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The Application of Genetic and Genomic Biotechnology in Aquaculture
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The Application of Genetic and Genomic Biotechnology in Aquaculture

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Marine Biology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 35325

Special Issue Editors

Dr. Baofeng Su

E-Mail Website
Guest Editor
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
Interests: fish breeding and physiology; genome editing; transgenics; applied bioinformatics and genomics; gene function and characterization; mucosal immunity
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Rex Dunham

E-Mail Website
Guest Editor
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
Interests: selective breeding; hybridization; gene transfer; gene mapping and genomics; reproductive physiology
Special Issues, Collections and Topics in MDPI journals
Dr. Xu Wang

E-Mail Website
Guest Editor
Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
Interests: comparative genomics; evolutionary genomics; metagenomics; reproduction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce a Special Issue entitled “The Application of Genetic and Genomic Biotechnology in Aquaculture” in the MDPI journal Biology. We welcome research papers, communications, and review articles focusing on the applications of biotechnological and/or genomic tools to improve our understanding of sustainable development of aquaculture. The goal is to facilitate genetic enhancement program information in the aquaculture industry. Biotechnology has shaped aquaculture, which is the fastest-growing farmed food sector worldwide. Aquaculture has become a major source of concern in animal-based protein sources, food security, and economic stability. The advancement of next-generation sequencing technology, genomics, and genome editing has enabled innovations with a broad range of applications in aquaculture.

This issue on genetics and genomics biotechnology in aquaculture would emphasize improving/exploring important production traits in aquaculture, such as growth, flavor, and disease resistance, among other traits, or using model fish species to study traditional/molecular/quantitative genetics or advanced genomics.

Transgenesis and gene/genome editing have demonstrated the potential to introduce intended genetic changes and corresponding functionalities. Any effort on elucidating the causal associations between genotype and phenotype will be appreciated. As a few massively parallel genome editing platforms or CRISPR arrays have been tested and reprogrammed on model species, we would be glad to evaluate any such reports on aquaculture species.

Traditional selective breeding has increased the efficiency of genetic improvement. Aquaculture species have seen some success in the molecular genetic and genomic application of marker-assisted selection, genomic selection, and multiple trait selection. We would like to explore further the potential on how genomic selection utilizes fish reproduction, fecundity, and external fertilization, and fuels selective breeding programs, and expedites genetic gain for aquaculture production traits.

Understanding the interaction between fishes and environmental pathogens/stressors would facilitate future manipulations of the resistibility of fish and sustainable development of aquaculture. Therefore, efforts on fish immune system, induction, and suppression mechanism of immune effector molecules, pattern recognition receptors, coding, and non-coding RNA molecules on an immune response would be considered. 

The advancement of next-generation sequencing and the decreasing of sequence cost has greatly facilitated the genetic dissection of important traits in aquaculture and exploration regulatory mechanism. A combination of various genomic tools and technologies is more likely to better illustrate the key molecules, pathways, and genetic networks.

Lastly, reviews on biotechnologies or genomics tools for potential future aquaculture research avenues will be considered. Should you have any concerns regarding whether your manuscripts are fit for this Special Issue, please feel free to contact us. We are looking forward to communicating with you for your research and viewpoints.

Any inquiry about paper submission, please feel free to contact the editorial office ([email protected]).

Dr. Baofeng Su
Dr. Rex Dunham
Dr. Xu Wang
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. Biology 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 2700 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

  • selection
  • breeding
  • genetics
  • transgenics
  • genome editing
  • physiology
  • immunity
  • genomics

Published Papers (15 papers)

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Editorial

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4 pages, 217 KiB  
Editorial
The Application of Genetic and Genomic Biotechnology in Aquaculture
by Baofeng Su, Xu Wang and Rex A. Dunham
Biology 2023, 12(1), 127; https://0-doi-org.brum.beds.ac.uk/10.3390/biology12010127 - 13 Jan 2023
Cited by 1 | Viewed by 1571
Abstract
This Special Issue, “The Application of Genetic and Genomic Biotechnology in Aquaculture,” collates 14 published manuscripts covering different aspects of implementing advanced molecular genetics and genomic science in aquaculture [...] Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)

