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Genes
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Genetic and Genomic Studies of Marine Animals
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Genetic and Genomic Studies of Marine Animals

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

Deadline for manuscript submissions: 20 February 2025 | Viewed by 4309

Special Issue Editors

Dr. Bingjian Liu

E-Mail Website
Guest Editor
Marine Science And Technology College, Zhejiang Ocean University, Zhoushan, China
Interests: population genome; population genetics; adaptation evolution; marine animals; biodiversity
Special Issues, Collections and Topics in MDPI journals
Dr. Yifan Liu

E-Mail Website
Guest Editor
National Engineering Research Center For Marine Aquaculture, Zhoushan, China
Interests: gene; marine organisms; evolution; reproduction; development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Research on marine animal genetics, reproduction and development can help identify the general patterns and causes of adaptation and understand the genetic mechanisms of marine organisms; at the same time, it can also scientifically predict the development and evolutionary direction of marine organisms and help formulate a more reasonable strategy for the exploitation of marine biological resources. This Special Issue will cover aspects of the genetic, reproduction and development of marine animals, e.g. population genetics, genomes, transcriptome, genes, reproduction and development. We invite both conceptual reviews and case studies that expand our knowledge in the molecular and genetic mechanisms underlying the adaptive evolution of marine animals.

Dr. Bingjian Liu
Dr. Yifan Liu
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

  • population genetics
  • genomes
  • transcriptome
  • genes
  • reproduction
  • development
  • adaptation evolution
  • marine animals
  • biodiversity

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Published Papers (4 papers)

