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Genetics and Genomics Applied to Aquatic Animal Science
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Genetics and Genomics Applied to Aquatic Animal Science

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

Deadline for manuscript submissions: closed (20 November 2023) | Viewed by 4603

Special Issue Editors

Dr. Shaokui Yi

E-Mail Website
Guest Editor
College of Life Sciences, Huzhou University, Huzhou 313000, China
Interests: RNA-seq; bioinformatics; functional genomics; GWAS; livestock genomics; conservation of animal genetic resources
Dr. Cong Zeng

E-Mail Website
Guest Editor
School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: marine conservation; aquatic animals; integrating ecology; evolution; genetics; spatial analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquatic animals play critical roles in global food supply and have become one of the primary sources for human diets. Compared to crops and livestock, the production of aquatic animals is fast-growing due to modern aquaculture and genetic improvement of aquatic animals. Genetic improvement of economic traits via molecular selective breeding has become increasingly important to help meet the rising food demand driven by human population growth. In particular, the genetics and genomics of aquatic animals provide huge opportunities for genetic gains in breeding programmes.

With the continuous advances in sequencing techniques and bioinformatics, genetics and genomics have been widely used in breeding studies of aquatic animals in recent years. For instance, ultra-long reads generated by PacBio or Nanopore sequencing platforms allow us to obtain a large number of genetic variations and candidate functional genes associated with breeding traits. Additionally, with the aid of RNA-seq and whole genome sequencing or resequencing methods, we could accurately evaluate the genetic regulation patterns and genetic backgrounds of aquatic resources.

In this Special Issue, we welcome papers in the field of the genetics and genomics of aquatic animals, such as fish, crustaceans, and turtles, including the identification of candidate functional genes or QTLs related to important traits and genetic resource evaluation with genome-wide markers. Manuscripts focusing on the application of high-throughput sequencing approaches and biotechnological innovations, such as RNA-seq, gene editing, WGS, genome resequencing in genome selection, and BS-seq, will be appreciated.

Dr. Shaokui Yi
Dr. Cong Zeng
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

  • breeding trait
  • gene function
  • genetic map
  • gene editing
  • transcriptome
  • GWAS
  • QTL
  • genome resequencing
  • molecular marker

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Published Papers (3 papers)

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Research

16 pages, 13071 KiB  
Article
Comparative Transcriptomic Analysis of Largemouth Bass (Micropterus salmoides) Livers Reveals Response Mechanisms to High Temperatures
by Fan Zhou, Ming Qi, Jiapeng Li, Yuanfei Huang, Xiaoming Chen, Wei Liu, Gaohua Yao, Qinghui Meng, Tianlun Zheng, Zhanqi Wang and Xueyan Ding
Genes 2023, 14(11), 2096; https://doi.org/10.3390/genes14112096 - 17 Nov 2023
Cited by 3 | Viewed by 1470
Abstract
High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for [...] Read more.
High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the ‘ECM-receptor interaction’ pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the ‘ECM-receptor interaction’ pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science)
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15 pages, 3739 KiB  
Article
Characterization and Expression Analysis of Genes from Megalobrama amblycephala Encoding Hemoglobins with Extracellular Microbicidal Activity
by Qijun Wang, Xiaoheng Zhao, Yunlong Liu, Juan Zheng, Hujun Cui, Haotong Wang, Houxu Ding, Hong Liu and Zhujin Ding
Genes 2023, 14(10), 1972; https://doi.org/10.3390/genes14101972 - 22 Oct 2023
Cited by 2 | Viewed by 1294
Abstract
Hemoglobin (Hb) usually comprises two α and two β subunits, forming a tetramer responsible for oxygen transportation and storage. Few studies have elucidated fish hemoglobin immune functions. Megalobrama amblycephala is a freshwater-cultured fish prevalent in China. We identified two M. amblycephala hemoglobin subunits [...] Read more.
Hemoglobin (Hb) usually comprises two α and two β subunits, forming a tetramer responsible for oxygen transportation and storage. Few studies have elucidated fish hemoglobin immune functions. Megalobrama amblycephala is a freshwater-cultured fish prevalent in China. We identified two M. amblycephala hemoglobin subunits and analyzed their expression patterns and antibacterial activities. The respective full-length cDNA sequences of the M. amblycephala Hb α (MaHbα) and β (MaHbβ) subunits were 588 and 603 bp, encoding 143 and 148 amino acids. MaHbα and MaHbβ were highly homologous to hemoglobins from other fish, displaying typical globin-like domains, most heme-binding sites, and tetramer interface regions highly conserved in teleosts. In phylogenetic analyses, the hemoglobin genes from M. amblycephala and other cypriniformes clustered into one branch, and those from other fishes and mammals clustered into other branches, revealing fish hemoglobin conservation. These M. amblycephala Hb subunits exhibit different expression patterns in various tissues and during development. MaHbα is mainly expressed in the blood and brain, while MaHbβ gene expression is highest in the muscle. MaHbα expression was detectable and abundant post-fertilization, with levels fluctuating during the developmental stages. MaHbβ expression began at 3 dph and gradually increased. Expression of both M. amblycephala Hb subunits was down-regulated in most examined tissues and time points post-Aeromonas hydrophila infection, which might be due to red blood cell (RBC) and hematopoietic organ damage. Synthetic MaHbα and MaHbβ peptides showed excellent antimicrobial activities, which could inhibit survival and growth in five aquatic pathogens. Two M. amblycephala hemoglobin subunits were identified, and their expression patterns and antibacterial activities were analyzed, thereby providing a basis for the understanding of evolution and functions of fish hemoglobins. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science)
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14 pages, 3156 KiB  
Article
The Dynamics of Gene Expression Unraveling the Immune Response of Macrobrachium rosenbergii Infected by Aeromonas veronii
by Xin Peng, Xuan Lan, Zhenxiao Zhong, Haihui Tu, Xinyi Yao, Qiongying Tang, Zhenglong Xia, Guoliang Yang and Shaokui Yi
Genes 2023, 14(7), 1383; https://doi.org/10.3390/genes14071383 - 30 Jun 2023
Cited by 2 | Viewed by 1392
Abstract
To further investigate the immune response of Macrobrachium rosenbergii against Aeromonas veronii, comparative transcriptomic analyses of the M. rosenbergii hepatopancreas were conducted on challenge and control groups at 6, 12, and 24 h post-infection (hpi), independently. A total of 51,707 high-quality unigenes [...] Read more.
To further investigate the immune response of Macrobrachium rosenbergii against Aeromonas veronii, comparative transcriptomic analyses of the M. rosenbergii hepatopancreas were conducted on challenge and control groups at 6, 12, and 24 h post-infection (hpi), independently. A total of 51,707 high-quality unigenes were collected from the RNA-seq data, and 8060 differentially expressed genes (DEGs) were discovered through paired comparisons. Among the three comparison groups, a KEGG pathway enrichment analysis showed that 173 immune-related DEGs were considerably clustered into 28 immune-related pathways, including the lysosome, the phagosome, etc. Moreover, the expression levels of the four key immune-related genes (TOLL, PAK1, GSK3β, and IKKα) were evaluated at various stages following post-infection in the hepatopancreas, hemolymph, and gills. Both PAK1 and GSK3β genes were highly up-regulated in all three tissues at 6 hpi with A. veronii; TOLL was up-regulated in the hepatopancreas and hemolymph but down-regulated in the gill at 6 hpi, and IKKα was up-regulated in hemolymph and gill, but down-regulated in the hepatopancreas at 6 hpi. These findings lay the groundwork for understanding the immune mechanism of M. rosenbergii after contracting A. veronii. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science)
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