Research

Jump to: Editorial

16 pages, 6719 KiB  
Article
Acute Hypoxia Stress-Induced Apoptosis in Gill of Japanese Flounder (Paralichthys olivaceus) by Modulating the Epas1/Bad Pathway
by Guangling Li, Binghua Liu, Jun Yang, Xiaohui Li, Hao Wang, Haishen Wen and Feng He
Biology 2022, 11(11), 1656; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11111656 - 12 Nov 2022
Cited by 1 | Viewed by 1453
Abstract
The physiological responses and molecular mechanisms of apoptosis in Japanese flounder under hypoxic stress remain unclear. In the present study, we performed acute hypoxia stress on Japanese flounder (2.39 ± 0.84 mg/L) and detected gills responses in histomorphology and molecular mechanisms. The results [...] Read more.
The physiological responses and molecular mechanisms of apoptosis in Japanese flounder under hypoxic stress remain unclear. In the present study, we performed acute hypoxia stress on Japanese flounder (2.39 ± 0.84 mg/L) and detected gills responses in histomorphology and molecular mechanisms. The results showed that the volume of the interlamellar cell mass decreased and the gill lamellae prolonged, indicating the expansion of the respiratory surface area. Additionally, the fluorescence signal of apoptosis increased under hypoxic stress. In addition, the expression of two genes (EPAS1 and Bad) related to apoptosis increased about four-fold and two-fold, respectively, at 6 h of hypoxia. Meanwhile, the result of the dual-luciferase reporter assay showed that EPAS1 is a transcription factor, which could regulate (p < 0.05) the expression of the Bad gene, and we identified the binding site of EPAS1 was the AATGGAAAC sequence located near −766. DNA methylation assay showed that hypoxia affected the methylation status of CpG islands of EPAS1 and Bad genes. All results indicated that hypoxia could activate the EPAS1/Bad signal pathway to induce gill apoptosis of Japanese flounder. Our study provides new light on understanding the molecular mechanism of hypoxia-induced apoptosis in Japanese flounder. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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27 pages, 6046 KiB  
Article
Hypoxia Affects HIF-1/LDH-A Signaling Pathway by Methylation Modification and Transcriptional Regulation in Japanese Flounder (Paralichthys olivaceus)
by Binghua Liu, Haishen Wen, Jun Yang, Xiaohui Li, Guangling Li, Jingru Zhang, Shuxian Wu, Ian AE Butts and Feng He
Biology 2022, 11(8), 1233; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11081233 - 18 Aug 2022
Cited by 2 | Viewed by 2309
Abstract
Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype [...] Read more.
Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype through changes in blood physiology (RBC, HGB, WBC), biochemistry (LDH, ALP, ALT, GLU, TC, TG, ALB), and hormone (cortisol) indicators. Hypoxia inducible factor-1 (HIF-1), an essential oxygen homeostasis mediator in organisms consisting of an inducible HIF-1α and a constitutive HIF-1β, and its target gene LDH-A were deeply studied. Results showed that HIF-1α and LDH-A genes were co-expressed and significantly affected by hypoxic stress. The dual-luciferase reporter assay confirmed that transcription factor HIF-1 transcriptionally regulated the LDH-A gene, and its transcription binding sequence was GGACGTGA located at −2343~−2336. The DNA methylation status of HIF-1α and LDH-A genes were detected to understand the mechanism of environmental stress on genes. It was found that hypoxia affected the HIF-1α gene and LDH-A gene methylation levels. The study uncovered HIF-1/LDH-A signaling pathway responsive mechanisms of Japanese flounder to hypoxia in epigenetic modification and transcriptional regulation. Our study is significant to further the understanding of environmental responsive mechanisms as well as providing a reference for aquaculture. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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19 pages, 2082 KiB  
Article
Full-Length Transcriptome Reconstruction Reveals the Genetic Mechanisms of Eyestalk Displacement and Its Potential Implications on the Interspecific Hybrid Crab (Scylla serrata ♀ × S. paramamosain ♂)
by Shaopan Ye, Xiaoyan Yu, Huiying Chen, Yin Zhang, Qingyang Wu, Huaqiang Tan, Jun Song, Hafiz Sohaib Ahmed Saqib, Ardavan Farhadi, Mhd Ikhwanuddin and Hongyu Ma
