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Explore Marine Biodiversity: Discover Insights from Genomics and Transcriptomics
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Explore Marine Biodiversity: Discover Insights from Genomics and Transcriptomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 April 2026 | Viewed by 2640

Special Issue Editors

Dr. Maria Sirakov

E-Mail Website
Guest Editor
Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
Interests: gut physiology; signalling pathways; marine organisms; gene expression; transcriptomics; emerging contaminants
Special Issues, Collections and Topics in MDPI journals
Dr. Ambrosino Luca

E-Mail Website
Guest Editor
Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
Interests: bioinformatics; genomics; transcriptomics; proteomics; comparative genomics; gene expression; homology modeling

Special Issue Information

Dear Colleagues,

We gladly invite colleagues to submit papers to the Special Issue “Explore Marine Biodiversity: Discover Insights from Genomics and Transcriptomics”.

This Special Issue aims to focus on marine biodiversity ranging from the studies focused on the evolution to the studies devoted to the maintenance of biodiversity in the different marine systems. Indeed, the role of the different species is pivotal for marine ecosystem structure and functioning. Thus, we will consider original research papers and reviews providing new insight into marine biodiversity.

Comparative studies investigating gene identification and function are highly recommended. In particular, studies including mechanisms of gene expression and regulation may shed light on the molecular bases of important mechanisms to maintain marine biodiversity. All the scientific work taking into account the evolution or the adaptation of marine species with -omics approaches is especially welcomed according to the IJMS policy.

Dr. Maria Sirakov
Dr. Ambrosino Luca
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • comparative genomics
  • functional genomics
  • transcriptomics
  • gene expression
  • adaptation
  • population genomics
  • marine biodiversity
  • evolution

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Published Papers (2 papers)

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Research

19 pages, 6722 KB  
Article
Knockdown-Induced Fasting Phenotypes in Flatworms: Insights into Underlying Mechanisms of Feeding Behavior
by Mikhail Biryukov, Anastasia Dmitrieva, Grigory Chepurnov and Kira S. Zadesenets
Int. J. Mol. Sci. 2025, 26(24), 11934; https://doi.org/10.3390/ijms262411934 - 11 Dec 2025
Abstract
The intestine is a multifunctional organ responsible for digestion, nutrient absorption, metabolic regulation, and innate immunity. In flatworms, recent studies have highlighted the importance of intestine-enriched genes expressed strongly in cells of the digestive tract. These genes are not only involved in digestion, [...] Read more.
The intestine is a multifunctional organ responsible for digestion, nutrient absorption, metabolic regulation, and innate immunity. In flatworms, recent studies have highlighted the importance of intestine-enriched genes expressed strongly in cells of the digestive tract. These genes are not only involved in digestion, nutrient uptake, transport, metabolism, and feeding behavior, but also in the modulating dynamics of stem cells (neoblasts). In Macrostomum lignano, the molecular mechanisms regulating interaction between digestive and neural processes remain poorly understood, as in other free-living flatworms. Therefore, identifying the genes required for intestinal integrity and feeding behavior is essential for understanding the underpinning mechanisms. In this study, we examined intestine-enriched candidate genes predicted to be involved in cell differentiation and maintenance of the intestine in M. lignano and whether the knockdown of these genes affects other tissues’ functioning. Using RNAi-mediated gene silencing, we identified four genes (kri1, wbp2nl, Mlig-tuf1, and Mlig-tuf2) whose knockdown causes pronounced phenotypes, including reduced feeding, fasting behavior, decreased body size and cell proliferation, low reproduction, and altered expression of an intestine-specific apob promoter. We have characterized their roles in intestinal homeostasis and neoblast dynamics and discussed potential mechanisms linking gene disruption to changes in feeding behavior. Full article
(This article belongs to the Special Issue Explore Marine Biodiversity: Discover Insights from Genomics and Transcriptomics)
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16 pages, 2874 KB  
Article
Transcriptomic Insights into Post-Spawning Death and Muscle Atrophy in Ayu (Plecoglossus altivelis)
by Jiancheng Liang, Minoru Fujisawa, Shogo Toma, Shuichi Asakawa, Kazutoshi Yoshitake, Yoji Igarashi, Shunsuke Saito, Takashi Akutsu, Kyuma Suzuki and Shigeharu Kinoshita
Int. J. Mol. Sci. 2025, 26(2), 434; https://doi.org/10.3390/ijms26020434 - 7 Jan 2025
Viewed by 2106
Abstract
In semelparous species like the ayu (Plecoglossus altivelis), spawning is followed by rapid physiological decline and death; yet, the underlying molecular mechanisms remain largely unexplored. This study examines transcriptomic changes in ayu skeletal muscle before and after spawning, with a focus [...] Read more.
In semelparous species like the ayu (Plecoglossus altivelis), spawning is followed by rapid physiological decline and death; yet, the underlying molecular mechanisms remain largely unexplored. This study examines transcriptomic changes in ayu skeletal muscle before and after spawning, with a focus on key genes and pathways contributing to muscle atrophy and metabolic dysfunction. Through RNA sequencing and DEG analysis, we identified over 3000 DEGs, and GSEA and KEGG pathway analysis revealed significant downregulation of energy metabolism and protein degradation. In post-spawning ayu, a rapid decrease in body weight was observed, accompanied by a decline in the expression of myosin heavy chain genes, which are major muscle protein genes, and gene expression changes indicative of muscle atrophy. Decreased expression of AP-1 transcription factors associated with muscle development and aging was also evident. PPI network analysis identified carbohydrate catabolism protein gapdh may be the key factor that led to muscle atrophy and accelerated aging in ayu. Our study revealed that after spawning, the ayu muscle tissue undergoes strong metabolic disorders and cellular stress responses, providing special insights into the mechanisms through the post-spawning death of ayu. Full article
(This article belongs to the Special Issue Explore Marine Biodiversity: Discover Insights from Genomics and Transcriptomics)
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