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Fishes
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Application of Transcriptomics in Fish
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Application of Transcriptomics in Fish

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

Deadline for manuscript submissions: closed (8 September 2023) | Viewed by 8478

Special Issue Editor

Prof. Dr. Qiuning Liu

E-Mail Website
Guest Editor
School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
Interests: fish; genomics; immunity; transcriptome; toxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As the most diverse and abundant group of extant vertebrates, fishes are of great economic and medical value as a primary source of protein for people worldwide and are of great evolutionary, ecological, and economic importance. Transcriptome analysis is a powerful tool, providing better understanding of the molecular mechanisms underlying adaptation to extreme conditions (temperature, pH, etc.), sex determination, defense, molecular breeding, nutrition regulation, etc., especially in non-model fish organisms. However, the transcriptome data of fishes are relatively underrepresented, and the published genetic data represent only a small fraction of extant fish species. To enhance the study of fish biology and contribute efforts toward fish biodiversity conservation and the sustainable utilization of natural fish resources, we are pleased to invite you to contribute to this Special Issue on “Application of Transcriptomics in Fish” in the Fishes journal.

Dr. Qiuning Liu
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. 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

  • fish
  • transcriptomics
  • acclimatization
  • molecular mechanisms

Published Papers (6 papers)

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Research

20 pages, 8974 KiB  
Article
Comparative Analysis of Hepatopancreas RNA-Seq of Juvenile Grass Carp (Ctenopharyngodon idella) Fed Different Starch Diets
by Jingjing Zhang, Xue Guo, Zhen Han, Letian Qu, Teng Xia, Xiangning Chen, Jianhe Xu, Zhujin Ding, Chaoqing Wei and Hanliang Cheng
Fishes 2023, 8(10), 495; https://doi.org/10.3390/fishes8100495 - 03 Oct 2023
Cited by 1 | Viewed by 974
Abstract
This study aimed to explore the effects of different starch source diets on the growth performance and hepatopancreas RNA-seq of grass carp. Juvenile grass carp (initial body weight of 39.4 ± 1.6 g) were fed diets containing 25% corn (CO), potato (PO), and [...] Read more.
This study aimed to explore the effects of different starch source diets on the growth performance and hepatopancreas RNA-seq of grass carp. Juvenile grass carp (initial body weight of 39.4 ± 1.6 g) were fed diets containing 25% corn (CO), potato (PO), and wheat (WH) starch for 8 weeks, respectively. The weight gain ratio (WGR) was significantly lower, whereas the visceral somatic index (VSI) and feed conversion ratio (FCR) were significantly higher in the CO group than those in the PO and WH groups. These indicators did not significantly differ between the PO and WH groups. Hepatopancreas RNA-seq analysis showed that 536, 514, and 647 differentially expressed genes (DEGs) were screened out in the comparisons of PO vs. WH, PO vs. CO, and CO vs. WH. The DEGs were mainly enriched in the several known pathways involved in steroid biosynthesis, cell cycle, fatty acid metabolism, and fat digestion and absorption according to Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis. The major DEGs related to lipid and carbohydrate metabolism were analyzed, in which lipogenesis-related DEGs (fasn, acc1, scd1, elovl6, and me1), fat digestion and absorption-related DEGs (fabp7, apoa1, apoa4, and pla2), and glycometabolism-related DEGs (gk, g6pd, and pepck) were down-regulated in the PO group compared with those in the CO and WH groups. Conversely, steroid synthesis-related DEGs (hmgcs, fdft1, sqle, lss, cyp51, msmo1, nsdhl, ugt, cyp1b1, and cyp7a1) were up-regulated in the PO group. These results indicate that the long-term PO ingestion could modulate hepatic lipid metabolism by reducing fatty acid biosynthesis and increasing bile acid biosynthesis. PO may be healthier in contrast to CO alone, which may not be suitable as a starch source in grass carp diet. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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13 pages, 3547 KiB  
Article
Molecular Identification and Expression Analysis of an Intelectin Gene in the Yellow Catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae)
by Senhao Jiang, Yuting Lei, Yanxuan Li, Wanyan Sun, Ti Wang, Ruiting Ma, Qiuning Liu and Boping Tang
Fishes 2023, 8(10), 492; https://doi.org/10.3390/fishes8100492 - 02 Oct 2023
Cited by 1 | Viewed by 942
Abstract
Intelectins (ITLNs) are a family of calcium-dependent lectins with carbohydrate-binding capacity, are distributed across various vertebrates, and play an important role in the innate immune response against pathogen infection. The yellow catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae) is an economically important fish [...] Read more.