Biology 2022, 11(7), 1026; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11071026 - 07 Jul 2022
Cited by 3 | Viewed by 1800
Abstract
The lack of high-quality juvenile crabs is the greatest impediment to the growth of the mud crab (Scylla paramamosain) industry. To obtain high-quality hybrid offspring, a novel hybrid mud crab (S. serrata ♀ × S. paramamosain ♂) was successfully produced [...] Read more.
The lack of high-quality juvenile crabs is the greatest impediment to the growth of the mud crab (Scylla paramamosain) industry. To obtain high-quality hybrid offspring, a novel hybrid mud crab (S. serrata ♀ × S. paramamosain ♂) was successfully produced in our previous study. Meanwhile, an interesting phenomenon was discovered, that some first-generation (F1) hybrid offspring’s eyestalks were displaced during the crablet stage I. To uncover the genetic mechanism underlying eyestalk displacement and its potential implications, both single-molecule real-time (SMRT) and Illumina RNA sequencing were implemented. Using a two-step collapsing strategy, three high-quality reconstructed transcriptomes were obtained from purebred mud crabs (S. paramamosain) with normal eyestalks (SPA), hybrid crabs with normal eyestalks (NH), and hybrid crabs with displaced eyestalks (DH). In total, 37 significantly differential alternative splicing (DAS) events (17 up-regulated and 20 down-regulated) and 1475 significantly differential expressed transcripts (DETs) (492 up-regulated and 983 down-regulated) were detected in DH. The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant GO terms were related to the cuticle or chitin. Overall, high-quality reconstructed transcriptomes were obtained for the novel interspecific hybrid crab and provided valuable insights into the genetic mechanisms of eyestalk displacement in mud crab (Scylla spp.) crossbreeding. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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23 pages, 4724 KiB  
Article
Masculinization of Adult Gambusia holbrooki: A Case of Recapitulation of Protogyny in a Gonochorist?
by Ngoc Kim Tran, Tzu Nin Kwan, John Purser and Jawahar G. Patil
Biology 2022, 11(5), 694; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11050694 - 30 Apr 2022
Cited by 4 | Viewed by 2185
Abstract
17α-Methyltestosterone (MT) is a synthetic steroid that has been widely used to masculinize many fish species when administered early during larval development, however, reports on its efficacy on adults is limited. To this end, this study investigated the efficacy of MT in the [...] Read more.
17α-Methyltestosterone (MT) is a synthetic steroid that has been widely used to masculinize many fish species when administered early during larval development, however, reports on its efficacy on adults is limited. To this end, this study investigated the efficacy of MT in the masculinization of the eastern mosquitofish (G. holbrooki) at two adult stages (maiden and repeat gravid females). The treated females were fed control or respective MT incorporated feed (0–200 mg/kg diet) for 50 days. Effects of the hormone on secondary sexual characteristics, internal gonad morphology, expression of the Anti-Müllerian Hormone (amh) gene and sexual behavior of the treated females were investigated. The results showed that MT at the dose of 50 mg/kg feed stimulated secondary sexual character development, upregulated expression of amh, formation of testicular tissue and a shift in the behavior similar to those of normal males, prominently so in treated maiden gravid females. Post-treatment, long-term observations indicated that only two masculinized females reverted back to being females and gave birth to young. Induction of masculinizing effects in most individuals suggests that the sexual phenotype of this species appears to be highly plastic with potential to sex reverse at adulthood. This in combination with its small size and short reproductive cycle could provide an ideal system to explore the mechanisms of sequential hermaphroditism in fish and contribute to genetic control of this pest fish. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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20 pages, 2217 KiB  
Article
