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Fishes
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Omics Analysis in Marine Invertebrate Biology
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Omics Analysis in Marine Invertebrate Biology

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (16 October 2023) | Viewed by 8410

Special Issue Editors

Prof. Dr. Eric Hallerman

E-Mail Website
Guest Editor
Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, 100 Cheatham Hall, Blacksburg, VA 24061, USA
Interests: genetics education; population genetics; aquaculture; biotechnology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Supawadee Poompuang

E-Mail Website
Guest Editor
Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
Interests: aquaculture genetics; selective breeding; genomic prediction; transcriptomics; Asian seabass; white shrimp; tilapia

Special Issue Information

Dear Colleagues,

The application of genomics, transcriptomics, proteomics, and metabolomics—or omics analyses—across diverse fields has increased rapidly in recent decades. These technologies are increasingly applied to non-model organisms, such as marine invertebrates, to understand molecular mechanisms behind observed phenotypes. The knowledge gained from these studies depends upon rigorous attention to quality across the stages of experimental planning, execution, sample preparation, analysis, and interpretation. We solicit papers that apply omics techniques to expand our knowledge of life history, adaptations, phenotypic plasticity, and projected responses to climate change across diverse marine invertebrate tax. We are especially interested in studies that integrate across biological hierarchy and/or convey the potential and weaknesses of the omics technique applied through careful data analysis and interpretation.

Prof. Dr. Eric Hallerman
Prof. Dr. Supawadee Poompuang
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. Fishes 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.

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Published Papers (4 papers)

