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Omics in Economic Aquatic Animals: Second Edition
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Omics in Economic Aquatic Animals: Second Edition

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

Deadline for manuscript submissions: closed (5 August 2026) | Viewed by 46199

Editors

Dr. Changxu Tian

E-Mail Website
Guest Editor
Fisheries College, Guangdong Ocean University, Zhanjiang, China
Interests: genome; aquaculture; fish; sequencing; molecular biology; genetics; breeding; molecular marker; qtl
Special Issues, Collections and Topics in MDPI journals
Dr. Xinxin You

E-Mail Website
Guest Editor
College of Fisheries, Guangdong Ocean University, Zhanjiang, China
Interests: marine genomics research; genetic breeding technology development; deep-sea aquaculture technology development

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 a broader scope of 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
Dr. Xinxin You
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issue

Published Papers (6 papers)

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Research

13 pages, 3283 KB  
Article
Proteomic Analysis of Biomineralization Proteins in the Shell Plates and Spicules of Chiton Acanthochitona rubrolineata
by Jinzhe Du, Jinzhe Zhang, Jingliang Huang, Xue Liu and Chuang Liu
Animals 2026, 16(17), 2651; https://doi.org/10.3390/ani16172651 - 24 Aug 2026
Abstract
Chitons, ancient polyplacophoran mollusks, are ideal models for studying biomineralization evolution due to their conserved morphology since the Cambrian. This study investigates the matrix proteins in shell plates and spicules of Acanthochitona rubrolineata using liquid chromatography–tandem mass spectrometry. By extracting proteins from 30 [...] Read more.
Chitons, ancient polyplacophoran mollusks, are ideal models for studying biomineralization evolution due to their conserved morphology since the Cambrian. This study investigates the matrix proteins in shell plates and spicules of Acanthochitona rubrolineata using liquid chromatography–tandem mass spectrometry. By extracting proteins from 30 individuals and using proteomic method, we identified 26 soluble proteins and 22 insoluble proteins in the shell plates and 25 insoluble proteins, and found domains such as von Willebrand factor type A, chitin-binding, ferritin, and cadherin. These domains, prevalent in molluscan biominerals, suggest conserved roles in organic matrix formation. Despite genomic dynamism, the conservation of key domains across species highlights a core biomineralization mechanism. Notably, eight of the shell proteins and eight of the spicule proteins were homologous between A. rubrolineata and chiton Acanthopleura loochooana, indicating functional conservation. Phylogenetic analysis further supported the evolutionary significance of these domains in chitons. The study advances understanding of biomineralization in Polyplacophora, emphasizing the interplay between morphological stasis and molecular evolution. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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21 pages, 10448 KB  
Article
Effects of Dietary CpG Oligodeoxynucleotides (CpG ODNs) Supplementation Levels on Growth Performance, Immunity, Digestive Capacity, Intestinal Microbiota, and Transcriptomic Response in Litopenaeus vannamei
by Hongming Wang, Cuihong Hou, Yudong Zheng, Hang Yuan, Beiping Tan, Lili Shi and Shuang Zhang
Animals 2026, 16(14), 2207; https://doi.org/10.3390/ani16142207 - 16 Jul 2026
Viewed by 416
Abstract
This study evaluated the effects of dietary CpG oligodeoxynucleotide (CpG ODNs) on growth performance, immunity, digestive function, intestinal microbiota, and transcriptomic responses in Litopenaeus vannamei. Shrimp with an initial body weight of 0.30 ± 0.02 g were fed diets supplemented with 0, [...] Read more.
This study evaluated the effects of dietary CpG oligodeoxynucleotide (CpG ODNs) on growth performance, immunity, digestive function, intestinal microbiota, and transcriptomic responses in Litopenaeus vannamei. Shrimp with an initial body weight of 0.30 ± 0.02 g were fed diets supplemented with 0, 0.1, 0.4, 1.6, 6.4, or 25.6 mg kg−1 CpG ODNs for 8 weeks. Dietary CpG ODNs did not significantly improve most growth parameters; however, shrimp fed the diet supplemented with 1.6 mg kg−1 CpG ODNs showed a lower feed conversion ratio. After white spot syndrome virus challenge, shrimp fed the diet supplemented with 25.6 mg kg−1 CpG ODNs showed higher survival than those in the control group, whereas survival after Vibrio parahaemolyticus challenge did not differ significantly among treatments. Dietary supplementation with CpG ODNs at levels above 0.4 mg kg−1 increased the activities of several serum immune-related and antioxidant