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Fishes
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Transcriptomics in Aquaculture: Current Status and Applications
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Transcriptomics in Aquaculture: Current Status and Applications

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

Deadline for manuscript submissions: closed (10 February 2023) | Viewed by 16645

Special Issue Editors

Dr. Changxu Tian

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Guest Editor
Fisheries College, Guangdong Ocean University, Zhanjiang 524091, China
Interests: fish; omics; breeding; genetics; environmental stressors; sex determination; reproductive biology
Special Issues, Collections and Topics in MDPI journals
Dr. Zihao Yuan

E-Mail
Guest Editor
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
Interests: pathogen–host interaction; aquatic animal immunology; immune system evolution; marine virus; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Transcriptome sequencing based on next-generation sequencing (NGS) has brought novel insights into our understanding of cell RNA expression from a global view. Transcriptome research has focused on various aquaculture research areas, targeting different aspects, including physiology and endocrinology, genetic breeding, nutrition, environmental stress response, disease, and health management. Notably, RNA sequencing technologies are an efficient approach for discovering novel and essential genes in an unbiased manner, which offers momentous potential for improving commercially important production traits in aquatic species. In this regard, this Special Issue focuses on the latest advances in the study of transcriptomes in aquaculture species via NGS-based technologies.

The scope of this Special Issue of Fishes covers a wide range of studies aimed at exploring various aspects of transcriptomics in aquaculture using NGS methods. Submissions may include original reports, reviews, perspectives, and methodology articles.

Dr. Changxu Tian
Dr. Zihao Yuan
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.

Keywords

  • aquaculture
  • RNA-seq
  • economic traits
  • gene expression regulation
  • next-generation sequencing

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Published Papers (7 papers)