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Research

27 pages, 7878 KiB  
Article
Effects of Cold Stress on the Hemolymph of the Pacific White Shrimp Penaeus vannamei
by Jianqiang Zhu, Wenjun Shi, Ran Zhao, Chen Gu, Hui Li, Libao Wang and Xihe Wan
Fishes 2024, 9(1), 36; https://doi.org/10.3390/fishes9010036 - 16 Jan 2024
Cited by 6 | Viewed by 2791
Abstract
Temperature is an important factor in the physiological processes of aquatic organisms and can seriously affect several chemical and biological processes in their bodies, including respiratory metabolism, antioxidant capacity, immune capacity, and signal transduction. In this study, physiological, transcriptomic, and metabolomic analyses were [...] Read more.
Temperature is an important factor in the physiological processes of aquatic organisms and can seriously affect several chemical and biological processes in their bodies, including respiratory metabolism, antioxidant capacity, immune capacity, and signal transduction. In this study, physiological, transcriptomic, and metabolomic analyses were used to investigate the response of Penaeus vannamei to cold stress. The results indicated that cold stress disrupted nucleotide metabolism and inhibited gluconeogenesis. However, shrimp exhibited response mechanisms in order to enhance cold tolerance, regulating changes in key genes and metabolites in amino acid and lipid metabolism to increase energy supply and protect cell membrane stability. In addition, the response included regulating Ca2+ pumps and ion channels to maintain intracellular ion homeostasis and osmotic balance. When the temperature dropped further, oxidative damage occurred due to overwhelming of the antioxidant defense system, and immune function was inhibited. This research provides some references regarding the molecular mechanisms involved in responding to cold stress and potential strategies to improve cold tolerance in P. vannamei; these are important references for studying the cold stress response of shrimp. Full article
(This article belongs to the Special Issue Omics Analysis in Marine Invertebrate Biology)
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17 pages, 2038 KiB  
Article
Transcriptome Sequencing Analysis of Sex-Related Genes in the Gonads of Mytilus unguiculatus
by Yanwen Ma, Yingying Ye, Ronghui Yao, Pengzhi Qi and Jiji Li
Fishes 2023, 8(9), 456; https://doi.org/10.3390/fishes8090456 - 11 Sep 2023
Cited by 2 | Viewed by 1483
Abstract
In the cultivation of Mytilus unguiculatus, the broodstock are shade-dried to stimulate sperm and egg production. To identify the functional genes affecting gonad development in M. unguiculatus, the transcriptome of gonads in mussels stimulated by shade-drying and those not stimulated were [...] Read more.
In the cultivation of Mytilus unguiculatus, the broodstock are shade-dried to stimulate sperm and egg production. To identify the functional genes affecting gonad development in M. unguiculatus, the transcriptome of gonads in mussels stimulated by shade-drying and those not stimulated were compared. Differential gene expression analysis revealed that there were 22 differentially expressed genes (DEGs) in the testis and 70 DEGs in the ovary among the experimental groups. KEGG enrichment analysis identified a total of 11 pathways that might be related to environmental stimuli affecting gonadal development. Nicotinic acetylcholine receptors (AChRs), the cholecystokinin A receptor (CCKAR), hypocretin (orexin) receptor 2 (HCRTR2), and gamma-aminobutyric acid type B receptor (GABBR) were highly expressed in the neuroactive ligand-receptor interaction pathway, indicating that these genes might be involved in the transduction of environmental information that stimulates gonadal development. Meanwhile, nuclear receptor co-repressor 2 (NCoR2) was highly expressed in the notch signaling pathway, indicating that NCoR2 might be involved in the regulation of gonad development. To validate the transcriptome data, we selected five DEGs in the KEGG signaling pathway, including AChRs, CCKAR, HCRTR2, GABAB, and NCoR2, for real-time quantitative PCR (RT-qPCR), which produced results consistent with the RNA-Seq data. The transcriptome analysis and gene pathway identification in this study have enhanced our comprehension of the reproductive mechanisms in M. unguiculatus. Full article
(This article belongs to the Special Issue Omics Analysis in Marine Invertebrate Biology)
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19 pages, 1571 KiB  
Article
Comparative Transcriptomic Analysis Reveals Adaptive Traits in Antarctic Scallop Adamussium colbecki
by Samuele Greco, Giacomo Voltarel, Anastasia Serena Gaetano, Chiara Manfrin, Alberto Pallavicini, Piero Giulio Giulianini and Marco Gerdol
Fishes 2023, 8(6), 276; https://doi.org/10.3390/fishes8060276 - 23 May 2023
Cited by 3 | Viewed by 1605
Abstract
Antarctica is the most extreme continent of Earth, with strong winds, freezing temperatures on land, and ocean temperatures constantly below 0 °C. Nonetheless, the Antarctic Ocean is home to an astounding diversity of living organisms that adapted to the multiple challenges posed by [...] Read more.
Antarctica is the most extreme continent of Earth, with strong winds, freezing temperatures on land, and ocean temperatures constantly below 0 °C. Nonetheless, the Antarctic Ocean is home to an astounding diversity of living organisms that adapted to the multiple challenges posed by this environment via a diverse set of evolutionary traits. Although the recent advancements in sequencing technologies clarified the molecular bases of such adaptations in Antarctic fishes, little information is available for Antarctic invertebrates. In this preliminary study, we address this knowledge gap with a comparative transcriptomic approach to obtain insights into some of the adaptations that allow the Antarctic scallop Adamussium colbecki to survive and thrive in the freezing waters of the Antarctic Ocean. Despite some limitations, our analyses highlighted significant over-expression of genes involved in regulation of mRNA transcription, maturation, and degradation, which might compensate for a reduced efficiency of these processes at low temperatures. Other alterations detected in the Antarctic scallop transcriptome include enhanced expression of genes that regulate degradation of misfolded protein products and allow maintenance of cytoskeletal structure and function at subzero temperatures. Altogether, these observations support the presence of multiple previously unreported molecular adaptive traits in A. colbecki, which have important implications for our understanding of adaptation of this important component of the Antarctic trophic chain to such an extreme, but stable environment. Full article
(This article belongs to the Special Issue Omics Analysis in Marine Invertebrate Biology)
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24 pages, 2022 KiB  
Article
Transcriptional Profiling of Populations in the Clam Ruditapes decussatus Suggests Genetically Determined Differentiation in Gene Expression along Parallel Temperature Gradients and between Races of the Atlantic Ocean and West Mediterranean Sea
by Carlos Saavedra, Massimo Milan, Ricardo B. Leite, David Cordero, Tomaso Patarnello, M. Leonor Cancela and Luca Bargelloni
Fishes 2023, 8(4), 203; https://doi.org/10.3390/fishes8040203 - 14 Apr 2023
Cited by 1 | Viewed by 2001
Abstract
Ongoing ocean warming due to climate change poses new challenges for marine life and its exploitation. We have used transcriptomics to find genetically based responses to increased temperature in natural populations of the marine clam Ruditapes decussatus, which lives along parallel thermal [...] Read more.
Ongoing ocean warming due to climate change poses new challenges for marine life and its exploitation. We have used transcriptomics to find genetically based responses to increased temperature in natural populations of the marine clam Ruditapes decussatus, which lives along parallel thermal gradients in southern Europe. Clams of the Atlantic and West Mediterranean races were collected in northern (cool) and a southern (warm) localities. The animals were kept in running seawater in the warm, southern Atlantic locality for a 15-week period. During this period, water temperature was raised to typical southern European summer values. After this period, an expression profile was obtained for a total of 34 clams and 11,025 probes by means of an oligonucleotide microarray. We found distinct transcriptional patterns for each population based on a total of 552 differentially expressed genes (DEGs), indicating innate differences which probably have a genetic basis. Race and latitude contributed significantly to gene expression differences, with very different sets of DEGs. A gene ontology analysis showed that races differed mainly in the genes involved in ribosomal function and protein biosynthesis, while genes related to glutathione metabolism and ATP synthesis in the mitochondria were the most outstanding with respect to north/south transcriptional differences. Full article
(This article belongs to the Special Issue Omics Analysis in Marine Invertebrate Biology)
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