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Molecular Insights into Zoology
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Molecular Insights into Zoology

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

Deadline for manuscript submissions: 20 July 2025 | Viewed by 4277

Special Issue Editor

Dr. Valeria Maselli

E-Mail Website
Guest Editor
Campus Monte Sant’Angelo, Department of Biology, University of Naples Federico II, Naples, Italy
Interests: zoology; molecular evolution; ethology

Special Issue Information

Dear Colleagues,

The study of animals, including their structure, physiology, classification, and ecological and evolutionary processes, has always interested researchers. The classical zoological approach can be improved by contemporary molecular biology tools that could provide important answers to classic problems. This integrated and transformative approach can be used not only for living species but also for extinct species, reconstructing the phylogeny and evolution at the genomic and molecular levels.

The advent of omics sciences and other emerging technologies has totally altered the scientific research approach, first with transcriptomic and genomic analysis but also with metagenomic analysis from environmental samples. The most important challenges could be data integration, technical limitations due to protocol adaptation, and animal welfare restrictions. Moreover, it is possible to consider the integration with other disciplines as ecological dynamics that enhance our understanding of biodiversity, ecosystem health, and the adaptive responses of species to environmental changes.

This multidisciplinary perspective is captured altogether in a Special Issue of the International Journal of Molecular Sciences, collecting some examples of how zoology can be integrated with the enormous potential of molecular science.

Dr. Valeria Maselli
Guest Editor

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. 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

  • zoology
  • genomics
  • transcriptomics
  • phylogeny
  • molecular evolution
  • mtDNA
  • eDNA
  • RNA
  • molecular zoolog

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Published Papers (4 papers)