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15 pages, 2947 KiB  
Article
Metabonomic Analysis of Macrobrachium rosenbergii with Iron Prawn Syndrome (IPS)
by Xi-Lian Li, Pei-Jing Shen, Wen-Ping Jiang, Ji-Lun Meng, Hai-Hua Cheng and Qiang Gao
Fishes 2023, 8(4), 196; https://doi.org/10.3390/fishes8040196 - 9 Apr 2023
Viewed by 1969
Abstract
We previously reported on the comparison of proteomic data between seven tissue types of a novel “iron prawn” species. However, no transcripts or metabolic information are available for this species. We therefore performed shotgun LC–MS/MS metabonomic and RNA-seq analyses of the total protein [...] Read more.
We previously reported on the comparison of proteomic data between seven tissue types of a novel “iron prawn” species. However, no transcripts or metabolic information are available for this species. We therefore performed shotgun LC–MS/MS metabonomic and RNA-seq analyses of the total protein from “iron prawns”. KEGG analysis revealed that the largest group consisted of a total of 114 KEGG pathway proteins, comparing the “iron prawns” with the normal prawns. A total of 423 peptides, corresponding to metabolic pathways, ABC transporters, starch and sucrose metabolism, insulin resistance/secretion, fatty digestion and absorption, and lipid metabolism, were identified. The pathways of carbohydrate and amino acid metabolism decreased in female iron prawns, while organic acid and its derivatives increased. However, the pathway of organic acid and its derivatives decreased and lipid metabolism increased in the male iron prawns. The pathways of choline metabolism in cancer and glycerophospholipid/histidine/propanoate metabolism have been significantly affected in iron prawns. Our work provides insight into the understanding of the formation mechanism of the “iron prawn”. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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17 pages, 3102 KiB  
Article
Transcriptomic Analysis and Functional Gene Expression in Different Stages of Gonadal Development of Macrobrachium rosenbergii
by Zhenxiao Zhong, Guozhu Chen, Haihui Tu, Xinyi Yao, Xin Peng, Xuan Lan, Qiongying Tang, Shaokui Yi, Zhenglong Xia, Miaoying Cai and Guoliang Yang
Fishes 2023, 8(2), 94; https://doi.org/10.3390/fishes8020094 - 5 Feb 2023
Cited by 7 | Viewed by 2264
Abstract
In order to decipher the functional genes and reveal the molecular mechanism of gonadal development in Macrobrachium rosenbergii, a comparative transcriptome analysis was performed on the testes and ovaries at different developmental stages. A total of 146,537 unigenes with an N50 of [...] Read more.
In order to decipher the functional genes and reveal the molecular mechanism of gonadal development in Macrobrachium rosenbergii, a comparative transcriptome analysis was performed on the testes and ovaries at different developmental stages. A total of 146,537 unigenes with an N50 of 2008 bp and an average length of 1144 bp were obtained from the sequencing raw data via quality control and denovo assembly. Identification of differentially expressed genes (DEGs) showed that there were 339 and 468 DEGs among the different developmental stages of testes and ovaries, respectively, and 7993 DEGs between the testes and ovaries. The KEGG enrichment analysis identified 13 candidate pathways related to gonadal development, including insulin synthesis, oocyte maturation, and steroid biosynthesis, which were involved in biological processes such as regulation of hormone metabolism, sex cell proliferation and development, and amino acid metabolism. The DEGs related to the above pathways such as insulin-like growth factor 1 receptor (IGF1R), heat shock protein 90 (Hsp 90), and cyclooxygenase (COX) genes were highly expressed during yolk protein synthesis, indicating that these genes might be involved in yolk accumulation and oogenesis. Meanwhile, calmodulin (CaM) and other genes were highly expressed during spermatogenesis, suggesting that these genes might play an important role in spermatogenesis. Ten differentially expressed genes in the KEGG signaling pathway, including CRQ, COX, APP, Cdc42, Hsd17b12, Art-1, Hsp70, Hsp90, PRMT1, and GP, were selected for real-time quantitative PCR (RT- qPCR) to validate the transcriptome data, and the results showed that RT- qPCR obtained consistent results with the RNA-Seq data. The present findings provide new insights into the molecular regulation mechanism of gonadal development in M. rosenbergii. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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13 pages, 2593 KiB  
Article
Transcriptomic and Metabolomic Analyses of Palaemon carinicauda Hepatopancreas in Response to Enterocytozoon hepatopenaei (EHP) Infection
by Guangwei Hu, Weili Wang, Kai Xu, Chao Wang, Dexue Liu, Jing Xu, Binlun Yan, Nanjing Ji and Huan Gao
Fishes 2023, 8(2), 92; https://doi.org/10.3390/fishes8020092 - 5 Feb 2023
Cited by 7 | Viewed by 2515
Abstract
