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Animals
Special Issues
Functional Genomics in Aquatic Species – Gene Expression and Epigenetic Modifications
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Functional Genomics in Aquatic Species – Gene Expression and Epigenetic Modifications

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 June 2023) | Viewed by 1413

Special Issue Editors

Dr. Emmanouil Malandrakis

E-Mail Website
Guest Editor
Laboratory of Applied Hydrobiology, Department of Animal Science, Agricultural University of Athens, 11855 Athens, Greece
Interests: aquaculture; fish welfare; fish transcriptomics; gene expression
Dr. Ioannis Konstantinidis

E-Mail Website
Guest Editor
Faculty of Biosciences and Aquaculture, Nord University, 8006 Bodø, Norway
Interests: aquaculture; genomics; epigenetics; epitranscriptomics

Special Issue Information

Dear Colleagues, 

Aquatic animals are of great ecological and economic importance and are studied with the aim of understanding basic biological processes by providing insights into the structure and function of higher vertebrate systems. Furthermore, such studies intend to answer questions mainly related to animal production or environmental interactions. Technological advances, mainly in sequencing technologies, enhanced our ability to study various molecular components and expanded our knowledge in transcriptomics and epitranscriptomics across many aquatic organisms. Cultured aquatic animals are studied mainly focusing on reproduction, development, nutrition, growth and responses to stress and diseases. In addition, model aquatic organisms are broadly used for the study of fundamental systems in biology, as well as environmental stressors such as toxicology and infection. The aim of this Special Issue is to collect the most recent advances in interdisciplinary research conducted in functional genomics of aquatic animals. We invite you to share your scientific expertise in transcriptomics and epigenetics of aquatic organisms.

We look forward to receiving your contributions.

Dr. Emmanouil Malandrakis
Dr. Ioannis Konstantinidis
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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • aquatic animals
  • transcriptomics
  • epigenetics
  • epitranscriptomics
  • gene expression
  • aquaculture
  • meta-genomics

Published Papers (1 paper)

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Research

13 pages, 3100 KiB  
Article
Candidate Regulatory Genes for Hindlimb Development in the Embryos of the Chinese Alligator (Alligator sinensis)
by Liuyang Yang, Mengqin Liu, Yunzhen Zhu, Yanan Li, Tao Pan, En Li and Xiaobing Wu
Animals 2023, 13(19), 3126; https://doi.org/10.3390/ani13193126 - 06 Oct 2023
Viewed by 1009
Abstract
Crocodilians, which are a kind of animal secondary adaptation to an aquatic environment, their hindlimb can provide the power needed to engage in various life activities, even in low-oxygen water environments. The development of limbs is an important aspect of animal growth and [...] Read more.
Crocodilians, which are a kind of animal secondary adaptation to an aquatic environment, their hindlimb can provide the power needed to engage in various life activities, even in low-oxygen water environments. The development of limbs is an important aspect of animal growth and development, as it is closely linked to body movement, support, heat production, and other critical functions. For the Chinese alligator, the hindlimb is one of the main sources of power, and its development and differentiation will directly influence the survival ability in the wild. Furthermore, a better understanding of the hindlimb developmental process will provide data support for the comparative evolutionary and functional genomics of crocodilians. In this study, the expression levels of genes related to hindlimb development in the Chinese alligator embryos during fetal development (on days 29, 35, 41, and 46) were investigated through transcriptome analysis. A total of 1675 differentially expressed genes (DEGs) at different stages were identified by using limma software. These DEGs were then analyzed using weighted correlation network analysis (WGCNA), and 4 gene expression modules and 20 hub genes were identified that were associated with the development of hindlimbs in the Chinese alligator at different periods. The results of GO enrichment and hub gene expression showed that the hindlimb development of the Chinese alligator embryos involves the development of the embryonic structure, nervous system, and hindlimb muscle in the early stage (H29) and the development of metabolic capacity occurs in the later stage (H46). Additionally, the enrichment results showed that the AMPK signaling pathway, calcium signaling pathway, HIF-1 signaling pathway, and neuroactive ligand–receptor interaction are involved in the development of the hindlimb of the Chinese alligator. Among these, the HIF-1 signaling pathway and neuroactive ligand–receptor interaction may be related to the adaptation of Chinese alligators to low-oxygen environments. Additionally, five DEGs (CAV1, IRS2, LDHA, LDB3, and MYL3) were randomly selected for qRT-PCR to verify the transcriptome results. It is expected that further research on these genes will help us to better understand the process of embryonic hindlimb development in the Chinese alligator. Full article
(This article belongs to the Special Issue Functional Genomics in Aquatic Species – Gene Expression and Epigenetic Modifications)
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