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Advances in Genes and Genomics of Aquatic Animals and Pathogens
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Advances in Genes and Genomics of Aquatic Animals and Pathogens

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

Deadline for manuscript submissions: closed (15 February 2025) | Viewed by 14770

Special Issue Editors

Dr. Erlong Wang

E-Mail Website
Guest Editor
College of Animal Science and Technology, Northwest A&F University, Yangling 712000, China
Interests: aquatic bacteriology; aquatic virology; aquatic animal immunology; fish vaccines; fish disease resistance genes; host–pathogen interaction
Special Issues, Collections and Topics in MDPI journals
Dr. Zihao Yuan

E-Mail
Guest Editor
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
Interests: pathogen–host interaction; aquatic animal immunology; immune system evolution; marine virus; evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Zehui Yu

E-Mail Website
Guest Editor
Laboratory Animal Center, Southwest Medical University, Luzhou 646099, China
Interests: virus evolution; virus classification; pathogen identification; bacterial genome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the course of million years of co-evolution, both pathogens and hosts have developed distinct traits for infection and defense. In aquatic species, the innate immune system serves as the primary defense against pathogens. In fish, the mucosal immune system, particularly in the gastrointestinal tract, serves as the primary portal for pathogen invasion. Aquatic invertebrates, such as mollusks, have developed natural immunity via chemical protective products. Microorganisms also play a role in regulating intestinal flora, altering host metabolism and immunity. Comparative analysis of host responses to microorganisms across species is key to understand the function and evolution of immune systems.

Hosts have evolved multiple defense mechanisms involving various genes against pathogen infections. Pattern recognition receptors (PRRs) specifically recognize pathogen-related molecular patterns (PAMPs) of microorganisms. PRRs activate immune responses via multiple signaling pathways to regulate host immunity and influence pathogen survival. Thus, it is worth investigating to explore how hosts respond to microorganisms and vice versa at the gene and genomic level. In addition, intestinal microbes regulate host food intake through the gut–brain axis, and their response to host immune capacity has become a hot research topic.

The Special Issue, "Advances in Genes and Genomics of Aquatic Animals and Pathogens", focuses on the evolution and interaction between microorganisms and hosts in aquatic species. Topics related to the gene and genomic mechanisms of microbial influence on host immunity, the role of pattern recognition receptors in microbial–host interactions, the evolution of pathogenic microbes, and the mechanisms of microorganisms for avoiding host immunity are also welcome. This research topic aims to facilitate the study of microorganism–host interactions and advance the research of genes and genomics in aquatic species.

Dr. Erlong Wang
Dr. Zihao Yuan
Dr. Zehui Yu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly 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 2600 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

  • disease resistance genes
  • aquatic animal genomics
  • evolutions in aquatic pathogens
  • aquatic animal viruses
  • aquatic animal bacteria
  • host–pathogen interactions

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Published Papers (7 papers)