Enterocytozoon hepatopenaei (EHP), a microsporidian responsible for hepatopancreatic microsporidiosis, is a major pathogen in commercial shrimp production. Among the affected species, Palaemon carinicauda (formerly Exopalaemon carinicauda) is commercially important in China and represents a potential research model for studying crustaceans. However, little [...] Read more.
Enterocytozoon hepatopenaei (EHP), a microsporidian responsible for hepatopancreatic microsporidiosis, is a major pathogen in commercial shrimp production. Among the affected species, Palaemon carinicauda (formerly Exopalaemon carinicauda) is commercially important in China and represents a potential research model for studying crustaceans. However, little information is available on its response to EHP infection. Hence, this study analyzed the transcriptome and metabolome of P. carinicauda’s hepatopancreas using high-throughput sequencing and liquid chromatograph-mass spectrometry (LC-MS) to determine its response during the early stage of infection. The transcriptomic analyses identified 730 differentially expressed genes, of which those associated with EHP infection were enriched in metabolic pathways as well as detoxification and antioxidant pathways. In addition, 144 differential metabolites were identified using a combination of positive and negative ion modes in LC-MS. The Kyoto encyclopedia of genes and genomes pathway analyses further indicated that the degradation of aromatic compounds, the AMP-activated protein kinase signaling pathway and C5-branched dibasic acid metabolism were significantly enriched after EHP infection. These results could provide useful insights into the effects of EHP on shrimps during the early stages of infection and help to understand the mechanisms underlying the stunted growth of shrimps after infection. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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21 pages, 6144 KiB  
Article
The Pathology and Splenic Transcriptome Profiling of Trionyx sinensis Challenged with Bacillus cereus
by Jinbiao Jiao, Jing Chen, Jiayun Yao, Yanli Li, Xuemei Yuan, Lei Huang, Shengqi Su and Haiqi Zhang
Fishes 2023, 8(2), 84; https://doi.org/10.3390/fishes8020084 - 31 Jan 2023
Cited by 2 | Viewed by 2524
Abstract
The pathogenic Bacillus cereus strain XS0724 isolated from China can cause high lethality to Trionyx sinensis, but little information is available on their detailed interactions. In this study, histopathologic profiling indicated that B. cereus caused vacuolization and cell necrosis in the liver, [...] Read more.
The pathogenic Bacillus cereus strain XS0724 isolated from China can cause high lethality to Trionyx sinensis, but little information is available on their detailed interactions. In this study, histopathologic profiling indicated that B. cereus caused vacuolization and cell necrosis in the liver, spleen, kidney, and intestine. The identification of the virulence factor genes non-hemolytic enterotoxin (Nhe), hemolysin BL (Hbl), and enterotoxin FM (entFM) confirmed bacterial pathogenicity. Splenic transcriptomic sequencing at 96 h post-infection identified various immune-related genes mapped to diverse gene families, including interleukin, complement, chemokine, and interferon. The differentially expressed genes (DEGs) were enriched in 2174 GO terms: 1694 in biological processes, 138 in cellular components, and 342 in molecular functions. Further KEGG enrichment indicated that DEGs were primarily associated with the phagosome, NF-kappa B signaling pathway, and PI3K-Akt signaling pathway. The DEGs and enriched pathways may be involved in the elimination of invasive B. cereus. These data laid the foundation for elucidating the potential molecular mechanisms in this bacterial infection process, and provided robust genetic evidence for subsequent work on resistance genes of T. sinensis. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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11 pages, 2436 KiB  
Article
Physiological and Transcriptomic Response of Asiatic Hard Clam Meretrix meretrix to the Harmful Alga Heterosigma akashiwo
by Nanjing Ji, Mingyang Xu, Junyue Wang, Junjia Li, Shishi Liu, Xueyao Yin, Xin Shen and Yuefeng Cai
Fishes 2023, 8(2), 67; https://doi.org/10.3390/fishes8020067 - 22 Jan 2023
Cited by 4 | Viewed by 1938
Abstract
The ichthyotoxic raphidophyte Heterosigma akashiwo is associated with harmful algal blooms (HABs). Although the influence of H. akashiwo on fish has been reported, little is known of its effects on other marine organisms, such as shellfish. In this study, the physiological and [...] Read more.