Gene Editing of the Catfish Gonadotropin-Releasing Hormone Gene and Hormone Therapy to Control the Reproduction in Channel Catfish, Ictalurus punctatus
by Guyu Qin, Zhenkui Qin, Cuiyu Lu, Zhi Ye, Ahmed Elaswad, Max Bangs, Hanbo Li, Yiliu Zhang, Yingqi Huang, Huitong Shi, Kamal Gosh, Nermeen Y. Abass, Khoi Vo, Ramjie Odin, William S. Bugg, Nathan J. C. Backenstose, David Drescher, Zachary Taylor, Timothy Braden, Baofeng Su and Rex A. Dunhamadd Show full author list remove Hide full author list
Biology 2022, 11(5), 649; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11050649 - 24 Apr 2022
Cited by 6 | Viewed by 2984
Abstract
Transcription activator-like effector nuclease (TALEN) plasmids targeting the channel catfish gonadotropin-releasing hormone (cfGnRH) gene were delivered into fertilized eggs with double electroporation to sterilize channel catfish (Ictalurus punctatus). Targeted cfGnRH fish were sequenced and base deletion, substitution, and insertion were detected. [...] Read more.
Transcription activator-like effector nuclease (TALEN) plasmids targeting the channel catfish gonadotropin-releasing hormone (cfGnRH) gene were delivered into fertilized eggs with double electroporation to sterilize channel catfish (Ictalurus punctatus). Targeted cfGnRH fish were sequenced and base deletion, substitution, and insertion were detected. The gene mutagenesis was achieved in 52.9% of P1 fish. P1 mutants (individuals with human-induced sequence changes at the cfGnRH locus) had lower spawning rates (20.0–50.0%) when there was no hormone therapy compared to the control pairs (66.7%) as well as having lower average egg hatch rates (2.0% versus 32.3–74.3%) except for one cfGnRH mutated female that had a 66.0% hatch rate. After low fertility was observed in 2016, application of luteinizing hormone-releasing hormone analog (LHRHa) hormone therapy resulted in good spawning and hatch rates for mutants in 2017, which were not significantly different from the controls (p > 0.05). No exogenous DNA fragments were detected in the genome of mutant P1 fish, indicating no integration of the plasmids. No obvious effects on other economically important traits were observed after the knockout of the reproductive gene in the P1 fish. Growth rates, survival, and appearance between mutant and control individuals were not different. While complete knock-out of reproductive output was not achieved, as these were mosaic P1 brood stock, gene editing of channel catfish for the reproductive confinement of gene-engineered, domestic, and invasive fish to prevent gene flow into the natural environment appears promising. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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15 pages, 3591 KiB  
Article
Identification and Characterization of MicroRNAs Involving in Initial Sex Differentiation of Chlamys farreri Gonads
by Xixi Li, Siyu Lin, Shutong Fan, Xiaoting Huang, Zhifeng Zhang and Zhenkui Qin
Biology 2022, 11(3), 456; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11030456 - 16 Mar 2022
Cited by 1 | Viewed by 2214
Abstract
Research on expressional regulation of genes at the initial sex differentiation of gonads will help to elucidate the mechanisms of sex determination and differentiation in animals. However, information on initial sex differentiation of gonads is limited in bivalves. MicroRNAs (miRNAs) are a class [...] Read more.
Research on expressional regulation of genes at the initial sex differentiation of gonads will help to elucidate the mechanisms of sex determination and differentiation in animals. However, information on initial sex differentiation of gonads is limited in bivalves. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that can regulate the target gene expression at the posttranscription level by degrading the mRNA or repressing the mRNA translation. In the present study, we investigated the small RNAs transcriptome using the testes and ovaries of Zhikong scallop Chlamys farreri juveniles with a shell height of 5.0 mm, a critical stage of initial sex differentiation of gonads. A total of 75 known mature miRNAs and 103 novel miRNAs were identified. By comparing the expression of miRNAs between the ovary and testis, 11 miRNAs were determined to be differentially expressed. GO annotations and KEGG analyses indicated that many putative target genes that matched to these differentially expressed miRNAs participated in the regulation of sex differentiation. Furthermore, two selected miRNAs, cfa-novel_miR65 and cfa-miR-87a-3p_1, were confirmed to downregulate expressions of Foxl2 (a female-critical gene) and Klf4 (a male-critical gene), respectively, using a dual-luciferase reporter analysis. Our findings provided new insights into the initial sex differentiation of gonads regulated by miRNAs in bivalves. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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16 pages, 2940 KiB  