Intelectins (ITLNs) are a family of calcium-dependent lectins with carbohydrate-binding capacity, are distributed across various vertebrates, and play an important role in the innate immune response against pathogen infection. The yellow catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae) is an economically important fish in China. The aim of this study was to quantify the gene expression of ITLN in response to pathogen-associated molecular patterns (PAMPs) stimulation. Here, the ITLN gene of P. fulvidraco was characterized and named PfITLN. The full-length cDNA of PfITLN was 1132 bp, including a 5’-untranslated region (UTR) of 140 bp, a 3’-UTR of 110 bp, and an open reading frame (ORF) of 882 bp encoding a polypeptide of 293 amino acids, which contains a signal peptide and two fibrinogen-related domains (FReDs). PfITLN had a molecular weight of 32.39 kDa with a theoretical pI of 5.03. The deduced PfITLN amino acid sequence had 81%, 64%, and 55% homology with Ictalurus furcatus, Danio rerio, and Homo sapiens, respectively. Moreover, the predicted tertiary protein structure of PfITLN was highly similar to that of other animals, and phylogenetic analysis showed that the PfITLN protein was close to those of other Teleostei. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis showed PfITLN expression in all examined tissues, with the highest abundance seen in the liver, followed by the head kidney, spleen, trunk kidney, and muscle. After PAMP infection with lipopolysaccharide (LPS) and polyriboinosinic polyribocytidylic acid (poly I:C), the expression levels of PfITLN were significantly upregulated at different time points. These results suggested that PfITLN might be involved in innate immunity. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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20 pages, 8124 KiB  
Article
RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer
by Neetu Shahi, Bhupendra Singh, Sumanta Kumar Mallik, Debajit Sarma and Win Surachetpong
Fishes 2023, 8(7), 352; https://doi.org/10.3390/fishes8070352 - 05 Jul 2023
Viewed by 1268
Abstract
Golden mahseer (Tor putitora) is a critically endangered fish with significant economic importance. However, its reproductive challenges in a captive environment pose a limitation to the successful domestication and aquaculture potential of this species. To understand the role of various genes [...] Read more.
Golden mahseer (Tor putitora) is a critically endangered fish with significant economic importance. However, its reproductive challenges in a captive environment pose a limitation to the successful domestication and aquaculture potential of this species. To understand the role of various genes in gonad maturation and reproduction in golden mahseer, we conducted an RNA-sequencing (RNA-Seq) study on the brains of mature male and female specimens. Altogether, 20.6 and 21.5 million reads were generated from the brains of the male and female fish, respectively. A total of 26,989 and 55,600 cDNA coding sequences (CDS) were identified from the male and female brains, respectively, among which 26,258 CDS from the male brain and 53,446 CDS from the female brain demonstrated homology to known protein database sequences. A comprehensive analysis revealed a total of 1187 distinct differentially expressed upregulated genes (DEGs), encompassing 953 DEGs anticipated to exhibit upregulation in the female brain and 234 DEGs in the male brain. Furthermore, in the brain of female and male golden mahseer, a significant downregulation was observed in 492 and 744 genes, respectively, resulting in a cumulative count of 1236 downregulated genes. Validation of the RNA-Seq results was performed by quantitative real-time PCR (qPCR) using 24 genes. Sixteen candidate genes with differential expression levels between the male and female fish were then selected and analyzed via qPCR. The results confirmed that amh, foxl3, dax1, kif20, and tkt were upregulated in the male golden mahseer brain, while cyp19a1a, dmrt2a, gdf9, sox9b, wt-1a, and aqp1 were upregulated in the female golden mahseer brain. Our study elucidates the distinct gene expression profiles in male and female golden mahseer brains and thus offers valuable insights for potential reproductive manipulation strategies in this fish species. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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13 pages, 2170 KiB  
Article
Transcriptome Analysis Reveals Differences in Gene Expression in the Muscle of the Brown-Marbled Grouper (Epinephelus fuscoguttatus) with Different Growth Rates
by Tong Wang, Yang Yang, Shirui Gong, Xi Wu, Leilei Zeng, Yuhao Tao, Chaoyue Zhong, Leling Song and Xiaochun Liu
Fishes 2023, 8(6), 309; https://doi.org/10.3390/fishes8060309 - 08 Jun 2023
Viewed by 1311
Abstract
Brown-marbled grouper is one of the most important mariculture species in China and is widely used as a crossbreeding parent in the grouper industry. Enhancing growth rates is a key target in fish breeding, and gaining insight into the underlying mechanisms responsible for [...] Read more.