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Research

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17 pages, 3080 KiB  
Article
The Complete Mitochondrial Genome of the Luciocyprinus langsoni (Cypriniformes: Cyprinidae): Characterization, Phylogeny, and Genetic Diversity Analysis
by Tiezhu Yang, Chenxi Tan, Liangjie Zhao, Zhiguo Hu, Chaoqun Su, Fan Li, Yuanye Ma, Wenchao Zhang, Xiaoyu Hao, Wenxu Zou, Jiayin Kang and Qingqing He
Genes 2024, 15(12), 1621; https://doi.org/10.3390/genes15121621 - 18 Dec 2024
Viewed by 674
Abstract
Background: Luciocyprinus langsoni is a species belonging to the Cyprinidae family. The objective of this study is to gain a comprehensive understanding of its evolutionary history and genetic characteristics. Methods: The complete mitochondrial genome of L. langsoni was determined using [...] Read more.
Background: Luciocyprinus langsoni is a species belonging to the Cyprinidae family. The objective of this study is to gain a comprehensive understanding of its evolutionary history and genetic characteristics. Methods: The complete mitochondrial genome of L. langsoni was determined using overlapping PCR. A phylogenetic analysis was conducted based on 13 protein-coding genes from 48 species. A population genetic diversity analysis using the COI gene and a selection analysis of 13 protein-coding genes were also performed. Results: The mitogenome is 16,586 base pairs long and consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two control regions. It has a high adenine-thymine (A + T) content. The phylogenetic analysis confirms the placement of L. langsoni within the subfamily Cyprininae. The population genetic diversity analysis reveals low variability in the Hechi Longjiang population. The selection analysis shows that all 13 protein-coding genes have evolved under purifying selection with Ka/Ks ratios below 1. Conclusions: These results enhance our understanding of L. langsoni’s evolutionary history and lay a genetic foundation for future studies in population genetics and phylogenetics. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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15 pages, 3252 KiB  
Article
Dynamic Alternative Polyadenylation during Litopenaeus Vannamei Metamorphosis Development
by Xueqin Yang, Xiuli Chen, Chengzhang Liu, Zezhong Wang, Wei Lei, Qiangyong Li, Yongzhen Zhao and Xia Wang
Genes 2024, 15(7), 837; https://doi.org/10.3390/genes15070837 - 26 Jun 2024
Viewed by 2228
Abstract
As an important mechanism in the post-transcriptional regulation of eukaryotic gene expression, alternative polyadenylation (APA) plays a key role in biological processes such as cell proliferation and differentiation. However, the role and dynamic pattern of APA during Litopenaeus vannamei metamorphosis are poorly understood. [...] Read more.
As an important mechanism in the post-transcriptional regulation of eukaryotic gene expression, alternative polyadenylation (APA) plays a key role in biological processes such as cell proliferation and differentiation. However, the role and dynamic pattern of APA during Litopenaeus vannamei metamorphosis are poorly understood. Here, RNA-seq data covering from the embryo to the maturation (16 time points) of L. vannamei were utilized. We identified 247 differentially expressed APA events between early and adult stages, and through fuzzy mean clustering analysis, we discovered five dynamic APA patterns. Among them, the gradual elongation of the 3′UTR is the major APA pattern that changes over time, and its genes are enriched in the pathways of protein and energy metabolism. Finally, we constructed mRNA-miRNA and PPI networks and detected several central miRNAs that may regulate L. vannamei development. Our results revealed the complex APA mechanisms in L. vannamei metamorphosis, shedding new light on post-transcriptional regulation of crustacean metamorphosis. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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20 pages, 2673 KiB  
Article
Discovery, Pathogenesis, and Complete Genome Characterization of Lates calcarifer Herpesvirus
by Bartjan Simmelink, Jordy P. M. Coolen, Wannes Vogels, Martin Deijs, Jessica L. M. van der Last-Kempkes, Kah Sing Ng, Siow Foong Chang, Koen Gevers, Liesbeth Harkema, Lia van der Hoek and Ad de Groof
Genes 2024, 15(3), 264; https://doi.org/10.3390/genes15030264 - 20 Feb 2024
Cited by 1 | Viewed by 2375
Abstract
In 2015 and 2016, two Barramundi (Lates calcarifer) farms in Singapore reported a disease outbreak characterized by lethargic behavior, pronounced inappetence, generalized skin lesions, erosions of the fins and tail, and ultimately high mortality in their fish. Next-generation sequencing and PCR [...] Read more.
In 2015 and 2016, two Barramundi (Lates calcarifer) farms in Singapore reported a disease outbreak characterized by lethargic behavior, pronounced inappetence, generalized skin lesions, erosions of the fins and tail, and ultimately high mortality in their fish. Next-generation sequencing and PCR confirmed presence of a novel virus belonging to the Alloherpesviridae family, Lates calcarifer herpesvirus (LCHV), which was subsequently isolated and cultured. We characterize, for the first time, the complete genome of two cultured LCHV isolates. The genome contains a long unique region of approximately 105,000 bp flanked by terminal repeats of approximately 24,800 bp, of which the first 8.2 kb do not show any similarity to described genomes in the Alloherpesviridae family. The two cultured isolates share 89% nucleotide identity, and their closest relatives are the viruses belonging to the genus Ictalurivirus. Experimental infections using one of the cultured LCHV isolates resulted in identical clinical signs as originally described in the index farm, both in intraperitoneal-injection infected fish and cohabitant fish, with mortality in both groups. Histopathological analysis showed pronounced abnormalities in the gills. Virus culture and PCR analysis confirmed the replication of LCHV in the infected fish, and thus Koch’s postulates were fulfilled. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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15 pages, 4636 KiB  
Article
Transcriptome Signatures of Atlantic Salmon—Resistant Phenotypes against Sea Lice Infestation Are Associated with Tissue Repair
by Valentina Valenzuela-Muñoz, Cristian Gallardo-Escárate, Diego Valenzuela-Miranda, Gustavo Nuñez-Acuña, Bárbara P. Benavente, Alejandro Alert and Marta Arevalo
Genes 2023, 14(5), 986; https://doi.org/10.3390/genes14050986 - 27 Apr 2023
Cited by 2 | Viewed by 2499
Abstract
Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity, including the sea louse Caligus rogercresseyi. This marine ectoparasite is mainly controlled through delousing drug treatments that have lost efficacy. Therein, strategies such as salmon breeding selection represent [...] Read more.
Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity, including the sea louse Caligus rogercresseyi. This marine ectoparasite is mainly controlled through delousing drug treatments that have lost efficacy. Therein, strategies such as salmon breeding selection represent a sustainable alternative to produce fish with resistance to sea lice. This study explored the whole-transcriptome changes in Atlantic salmon families with contrasting resistance phenotypes against lice infestation. In total, 121 Atlantic salmon families were challenged with 35 copepodites per fish and ranked after 14 infestation days. Skin and head kidney tissue from the top two lowest (R) and highest (S) infested families were sequenced by the Illumina platform. Genome-scale transcriptome analysis showed different expression profiles between the phenotypes. Significant differences in chromosome modulation between the R and S families were observed in skin tissue. Notably, the upregulation of genes associated with tissue repairs, such as collagen and myosin, was found in R families. Furthermore, skin tissue of resistant families showed the highest number of genes associated with molecular functions such as ion binding, transferase, and cytokine activity, compared with the susceptible. Interestingly, lncRNAs differentially modulated in the R/S families are located near genes associated with immune response, which are upregulated in the R family. Finally, SNPs variations were identified in both salmon families, where the resistant ones showed the highest number of SNPs variations. Remarkably, among the genes with SPNs, genes associated with the tissue repair process were identified. This study reported Atlantic salmon chromosome regions exclusively expressed in R or S Atlantic salmon families’ phenotypes. Furthermore, due to the presence of SNPs and high expression of tissue repair genes in the resistant families, it is possible to suggest mucosal immune activation associated with the Atlantic salmon resistance to sea louse infestation. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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12 pages, 1531 KiB  
Article
Japanese Flounder pol-miR-155 Is Involved in Edwardsiella tarda Infection via ATG3
by Zhanwei Zhang and Xiaolu Guan
Genes 2023, 14(5), 958; https://doi.org/10.3390/genes14050958 - 22 Apr 2023
Cited by 4 | Viewed by 1894
Abstract
MicroRNAs (miRNAs) are small RNA molecules that function in the post-transcriptionally regulation of the expression of diverse genes, including those involved in immune defense. Edwardsiella tarda can infect a broad range of hosts and cause severe disease in aquatic species, including Japanese flounder [...] Read more.
MicroRNAs (miRNAs) are small RNA molecules that function in the post-transcriptionally regulation of the expression of diverse genes, including those involved in immune defense. Edwardsiella tarda can infect a broad range of hosts and cause severe disease in aquatic species, including Japanese flounder (Paralichthys olivaceus). In this study, we examined the regulation mechanism of a flounder miRNA, pol-miR-155, during the infection of E. tarda. Pol-miR-155 was identified to target flounder ATG3. Overexpression of pol-miR-155 or knockdown of ATG3 expression suppressed autophagy and promoted the intracellular replication of E. tarda in flounder cells. Overexpression of pol-miR-155 activated the NF-κB signaling pathway and further promoted the expression of downstream immune related genes of interleukin (IL)-6 and IL-8. These results unraveled the regulatory effect of pol-miR-155 in autophagy and in E. tarda infection. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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18 pages, 2815 KiB  
Article
Comparative Transcriptomics in Atlantic Salmon Head Kidney and SHK-1 Cell Line Exposed to the Sea Louse Cr-Cathepsin
by Yeny Leal, Valentina Valenzuela-Muñoz, Antonio Casuso, Bárbara P. Benavente and Cristian Gallardo-Escárate
Genes 2023, 14(4), 905; https://doi.org/10.3390/genes14040905 - 13 Apr 2023
Cited by 3 | Viewed by 2659
Abstract
The development of vaccines against sea lice in salmon farming is complex, expensive, and takes several years for commercial availability. Recently, transcriptome studies in sea louse have provided valuable information for identifying relevant molecules with potential use for fish vaccines. However, the bottleneck [...] Read more.
The development of vaccines against sea lice in salmon farming is complex, expensive, and takes several years for commercial availability. Recently, transcriptome studies in sea louse have provided valuable information for identifying relevant molecules with potential use for fish vaccines. However, the bottleneck is the in vivo testing of recombinant protein candidates, the dosage, and the polyvalent formulation strategies. This study explored a cell-based approach to prospect antigens as candidate vaccines against sea lice by comparison with immunized fish. Herein, SHK-1 cells and Atlantic salmon head kidney tissue were exposed to the antigen cathepsin identified from the sea louse Caligus rogercresseyi. The cathepsin protein was cloned and recombinantly expressed in Escherichia coli, and then SHK-1 cell lines were stimulated with 100 ng/mL cathepsin recombinant for 24 h. In addition, Atlantic salmons were vaccinated with 30 ug/mL recombinant protein, and head kidney samples were then collected 30 days post-immunization. SHK-1 cells and salmon head kidney exposed to cathepsin were analyzed by Illumina RNA sequencing. The statistical comparisons showed differences in the transcriptomic profiles between SHK-1 cells and the salmon head kidney. However, 24.15% of the differentially expressed genes were shared. Moreover, putative gene regulation through lncRNAs revealed tissue-specific transcription patterns. The top 50 up and downregulated lncRNAs were highly correlated with genes involved in immune response, iron homeostasis, pro-inflammatory cytokines, and apoptosis. Also, highly enriched pathways related to the immune system and signal transduction were shared between both tissues. These findings highlight a novel approach to evaluating candidate antigens for sea lice vaccine development, improving the antigens screening in the SHK-1 cell line model. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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Review