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Research

16 pages, 3196 KiB  
Article
Effects of Alexandrium pacificum Exposure on Exopalaemon carinicauda: Hepatopancreas Histology, Antioxidant Enzyme Activity, and Transcriptome Analysis
by Wanyu Han, Weitao Cheng, Menghao Fan, Dexue Liu, Yanrong Cao, Xuao Mei, Jiaxuan Wan, Guangwei Hu, Huan Gao and Nanjing Ji
Int. J. Mol. Sci. 2025, 26(4), 1605; https://doi.org/10.3390/ijms26041605 - 13 Feb 2025
Viewed by 577
Abstract
Alexandrium pacificum, a dinoflagellate known for causing harmful algal blooms (HABs), has garnered significant attention due to its potential toxicity to marine ecosystems, fisheries, and human health. However, the effects of this toxin-producing alga on shrimp are not yet comprehensively understood. This [...] Read more.
Alexandrium pacificum, a dinoflagellate known for causing harmful algal blooms (HABs), has garnered significant attention due to its potential toxicity to marine ecosystems, fisheries, and human health. However, the effects of this toxin-producing alga on shrimp are not yet comprehensively understood. This study aimed to assess the hepatopancreas damage induced by A. pacificum in the economically important shrimp species E. carinicauda and to elucidate the underlying molecular mechanisms through histology, antioxidant enzyme activity, and transcriptome analysis. The shrimp were assigned to either a control group or an exposed group, with the latter involving exposure to A. pacificum at a concentration of 1.0 × 104 cells/mL for 7 days. A histological analysis subsequently revealed pathological changes in the hepatopancreas tissue of the exposed group, including lumen expansion and the separation of the basement membrane from epithelial cells, while antioxidant enzyme activity assays demonstrated that exposure to A. pacificum weakened the antioxidant defense system, as evidenced by the reduced activities of catalase, superoxide dismutase, and glutathione, along with increased malondialdehyde levels. Transcriptome analysis further identified 663 significantly upregulated genes and 1735 significantly downregulated ones in the exposed group, with these differentially expressed genes being primarily associated with pathways such as protein processing in the endoplasmic reticulum, mitophagy, glycolysis/gluconeogenesis, sphingolipid metabolism, and glycerophospholipid metabolism. This study provides novel insights into the toxicological effects of A. pacificum on aquatic organisms and enhances the current understanding of the ecotoxicological risks posed by HABs. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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31 pages, 5105 KiB  
Article
Decoding Local Adaptation in the Exploited Native Marine Mussel Mytilus chilensis: Genomic Evidence from a Reciprocal Transplant Experiment
by Marco Yévenes, Gonzalo Gajardo and Cristian Gallardo-Escárate
Int. J. Mol. Sci. 2025, 26(3), 931; https://doi.org/10.3390/ijms26030931 - 23 Jan 2025
Viewed by 713
Abstract
Local adaptations are important in evolution as they drive population divergence and preserve standing genetic diversity essential for resilience under climate change and human impacts. Protecting locally adapted populations is essential for aquaculture species. However, high larval connectivity and frequent translocations challenge this [...] Read more.
Local adaptations are important in evolution as they drive population divergence and preserve standing genetic diversity essential for resilience under climate change and human impacts. Protecting locally adapted populations is essential for aquaculture species. However, high larval connectivity and frequent translocations challenge this in Chilean blue mussel (Mytilus chilensis) aquaculture, a world-class industry in Chiloé Island. This study examined local adaptations in two ecologically distinct natural beds, Cochamó (northernmost inner sea of Chiloé) and Yaldad (southernmost tip), through a 91-day reciprocal transplant experiment and genomic evidence. Cochamó mussels grew faster in their native environment (0.015 g/day) than Yaldad (0.004 g/day), though growth declined upon transplantation. Mussels transplanted within and between beds displayed distinctive adaptive transcriptomic responses, with differentially expressed genes involved with immune function, osmoregulation, metabolism, and cellular balance. Additionally, 58 known outlier SNPs mapped over the species’ genome sequence were linked with adaptive genes involved with osmoregulation, oxidative stress, and oxygen management, revealing selection-targeted specific genome regions. This study highlights how translocations affect the adaptive genomic response of M. chilensis and the impact of local environments in counterbalancing its genetic connectivity, concluding that the genomic differences in natural beds should be monitored and conserved for sustainable aquaculture practices. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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15 pages, 6523 KiB  
Article
Complete Mitogenomes of Xinjiang Hares and Their Selective Pressure Considerations
by Ruijie Wang, Mayinur Tursun and Wenjuan Shan
Int. J. Mol. Sci. 2024, 25(22), 11925; https://doi.org/10.3390/ijms252211925 - 6 Nov 2024
Viewed by 868
Abstract
Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base [...] Read more.
Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares’ mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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19 pages, 6473 KiB  
Article
Mitogenomic Architecture of Atlantic Emperor Lethrinus atlanticus (Actinopterygii: Spariformes): Insights into the Lineage Diversification in Atlantic Ocean
by Shantanu Kundu, Hye-Eun Kang, Yunji Go, Gyurim Bang, Yengju Jang, Hsu Htoo, Sarifah Aini and Hyun-Woo Kim
Int. J. Mol. Sci. 2024, 25(19), 10700; https://doi.org/10.3390/ijms251910700 - 4 Oct 2024
Viewed by 1504
Abstract
The evolutionary history of emperors, particularly in the Atlantic and Indo-West Pacific Oceans, remains largely unmapped. This study explores the maternal lineage evolution of Lethrinids by examining the complete mitogenome of Lethrinus atlanticus, which is endemic to the Eastern Atlantic Ocean. Utilizing [...] Read more.
The evolutionary history of emperors, particularly in the Atlantic and Indo-West Pacific Oceans, remains largely unmapped. This study explores the maternal lineage evolution of Lethrinids by examining the complete mitogenome of Lethrinus atlanticus, which is endemic to the Eastern Atlantic Ocean. Utilizing advanced next-generation sequencing, we found that the mitogenome spans 16,789 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and an AT-rich control region (CR). Our analysis indicates a preference for AT base pairs in the L. atlanticus mitogenome (53.10%). Most PCGs begin with the ATG codon, except for COI, which starts with GTG. Relative synonymous codon usage reveals high frequencies for alanine, leucine, proline, serine, and threonine. The ratio of nonsynonymous to synonymous substitutions suggests strong negative selection across all PCGs in Lethrinus species. Most transfer RNAs exhibit typical cloverleaf structures, with the exception of tRNA-serine (GCT), which lacks a dihydrouracil stem. Comparative analysis of conserved sequence blocks across the CRs of three Lethrinus species shows notable differences in length and nucleotide composition. Phylogenetic analysis using concatenated PCGs clearly distinguishes all Lethrinus species, including L. atlanticus, and sheds light on the evolutionary relationships among Spariformes species. The estimated divergence time of approximately 20.67 million years between L. atlanticus and its Indo-West Pacific relatives provides insights into their historical separation and colonization during the late Oligocene. The distribution of Lethrinids may be influenced by ocean currents and ecological factors, potentially leading to their speciation across the Eastern Atlantic and Indo-West Pacific. This study enhances our understanding of the genetic diversity and phylogenetic relationships within Lethrinus species. Further exploration of other emperor fish mitogenomes and comprehensive genomic data could provide vital insights into their genetic makeup, evolutionary history, and environmental adaptability in marine ecosystems globally. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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