enzymes, reduced malondialdehyde content, and enhanced intestinal trypsin and amylase activities. In addition, this treatment increased microbial richness indices, while reducing the relative abundances of Vibrio and Photobacterium. Transcriptomic analysis showed that several pathways, including the AMPK signaling pathway and JAK–STAT signaling pathway, were significantly enriched in the CpG ODNs (above 0.4 mg kg−1) groups compared with the control group. In conclusion, dietary supplementation with CpG ODNs did not significantly improve the growth performance of L. vannamei. However, dietary supplementation with CpG ODNs at levels above 0.4 mg kg−1 may help enhance immune and digestive functions and modulate the intestinal microbiota composition of L. vannamei. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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19 pages, 21204 KB  
Article
Comparative Intestinal Transcriptomics Reveals Sex-Dependent Physiological Signatures in Mugilogobius chulae and Supports Sex-Aware Stress Evaluation
by Ning Zhang, Haiming Chen, Jiahao Gao, Yuhan Zhou, Qiwen Jiang, Jianjun Li, Jian Liao, Yanping Zhang, Zhongduo Wang, Yusong Guo and Zhongdian Dong
Animals 2026, 16(14), 2126; https://doi.org/10.3390/ani16142126 - 9 Jul 2026
Viewed by 355
Abstract
Sex is an important biological variable in animal physiology and environmental-stress research, but its influence on fish intestinal transcriptomic profiles remains insufficiently characterized. In this study, adult female and male Mugilogobius chulae were used to characterize baseline intestinal sex differences and to evaluate [...] Read more.
Sex is an important biological variable in animal physiology and environmental-stress research, but its influence on fish intestinal transcriptomic profiles remains insufficiently characterized. In this study, adult female and male Mugilogobius chulae were used to characterize baseline intestinal sex differences and to evaluate their relevance to short-term sulfamethoxazole exposure. Fish were assigned to solvent control or nominal 1 mg/L sulfamethoxazole exposure for 7 days, and intestinal tissues were analyzed by histology, RNA sequencing (RNA-Seq), functional enrichment analysis, gene set enrichment analysis, and quantitative real-time polymerase chain reaction validation. Representative histological sections showed qualitative sex-related differences in intestinal morphology. Transcriptomic analyses revealed that intestinal variation was more strongly associated with sex than with pooled treatment status. The pooled female-versus-male comparison identified 85 differentially expressed genes, whereas the pooled treatment-versus-control comparison yielded no significant differentially expressed genes under the current threshold. Functional enrichment and gene set enrichment analyses showed that female-biased intestinal profiles were mainly associated with nutrient absorption, lipid and sterol handling, membrane transport and epithelial interface-related pathways, whereas male-biased profiles were more closely related to RNA processing, oxidative metabolism, translation, protein targeting and mucosal immune signaling. These findings demonstrate sex-dependent intestinal transcriptomic signatures in M. chulae and support sex-aware intestinal transcriptomic analysis in aquatic animal omics and environmental-stress evaluation. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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17 pages, 4626 KB  
Article
Chromosome-Level Genome Assembly of Dybowski’s Frog (Rana dybowskii) Provides Insights into Environmental Adaptation and Evolutionary Genomics
by Yuting Liu, Linghao Kong, Jiayu Li and Yingdong Li
Animals 2026, 16(13), 2027; https://doi.org/10.3390/ani16132027 - 2 Jul 2026
Viewed by 550
Abstract
Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the [...] Read more.
Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the industry. Here, we integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C) technologies to assemble the first chromosome-level reference genome of R. dybowskii. The final assembled genome size is 3.77 Gb, with a contig N50 of 16.27 Mb and a scaffold N50 of 41.54 Mb. A total of 97.82% of the sequences were successfully anchored onto 12 definitive pseudochromosomes corresponding to haploid chromosome number. Repetitive elements account for 65.61% of the genome, characterized by an unusual dominance of DNA transposons (37.19%) over retrotransposons, suggesting a genomic landscape shaped by extreme cold adaptation. Combining multi-tissue transcriptomic evidence, we structurally predicted 26,862 protein-coding genes, and the predicted gene set showed a BUSCO completeness of 96.1%. Functional annotation successfully categorized 96.55% of the total genes. This genomic resource successfully fills a crucial phylogenetic gap in the Rana genus, driving high-efficiency molecular breeding and sustainable conservation of this economic amphibian. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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21 pages, 4672 KB  