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Research

15 pages, 3729 KiB  
Article
Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process
by Anqi Li, Zhentao Song, Mingzhi Zhang, Hu Duan, Liying Sui, Bin Wang and Tong Hao
Genes 2024, 15(8), 1083; https://doi.org/10.3390/genes15081083 - 16 Aug 2024
Viewed by 597
Abstract
Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, with [...] Read more.
Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, with little research on the molecular regulatory mechanism of Artemia embryonic reactivation. The first 5 h after embryonic diapause breaking has been proved to be most important for embryonic reactivation in Artemia. In this work, two high-throughput sequencing methods, ATAC-seq and RNA-seq, were integrated to study the signal regulation process in embryonic reactivation of Artemia at 5 h after diapause breaking. Through the GO and KEGG enrichment analysis of the high-throughput datasets, it was showed that after 5 h of diapause breaking, the metabolism and regulation of Artemia cyst were quite active. Several signal transduction pathways were identified in the embryonic reactivation process, such as G-protein-coupled receptor (GPCR) signaling pathway, cell surface receptor signaling pathway, hormone-mediated signaling pathway, Wnt, Notch, mTOR signaling pathways, etc. It indicates that embryonic reactivation is a complex process regulated by multiple signaling pathways. With the further protein structure analysis and RT-qPCR verification, 11 GPCR genes were identified, in which 5 genes function in the embryonic reactivation stage and the other 6 genes contribute to the diapause stage. The results of this work reveal the signal transduction pathways and GPCRs involved in the embryonic reactivation process of Artemia cysts. These findings offer significant clues for in-depth research on the signal regulatory mechanisms of the embryonic reactivation process and valuable insights into the mechanism of animal embryonic diapause. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Marine Animals)
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21 pages, 11382 KiB  
Article
Gonadal Transcriptome Sequencing Analysis Reveals the Candidate Sex-Related Genes and Signaling Pathways in the East Asian Common Octopus, Octopus sinensis
by Fenghui Li, Siqing Chen, Tao Zhang, Luying Pan, Changlin Liu and Li Bian
Genes 2024, 15(6), 682; https://doi.org/10.3390/genes15060682 - 24 May 2024
Viewed by 826
Abstract
The East Asian common octopus (Octopus sinensis) is an economically important species among cephalopods. This species exhibits a strict dioecious and allogamous reproductive strategy, along with a phenotypic sexual dimorphism, where the third right arm differentiates into hectocotylus in males. However, [...] Read more.
The East Asian common octopus (Octopus sinensis) is an economically important species among cephalopods. This species exhibits a strict dioecious and allogamous reproductive strategy, along with a phenotypic sexual dimorphism, where the third right arm differentiates into hectocotylus in males. However, our understanding of the molecular mechanisms that underlie sex determination and differentiation in this species remains limited. In the present study, we surveyed gene-expression profiles in the immature male and female gonads of O. sinensis based on the RNA-seq, and a total of 47.83 Gb of high-quality data were generated. Compared with the testis, we identified 8302 differentially expressed genes (DEGs) in the ovary, of which 4459 genes were up-regulated and 3843 genes were down-regulated. Based on the GO enrichment, many GO terms related to sex differentiation were identified, such as sex differentiation (GO: 0007548), sexual reproduction (GO: 0019953) and male sex differentiation (GO: 0046661). A KEGG classification analysis identified three conserved signaling pathways that related to sex differentiation, including the Wnt signaling pathway, TGF-β signaling pathway and Notch signaling pathway. Additionally, 21 sex-related DEGs were selected, of which 13 DEGs were male-biased, including Dmrt1, Foxn5, Foxj1, Sox30, etc., and 8 DEGs were female-biased, including Sox14, Nanos3, β-tubulin, Suh, etc. Ten DEGs were used to verify the expression patterns in the testis and ovary using the RT-qPCR method, and the results showed that the expression level shown by RT-qPCR was consistent with that from the RNA-seq, which confirmed the reliability of the transcriptome data. The results presented in this study will not only contribute to our understanding of sex-formation mechanisms in O. sinensis but also provide the foundational information for further investigating the molecular mechanisms that underline its gonadal development and facilitate the sustainable development of octopus artificial breeding. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Marine Animals)
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16 pages, 6457 KiB  
Article
Reconstruction of Metabolic–Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone Synthesis
by Tong Hao, Zhentao Song, Mingzhi Zhang, Lingrui Zhang, Jiarui Yang, Jingjing Li and Jinsheng Sun
Genes 2024, 15(4), 410; https://doi.org/10.3390/genes15040410 - 26 Mar 2024
Viewed by 941
Abstract
Integrated networks have become a new interest in genome-scale network research due to their ability to comprehensively reflect and analyze the molecular processes in cells. Currently, none of the integrated networks have been reported for higher organisms. Eriocheir sinensis is a typical aquatic [...] Read more.
Integrated networks have become a new interest in genome-scale network research due to their ability to comprehensively reflect and analyze the molecular processes in cells. Currently, none of the integrated networks have been reported for higher organisms. Eriocheir sinensis is a typical aquatic animal that grows through ecdysis. Ecdysone has been identified to be a crucial regulator of ecdysis, but the influence factors and regulatory mechanisms of ecdysone synthesis in E. sinensis are still unclear. In this work, the genome-scale metabolic network and protein–protein interaction network of E. sinensis were integrated to reconstruct a metabolic–protein interaction integrated network (MPIN). The MPIN was used to analyze the influence factors of ecdysone synthesis through flux variation analysis. In total, 236 integrated reactions (IRs) were found to influence the ecdysone synthesis of which 16 IRs had a significant impact. These IRs constitute three ecdysone synthesis routes. It is found that there might be alternative pathways to obtain cholesterol for ecdysone synthesis in E. sinensis instead of absorbing it directly from the feeds. The MPIN reconstructed in this work is the first integrated network for higher organisms. The analysis based on the MPIN supplies important information for the mechanism analysis of ecdysone synthesis in E. sinensis. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Marine Animals)
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13 pages, 2649 KiB  
Article
Transcriptomic Analysis of Liver Tissue of Black Sea Bass (Centropristis striata) Exposed to High Nitrogen Environment
by Bingjian Liu, Xun Jin, Kun Zhang, Yifan Liu, Shaowen Wang, Shiyi Chen, Shufei Zhang and Xiaolong Yin
Genes 2023, 14(7), 1440; https://doi.org/10.3390/genes14071440 - 13 Jul 2023
Viewed by 1578
Abstract
The black sea bass, Centropristis striata, is a potential candidate for commercial aquaculture. Due to inadequate removal of nitrogen in its breeding environment, C. striata exhibits increased nitrate concentration, which can cause acute toxicity, including energy metabolism damage and tissue damage. Therefore, [...] Read more.
The black sea bass, Centropristis striata, is a potential candidate for commercial aquaculture. Due to inadequate removal of nitrogen in its breeding environment, C. striata exhibits increased nitrate concentration, which can cause acute toxicity, including energy metabolism damage and tissue damage. Therefore, RNA-seq technology was applied to characterize genes associated with toxicity tolerance under nitrate stress. The nitrate treatment caused significant changes in a total of 8920 genes, of which 2949 genes were up-regulated and 5971 genes were down-regulated. It was found that significantly enriched GO terms and KEGG were associated with blood microparticles, inhibitors of enzyme activity, and complement and coagulation cascade pathways. Furthermore, through bioinformatics analysis, it was found that these different pathways obtained in GO and KEGG enrichment analysis were mostly related to the immune and inflammatory response of fish. This study expands our understanding of the mechanism of nitrate stress affecting the liver function of C. striata. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Marine Animals)
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