Brown-marbled grouper is one of the most important mariculture species in China and is widely used as a crossbreeding parent in the grouper industry. Enhancing growth rates is a key target in fish breeding, and gaining insight into the underlying mechanisms responsible for growth differences between individuals can aid in the improvement of grouper growth rates. However, the mechanism behind growth differences in this fish remains unclear. We analyzed the transcriptome profiles of muscle tissues between fast- and slow-growing brown-marbled grouper using RNA-seq and identified 77 significantly up-regulated genes and 92 significantly down-regulated genes in the extreme growth groups. Our findings suggest that up-regulated genes such as ghr and tnni2, as well as down-regulated genes such as stc2 and pdp1, are associated with growth advantages in brown-marbled grouper. We used differentially expressed genes (DEGs) for GO and KEGG enrichment analyses. The results of the GO enrichments showed that the significantly up-regulated genes in the fast-growing group were involved in protein folding, the actin cytoskeleton, the myosin complex, and other processes. The results of the KEGG enrichments showed that the significantly up-regulated genes in the fast-growing group were involved in various pathways such as glycolysis/gluconeogenesis, adipocytokine signaling, MAPK signaling, carbon metabolism, and PI3K-Akt signaling. Additionally, gene set enrichment analysis (GSEA) showed that the PI3K/AKT/mTOR pathway was up-regulated in the fast-growing group, which may be responsible for the higher nutrient absorption efficiency and muscle growth in these fish. Our results contribute to a better understanding of the molecular mechanisms and regulatory pathways underlying fast growth in brown-marbled grouper. However, further studies are necessary to fully elucidate the mechanisms behind growth differences between individuals. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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15 pages, 4395 KiB  
Article
De Novo Transcriptome Analysis of the Early Hybrid Triploid Loach (Misgurnus anguillicaudatus) Provides Novel Insights into Fertility Mechanism
by Ziyu Zhou, Gu Shan, Xin Li, Wenxuan Guo, Kexin Ma, Yueyao Yang, Yifan Li, Yunbang Zhang, He Zhou and Xiaojuan Cao
Fishes 2023, 8(2), 70; https://doi.org/10.3390/fishes8020070 - 23 Jan 2023
Cited by 2 | Viewed by 1401
Abstract
As a new freshwater aquaculture product, triploid loaches (Misgurnus anguillicaudatus) are characterized by fast growth, high-quality meat, high edibility, high resistance to disease, and sterility. In this study, a natural tetraploid loach (4n = 100) (♀) was crossed with a diploid [...] Read more.
As a new freshwater aquaculture product, triploid loaches (Misgurnus anguillicaudatus) are characterized by fast growth, high-quality meat, high edibility, high resistance to disease, and sterility. In this study, a natural tetraploid loach (4n = 100) (♀) was crossed with a diploid loach (2n = 50) (♂), thus creating the hybrid triploid loach (3n = 75). The histological observations of triploid offspring and diploid controls at 4 days post-hatching (dph), 15dph, 22dph, and 50dph showed that most of the hybrid triploid loaches were abortive in the early gonad differentiation process. To explore its fertility mechanism, through transcriptome analyses of triploid offspring and diploid controls at four periods, 10 differentially expressed genes related to the early fertility mechanism were identified: amh, hormad1, rec8, h2b, plvap, zp3, h2a, nrb0b1, ddx4, and esr2. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs, two pathways were identified that are closely related to the early fertility mechanism at 50dph: the estrogen signaling pathway and steroid biosynthesis. The findings laid a foundation for further exploration of their molecular inhibition mechanism in hybrid triploid loaches. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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17 pages, 2833 KiB  
Article
Transcriptome Analysis of the Immune Process of Golden Pompano (Trachinotus ovatus) Infected with Streptococcus agalactiae
by Jie Gao, Hua-Yang Guo, Ming-Jian Liu, Ke-Cheng Zhu, Bo Liu, Bao-Suo Liu, Nan Zhang, Shi-Gui Jiang and Dian-Chang Zhang
Fishes 2023, 8(1), 52; https://doi.org/10.3390/fishes8010052 - 13 Jan 2023
Cited by 7 | Viewed by 1834
Abstract
The golden pompano (Trachinotus ovatus) is one of the most economically valuable marine fishes in South China. Streptococcus agalactiae, an infectious Gram-positive bacterium that is highly destructive for golden pompano culture, has recently caused massive losses to the golden pompano [...] Read more.
The golden pompano (Trachinotus ovatus) is one of the most economically valuable marine fishes in South China. Streptococcus agalactiae, an infectious Gram-positive bacterium that is highly destructive for golden pompano culture, has recently caused massive losses to the golden pompano industry. This study aimed to investigate the dynamic immune response of golden pompano to S. agalactiae infection, using RNA-seq analysis at two different time points after infection. Abundances of differentially expressed genes (DEGs) gradually increased in the liver and spleen 48–120 h post-infection, whereas those in the head kidney were lower at 120 h than at 48 h. Pathway enrichment analysis of DEGs revealed that genes related to the complement system were continuously transcribed between 48 and 120 h. Metabolic and immune-regulation-related pathways were highly enriched in the liver 48 h after infection. Transcriptome analysis was verified using quantitative PCR for eight genes with similar expression trends. This study revealed the inflammatory response of golden pompano after S. agalactiae infection, including inflammation-related chemokines and signaling pathways. Our findings provide a theoretical basis for studying S. agalactiae resistance in golden pompano and provide a reliable resource for the genetic breeding of fish. Full article
(This article belongs to the Special Issue Application of Transcriptomics in Fish)
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