Article
Elucidation of the XX/XY Sex Determination System and Development of a Sex-Linked Molecular Marker in the Freshwater Snail Bellamya purificata
by Yajun Gao, Yanhong Wen, Shaokui Yi, Yong Lin, Jinxia Peng, Xianhui Pan and Xiaoyun Zhou
Animals 2026, 16(6), 916; https://doi.org/10.3390/ani16060916 - 14 Mar 2026
Viewed by 43144
Abstract
The freshwater snail Bellamya purificata is both ecologically and economically significant, exhibiting notable sexual dimorphism in growth and nutritional traits that underscore the importance of breeding of monosex stocks. However, the genetic basis of sex determination remains unclear. Herein, genome-wide association studies (GWASs) [...] Read more.
The freshwater snail Bellamya purificata is both ecologically and economically significant, exhibiting notable sexual dimorphism in growth and nutritional traits that underscore the importance of breeding of monosex stocks. However, the genetic basis of sex determination remains unclear. Herein, genome-wide association studies (GWASs) combined with transcriptomic analysis were conducted to identify sex-linked markers and candidate genes for this species. GWAS generated 571 significantly sex-associated SNPs and 1853 InDels, corresponding to 44 candidate genes. Multiple significant SNP peaks were detected on chromosomes 1 and 2, with mrc2 and mis18bp1 as key candidate genes. A sex-linked InDel marker located within mis18bp1 can distinguish males and females cost-effectively. Genotype analysis of the sex-associated loci revealed that most females were homozygous while males were heterozygous, suggesting that B. purificata has a primarily XX/XY sex determination system. Comparative gonadal transcriptome analyses identified 2996 female-biased and 4281 male-biased genes. Among them, sry, sox8, dmrt1 and dmrt2 may be critical in male sex differentiation, while β-catenin, foxl2, esr1 and nr5a2 may be important in female sex differentiation. Integration of GWAS and transcriptomic data highlighted four pronounced sex-associated candidate genes, including mis18bp1, rnf216, tbx1 and mrc2. These results provide a valuable foundation for elucidating the genetic mechanisms underlying sex determination and for the development of monosex stocks in B. purificata. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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15 pages, 1884 KB  
Article
Genomic Characterization and Phylogenetic Relationships of Procypris rabaudi Revealed by Whole-Genome Survey Analysis
by Xiaolu Han, Renhui Luo, Qi Liu, Zengbao Yuan and Wenping He
Animals 2026, 16(2), 246; https://doi.org/10.3390/ani16020246 - 14 Jan 2026
Viewed by 764
Abstract
Procypris rabaudi, a member of the Cyprinidae family and genus Procypris, has been designated as a national second-class protected wildlife species in China due to a significant decline in its wild populations. Understanding its genomic characteristics and mitochondrial genome structure is [...] Read more.
Procypris rabaudi, a member of the Cyprinidae family and genus Procypris, has been designated as a national second-class protected wildlife species in China due to a significant decline in its wild populations. Understanding its genomic characteristics and mitochondrial genome structure is crucial for germplasm conservation and systematic classification. In this study, we utilized high-throughput sequencing to investigate the genome of P. rabaudi. The genome size was 1.5 Gb, with a heterozygosity rate of 0.44% and 61.47% of repetitive sequences. We identified 1,151,980 simple sequence repeats (SSRs), with mononucleotide repeats being the most abundant at 55.34%. The complete mitochondrial genome was assembled with 16,595 bp length. A phylogenetic tree constructed from 13 mitochondrial protein-coding genes indicated that genus Procypris was most closely related to genus Luciocyprinus and formed a monophyletic group with Cyprinus, Carassioides, and Carassius. Pairwise Sequentially Markovian Coalescent (PSMC) analysis revealed a rapid population expansion prior to the Last Interglacial Period, followed by a decline after reaching its peak during Last Glacial Period. Notably, P. rabaudi exhibited a two-peak demographic pattern during both the Last Glacial Period. These genomic data provide valuable resources for the conservation of P. rabaudi germplasm and for future studies on cyprinid classification and evolution. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals: Second Edition)
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