic pressure, and energy metabolism. For example, DST was upregulated in the aquatic environment compared to the semi-terrestrial one, and SPAST was downregulated in some groups. ATP2A and SLC6A3 were upregulated with osmotic regulation, and IDH3 was upregulated when comparing the aquatic and semi-terrestrial habitats; at the same time, many energy-related genes were downregulated between the terrestrial and semi-terrestrial habitats. Regarding the gut microbiota, no significant differences in alpha diversity were found between habitats, but there were differences at the genus level. Pseudomonas and Malaciobacter were more abundant in the aquatic habitat, and Dietzia in the semi-terrestrial one. These results provide insights into H. tientsinensis’ terrestrial adaptation, benefiting crustacean evolution study and aquaculture. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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14 pages, 1096 KiB  
Article
Whole-Genome Sequencing of Hexagrammos otakii Provides Insights into Its Genomic Characteristics and Population Dynamics
by Dong Liu, Xiaolong Wang, Jifa Lü, Yijing Zhu, Yuxia Jian, Xue Wang, Fengxiang Gao, Li Li and Fawen Hu
Animals 2025, 15(6), 782; https://doi.org/10.3390/ani15060782 - 10 Mar 2025
Viewed by 628
Abstract
Hexagrammos otakii, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In [...] Read more.
Hexagrammos otakii, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70–15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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29 pages, 4666 KiB  
Article
Transcriptional Rearrangements Associated with Thermal Stress and Preadaptation in Baikal Whitefish (Coregonus baicalensis)
by Yulia P. Sapozhnikova, Anastasiya G. Koroleva, Tuyana V. Sidorova, Sergey A. Potapov, Alexander A. Epifantsev, Evgenia A. Vakhteeva, Lyubov I. Tolstikova, Olga Yu. Glyzina, Vera M. Yakhnenko, Valeria M. Cherezova and Lyubov V. Sukhanova
Animals 2024, 14(21), 3077; https://doi.org/10.3390/ani14213077 - 25 Oct 2024
Cited by 1 | Viewed by 1751
Abstract
In this work, we describe the transcriptional profiles of preadapted and non-adapted one-month-old juvenile Baikal whitefish after heat shock exposure. Preadapted fish were exposed to a repeated thermal rise of 6 °C above the control temperature every three days throughout their embryonic development. [...] Read more.
In this work, we describe the transcriptional profiles of preadapted and non-adapted one-month-old juvenile Baikal whitefish after heat shock exposure. Preadapted fish were exposed to a repeated thermal rise of 6 °C above the control temperature every three days throughout their embryonic development. One month after hatching, preadapted and non-adapted larvae were either kept at control temperatures (12 °C) or exposed to an acute thermal stress (TS) of 12 °C above the control temperature. In response to this acute stress, an increase in HSP gene expression (HSP-30, HSP-40, HSP-47, HSP-70, and HSP-90) and TRIM16 was detected, independent of preadaptation. The expression levels of genes responsible for the response to oxygen levels, growth factors and the immune response, HBA, HBB, Myosin VI, Myosin VII, MHC, Plumieribetin, TnI, CYP450, and LDB3 were higher in individuals that had previously undergone adaptation. Genes responsible for the regulation of metabolism, MtCK, aFGF, ARF, CRYGB, and D-DT, however, increased their activity in non-adapted individuals. This information on transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to their environment. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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18 pages, 2396 KiB  
Article
Acclimation during Embryogenesis Remodulates Telomerase Activity and Gene Expression in Baikal Whitefish Larvae, Mitigating the Effects of Acute Temperature Stress
by Anastasiya G. Koroleva, Eugenia A. Vakhteeva, Alexander A. Epifantsev, Lyubov V. Sukhanova, Vera M. Yakhnenko, Olga Yu. Glyzina, Lyubov I. Tolstikova, Valeria M. Cherezova, Tuyana V. Sidorova, Sergey A. Potapov, Sergey V. Kirilchik and Yulia P. Sapozhnikova
Animals 2024, 14(19), 2839; https://doi.org/10.3390/ani14192839 - 2 Oct 2024
Cited by 2 | Viewed by 1634
Abstract
Acclimation through the hormesis effect increases the plasticity of organisms, which has been shown for many ectothermic animals, including fish. We investigated the effect of temperature acclimation in Baikal whitefish Coregonus baicalensis (Dybowski, 1874). Telomere length, telomerase activity, and the expression of genes, [...] Read more.