Article
Genome-Wide Analysis of Alternative Splicing (AS) Mechanism Provides Insights into Salinity Adaptation in the Livers of Three Euryhaline Teleosts, including Scophthalmus maximus, Cynoglossus semilaevis and Oncorhynchus mykiss
by Yuan Tian, Qinfeng Gao, Shuanglin Dong, Yangen Zhou, Han Yu, Dazhi Liu and Wenzhao Yang
Biology 2022, 11(2), 222; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11020222 - 30 Jan 2022
Cited by 8 | Viewed by 2446
Abstract
Salinity is an important environmental factor that directly affects the survival of aquatic organisms, including fish. However, the underlying molecular mechanism of salinity adaptation at post-transcriptional regulation levels is still poorly understood in fish. In the present study, 18 RNA-Seq datasets were utilized [...] Read more.
Salinity is an important environmental factor that directly affects the survival of aquatic organisms, including fish. However, the underlying molecular mechanism of salinity adaptation at post-transcriptional regulation levels is still poorly understood in fish. In the present study, 18 RNA-Seq datasets were utilized to investigate the potential roles of alternative splicing (AS) in response to different salinity environments in the livers of three euryhaline teleosts, including turbot (Scophthalmus maximus), tongue sole (Cynoglossus semilaevis) and steelhead trout (Oncorhynchus mykiss). A total of 10,826, 10,741 and 10,112 AS events were identified in the livers of the three species. The characteristics of these AS events were systematically investigated. Furthermore, a total of 940, 590 and 553 differentially alternative splicing (DAS) events were determined and characterized in the livers of turbot, tongue sole and steelhead trout, respectively, between low- and high-salinity environments. Functional enrichment analysis indicated that these DAS genes in the livers of three species were commonly enriched in some GO terms and KEGG pathways associated with RNA processing. The most common DAS genes work as RNA-binding proteins and play crucial roles in the regulation of RNA splicing. The study provides new insights into uncovering the molecular mechanisms of salinity adaptation in teleosts. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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16 pages, 3321 KiB  
Article
Transcriptomic Analysis Reveals Functional Interaction of mRNA–lncRNA–miRNA in Steroidogenesis and Spermatogenesis of Gynogenetic Japanese Flounder (Paralichthys olivaceus)
by Jie Cheng, Fan Yang, Saisai Liu, Haitao Zhao, Wei Lu and Quanqi Zhang
Biology 2022, 11(2), 213; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11020213 - 28 Jan 2022
Cited by 10 | Viewed by 2581
Abstract
Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder (Paralichthys olivaceus) is an important marine cultured fish [...] Read more.
Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder (Paralichthys olivaceus) is an important marine cultured fish that presents significant sexual dimorphism with bigger females, in which gynogenesis has been applied for aquaculture industry. In order to reveal the regulatory mechanisms of sexual development in gynogenetic female and sex-reversed neo-male P. olivaceus, the lncRNA–miRNA–mRNA interactions were investigated using high-throughput sequencing. A total of 6772 differentially expressed mRNAs (DEmRNAs), 2284 DElncRNAs, and 244 DEmiRNAs were obtained between gynogenetic female ovaries and sex-reversed neo-male testes. Genes in the steroid hormone biosynthesis and secretion pathway were enriched and mostly significantly upregulated in neo-male testes. Subsequently, network analysis uncovered high functional specificity for gynogenetic