The ichthyotoxic raphidophyte Heterosigma akashiwo is associated with harmful algal blooms (HABs). Although the influence of H. akashiwo on fish has been reported, little is known of its effects on other marine organisms, such as shellfish. In this study, the physiological and transcriptomic responses of the Asiatic hard clam Meretrix meretrix to H. akashiwo were investigated. The results showed that clam survival was not influenced by H. akashiwo (at a concentration of 2 × 104 cells/mL), and M. meretrix eliminated the alga effectively after 48 h in co-culture. H. akashiwo did not alter the antioxidant capacity of the clams. However, 544 unigenes were found to be differentially expressed between the control and H. akashiwo-treated clams. Interestingly, the significant up-regulation of lysosome-related genes and transport proteins suggested remodeling of the clam metabolism possibly for digestion of H. akashiwo. In summary, our results indicate that the clam M. meretrix can effectively feed on H. akashiwo, and intensification of shellfish farming may be helpful to control and mitigate H. akashiwo blooms. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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16 pages, 2438 KiB  
Article
Evidence for the Growth Superiority and Delayed Ovarian Development in Tetraploid Loach Misgurnus anguillicaudatus
by Xiaoyun Zhou, Zexia Gao, Shuangshuang Luo, Junxiao Su and Shaokui Yi
Fishes 2022, 7(6), 322; https://doi.org/10.3390/fishes7060322 - 8 Nov 2022
Cited by 2 | Viewed by 2035
Abstract
The diploids and tetraploids of cyprinid loach Misgurnus anguillicaudatus coexist in many natural habits. The tetraploids generally exhibit superior growth performance and delayed gonadal development compared with diploids. To investigate the regulation mechanism of growth superiority and ovarian development in tetraploids, we first [...] Read more.
The diploids and tetraploids of cyprinid loach Misgurnus anguillicaudatus coexist in many natural habits. The tetraploids generally exhibit superior growth performance and delayed gonadal development compared with diploids. To investigate the regulation mechanism of growth superiority and ovarian development in tetraploids, we first conducted a long-term culture experiment and histological observation. The tetraploids exhibited a higher growth performance and delayed ovarian development. Meanwhile, at a genetic level, an average of 6891 differentially expressed genes (DEGs) between diploids and tetraploids were identified from the brain, pituitary, liver, gonad and muscle using the RNA-seq method. Among these DEGs, as expected, some candidate genes, including IGF family genes, somatostatin, leptin, cyp19a1b, gthα, lhβ and fshβ, were detected, which play critical roles in the regulation of growth and gonad development of fish. In particular, the genes related to GH/IGF axis and growth factors, signal transduction, gonadal hormone and appetite were significantly increased in tetraploids. The clustering analyses of the key candidate genes showed that most key genes were up-regulated in the pituitary and gonad of tetraploids instead of other tissues. The dynamics of these key genes provide valuable genetic evidence for clarifying the growth superiority and delayed gonadal development of tetraploids. Moreover, this study also provides some clues for unveiling the genetic superiority of polyploidy species in other phenotypes. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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19 pages, 2735 KiB  
Article
Effects of Glutamine Starvation on SHVV Replication by Quantitative Proteomics Analysis
by Junlin Liu, Yulei Zhang, Xiaoyan Liu, Hantao Zhang, Yi Liu, Keping Chen, Min Tang and Lindan Sun
Fishes 2022, 7(6), 315; https://doi.org/10.3390/fishes7060315 - 30 Oct 2022
Cited by 1 | Viewed by 2148
Abstract
Snakehead vesiculovirus (SHVV), a strain of negative-stranded RNA viruses extracted from sick snakehead fish (Ophicephalus striatus), may pose a threat to the health of snakehead fish. Previous research has proved that the replication of SHVV can be significantly inhibited by glutamine [...] Read more.
Snakehead vesiculovirus (SHVV), a strain of negative-stranded RNA viruses extracted from sick snakehead fish (Ophicephalus striatus), may pose a threat to the health of snakehead fish. Previous research has proved that the replication of SHVV can be significantly inhibited by glutamine starvation. To study how glutamine starvation inhibits SHVV replication, channel catfish ovary (CCO) cells with SHVV cultivated in the glutamine-free medium or the complete medium were used to investigate the differentially expressed proteins (DEPs). The results showed that 124 up-regulated and 246 down-regulated proteins were involved in many viral replication physiological processes, such as autophagy, post-translational modifications machinery, and functional pathways, including the PI3K-Akt signaling pathway and mTOR signaling pathway. Furthermore, a few proteins, such as Akt and Hsp90, which have been confirmed to be involved in the replication of RNA viruses, were also significantly differentially expressed. Taken together, our study demonstrated that glutamine starvation affects various functional pathways and the expression of some key proteins related to RNA viral replication, which will benefit future studies on the replication mechanisms of SHVV and the prevention of SHVV infection. Full article
(This article belongs to the Special Issue Transcriptomics in Aquaculture: Current Status and Applications)
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