Acclimation through the hormesis effect increases the plasticity of organisms, which has been shown for many ectothermic animals, including fish. We investigated the effect of temperature acclimation in Baikal whitefish Coregonus baicalensis (Dybowski, 1874). Telomere length, telomerase activity, and the expression of genes, whose products are involved in the regulation of telomere length and defense against reactive oxygen species, were selected to assess the state of the larvae. Acclimation and acute temperature stress (+12 °C) had no effect on telomere length, but altered telomerase activity (acclimation decreased it; stress increased it) and the levels of genes expression. Under stress, the expression of superoxide dismutase genes was increased in acclimated larvae and that of glutathione peroxidases in non-acclimated larvae, which may indicate lower reactive oxygen species formation and slower antioxidant responses in acclimated fish. The expression of some telomere-related genes was reduced under temperature stress, but the expression of the tzap and smg genes, whose products improve the control of telomere length by preventing them from lengthening or shortening, was increased in acclimated individuals. The data obtained indicate a positive effect of acclimation on the state of the Baikal whitefish larvae by remodulation of their telomerase activity and the transcriptional profile. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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17 pages, 5539 KiB  
Article
Effects of Chronic Heat Stress on Growth, Apoptosis, Antioxidant Enzymes, Transcriptomic Profiles, and Immune-Related Genes of Hong Kong Catfish (Clarias fuscus)
by Yong Liu, Changxu Tian, Zhihua Yang, Cailin Huang, Kaizhi Jiao, Lei Yang, Cunyu Duan, Zhixin Zhang and Guangli Li
Animals 2024, 14(7), 1006; https://doi.org/10.3390/ani14071006 - 26 Mar 2024
Cited by 13 | Viewed by 2849
Abstract
Chronic heat stress can have detrimental effects on the survival of fish. This study aimed to investigate the impact of prolonged high temperatures on the growth, antioxidant capacity, apoptosis, and transcriptome analysis of Hong Kong catfish (Clarias fuscus). By analyzing the [...] Read more.
Chronic heat stress can have detrimental effects on the survival of fish. This study aimed to investigate the impact of prolonged high temperatures on the growth, antioxidant capacity, apoptosis, and transcriptome analysis of Hong Kong catfish (Clarias fuscus). By analyzing the morphological statistics of C. fuscus subjected to chronic high-temperature stress for 30, 60, and 90 days, it was observed that the growth of C. fuscus was inhibited compared to the control group. The experimental group showed a significant decrease in body weight and body length compared to the control group after 60 and 90 days of high-temperature stress (p < 0.05, p < 0.01). A biochemical analysis revealed significant alterations in the activities of three antioxidant enzymes superoxide dismutase activity (SOD); catalase activity (CAT); glutathione peroxidase activity (GPx), the malondialdehyde content (MDA), and the concentrations of serum alkaline phosphatase (ALP); Aspartate aminotransferase (AST); and alanine transaminase (ALT) in the liver. TUNEL staining indicated stronger apoptotic signals in the high-temperature-stress group compared to the control group, suggesting that chronic high-temperature-induced oxidative stress, leading to liver tissue injury and apoptosis. Transcriptome analysis identified a total of 1330 DEGs, with 835 genes being upregulated and 495 genes being downregulated compared to the control group. These genes may be associated with oxidative stress, apoptosis, and immune response. The findings elucidate the growth changes in C. fuscus under chronic high temperature and provide insights into the underlying response mechanisms to a high-temperature environment. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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