P. olivaceus sperm motility, as co-expressed DEmRNAs were significantly enriched in microtubule and cytoskeleton-related biological processes. Clustered miRNAs were characterized in the P. olivaceus genome with examples of the largest conserved let-7 clusters. The 20 let-7 members are distributed in 11 clusters and may not transcribe together with their neighboring miR-125b, with let-7 repressing cyp11a and miR-125b repressing esr2b, both as key steroidogenesis pathway genes. In summary, this study provides comprehensive insights into the mRNA–miRNA–lncRNA functional crosstalk in teleost sexual development and gametogenesis and will expand our understanding of ncRNA biology in teleost gynogenesis. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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16 pages, 2872 KiB  
Article
Population Genomics of Megalobrama Provides Insights into Evolutionary History and Dietary Adaptation
by Jing Chen, Han Liu, Ravi Gooneratne, Yao Wang and Weimin Wang
Biology 2022, 11(2), 186; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11020186 - 25 Jan 2022
Cited by 4 | Viewed by 2606
Abstract
Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. [...] Read more.
Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. pellegrini. Population structure indicated that geographically divergent Megalobrama populations were separated into six subgroups. A phylogenetic tree showed that M. skolkovii was more closely related to M. pellegrini than other species and M. hoffmanni was clustered apart from other Megalobrama species, showing a high nucleotide diversity in geographic groups. Treemix validated gene flow from M. amblycephala to M. skolkovii, suggesting that introgression may provide an important source of genetic variation in the M. skolkovii populations. According to the demographic history analysis, it is speculated that Megalobrama might have been originally distributed in the Pearl River with some spread to Hainan Island and northern China due to lower sea levels during the glacial period. Whole-genome selective sweeps analysis demonstrated that M. amblycephala likely developed an enhanced energy metabolism mostly through fatty acid degradation pathways whereas M. hoffmanni possibly regulate lipid absorption via the cholesterol metabolism pathway. Taken together, this study provides a valuable genomic resource for future genetic investigations aiming to improve genome-assisted breeding of Megalobrama species. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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14 pages, 1318 KiB  
Article
Screening and Identification of Transcription Factors Potentially Regulating Foxl2 Expression in Chlamys farreri Ovary
by Shutong Fan, Xixi Li, Siyu Lin, Yunpeng Li, Huixin Ma, Zhifeng Zhang and Zhenkui Qin
Biology 2022, 11(1), 113; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11010113 - 11 Jan 2022
Cited by 5 | Viewed by 2034
Abstract
Foxl2 is an evolutionarily conserved female sex gene, which is specifically expressed in the ovary and mainly involved in oogenesis and ovarian function maintenance. However, little is known about the mechanism that regulates Foxl2 specific expression during the ovary development. In the present [...] Read more.
Foxl2 is an evolutionarily conserved female sex gene, which is specifically expressed in the ovary and mainly involved in oogenesis and ovarian function maintenance. However, little is known about the mechanism that regulates Foxl2 specific expression during the ovary development. In the present study, we constructed the gonadal yeast one-hybrid (Y1H) library of Chlamysfarreri with ovaries and testes at different developmental stages using the Gateway technology. The library capacity was more than 1.36 × 107 CFU, and the length of the inserted fragment was 0.75 Kb~2 Kb, which fully met the demand of yeast library screening. The highly transcriptional activity promoter sequence of C. farreri Foxl2 (Cf-Foxl2) was determined at −1000~−616 bp by dual-luciferase reporter (DLR) assay and was used as bait to screen possible transcription factors from the Y1H library. Eleven candidate factors, including five unannotated factors, were selected based on Y1H as well as their expressional differences between ovaries and testes and were verified for the first time to be involved in the transcriptional regulation of Cf-Foxl2 by RT-qPCR and DLR. Our findings provided valuable data for further studying the specific regulation mechanism of Foxl2 in the ovary. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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16 pages, 1318 KiB  