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14 pages, 8290 KiB  
Review
Mechanistic Role of TRIM26 in Viral Infection and Host Defense
by Mona Sharma, Ke Liu, Jianchao Wei, Zhiyong Ma and Yafeng Qiu
Genes 2024, 15(11), 1476; https://doi.org/10.3390/genes15111476 - 15 Nov 2024
Viewed by 1357
Abstract
Tripartite motif protein 26 (TRIM26) is an E3 ubiquitin ligase and a member of the TRIM family. Similar to other TRIM proteins, TRIM26 consists of three domains, collectively termed RBCC: a Really Interesting New Gene (RING) domain, one B-Box domain, and a C [...] Read more.
Tripartite motif protein 26 (TRIM26) is an E3 ubiquitin ligase and a member of the TRIM family. Similar to other TRIM proteins, TRIM26 consists of three domains, collectively termed RBCC: a Really Interesting New Gene (RING) domain, one B-Box domain, and a C terminal domain consisting of a PRY/SPRY domain. The PRY/SPRY domain exhibits relatively higher conservation compared with the RING and B-Box domains, suggesting potentially similar roles across TRIM26 proteins from various species. TRIM26 either directly interacts with viral proteins or modulates immune responses to engage with a viral infection, serving as either a protective or detrimental host factor depending on the circumvent of the viral infection. The present review focuses on understanding the mechanisms of TRIM26 during viral infection and its potential future applications. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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