Article
Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)
by Wei Cui, Da Huo, Shilin Liu, Lili Xing, Fang Su, Hongsheng Yang and Lina Sun
Biology 2022, 11(1), 50; https://0-doi-org.brum.beds.ac.uk/10.3390/biology11010050 - 30 Dec 2021
Cited by 10 | Viewed by 1957
Abstract
Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic [...] Read more.
Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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21 pages, 4635 KiB  
Article
Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection
by Min Zhang, Min Cao, Yunji Xiu, Qiang Fu, Ning Yang, Baofeng Su and Chao Li
Biology 2021, 10(10), 1015; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10101015 - 09 Oct 2021
Cited by 16 | Viewed by 2177
Abstract
The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and [...] Read more.
The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10× genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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21 pages, 3846 KiB  
Article
Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis
by Jing Li, Bao Shi, Chongnv Wang, Changwei Shao, Xuezhou Liu and Daiqiang Zhang
Biology 2021, 10(9), 830; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10090830 - 26 Aug 2021
Cited by 5 | Viewed by 2399
Abstract
CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative [...] Read more.
CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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18 pages, 5289 KiB  
Article
Revealing New Landscape of Turbot (Scophthalmus maximus) Spleen Infected with Aeromonas salmonicida through Immune Related circRNA-miRNA-mRNA Axis
by Ting Xue, Yiping Liu, Min Cao, Mengyu Tian, Lu Zhang, Beibei Wang, Xiaoli Liu and Chao Li
Biology 2021, 10(7), 626; https://0-doi-org.brum.beds.ac.uk/10.3390/biology10070626 - 06 Jul 2021
Cited by 4 | Viewed by 1930
Abstract
Increasing evidence suggests that non-coding RNAs (ncRNA) play an important role in a variety of biological life processes by regulating gene expression at the transcriptional and post-transcriptional levels. Turbot (Scophthalmus maximus) has been threatened by various pathogens. In this study, the [...] Read more.
Increasing evidence suggests that non-coding RNAs (ncRNA) play an important role in a variety of biological life processes by regulating gene expression at the transcriptional and post-transcriptional levels. Turbot (Scophthalmus maximus) has been threatened by various pathogens. In this study, the expression of circular RNAs (circRNAs), microRNAs (miRNAs), and mRNA in the immune organs spleen of turbot infected with Aeromonas salmonicida was analyzed by high-throughput sequencing, and a circRNA-miRNA-mRNA network was constructed, so as to explore the function of non-coding RNA in the immune system of teleost. Illumina sequencing was performed on the uninfected group and infected group. A total of 119 differential expressed circRNAs (DE-circRNAs), 140 DE-miRNAs, and 510 DE-mRNAs were identified in the four infected groups compared with the uninfected group. Most DE-mRNAs and the target genes of DE-ncRNAs were involved in immune-related pathways. The quantitative real-time PCR (qRT-PCR) results verified the reliability and accuracy of the high-throughput sequencing data. Ninety-six differentially expressed circRNA-miRNA-mRNA regulatory networks were finally constructed. Among them, 15 circRNA-miRNA-mRNA were presented in the form of “up (circRNA)-down (miRNA)-up (mRNA)” or “down-up-down”. Immune-related genes gap junction CX32.2, cell adhesion molecule 3, and CC chemokine were also found in these networks. These results indicate that ncRNA may regulate the expression of immune-related genes through the circRNA-miRNA-mRNA regulatory network and thus participate in the immune response of turbot spleen after pathogen infection. Full article
(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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