Biology

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22 pages, 7309 KiB

Open AccessArticle

Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates

by Tim Young, Olivier Laroche, Seumas P. Walker, Matthew R. Miller, Paula Casanovas, Konstanze Steiner, Noah Esmaeili, Ruixiang Zhao, John P. Bowman, Richard Wilson, Andrew Bridle, Chris G. Carter, Barbara F. Nowak, Andrea C. Alfaro and Jane E. Symonds

Biology 2023, 12(8), 1135; https://doi.org/10.3390/biology12081135 - 15 Aug 2023

Cited by 3 | Viewed by 2524

Abstract

Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging [...] Read more.

Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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17 pages, 3430 KiB

Open AccessArticle

Comprehensive Analysis of Whole-Transcriptome Profiles in Response to Acute Hypersaline Challenge in Chinese Razor Clam Sinonovacula constricta

by Wei Cao, Yinghui Dong, Yusong Geng, Siqi Bi, Zhihong Liu, Liqing Zhou, Xiujun Sun, Sudong Xia, Changfeng Chi and Biao Wu

Biology 2023, 12(1), 106; https://doi.org/10.3390/biology12010106 - 10 Jan 2023

Cited by 7 | Viewed by 2211

Abstract

The Chinese razor clam (Sinonovacula constricta) is an important for Chinese aquaculture marine bivalve that naturally occurs across intertidal and estuarine areas subjected to significant changes in salinity level. However, the information on the molecular mechanisms related to high salinity stress [...] Read more.

The Chinese razor clam (Sinonovacula constricta) is an important for Chinese aquaculture marine bivalve that naturally occurs across intertidal and estuarine areas subjected to significant changes in salinity level. However, the information on the molecular mechanisms related to high salinity stress in the species remain limited. In this study, nine gill samples of S. constricta treated with 20, 30, and 40 ppt salinity for 24 h were used for whole-transcriptome RNA sequencing, and a regulatory network of competing endogenous RNAs (ceRNAs) was constructed to better understand the mechanisms responsible for adaptation of the species to high salinity. A total of 83,262 lncRNAs, 52,422 mRNAs, 2890 circRNAs, and 498 miRNAs were identified, and 4175 of them displayed differential expression pattern among the three groups examined. The KEGG analyses of differentially expressed RNAs evidenced that amino acid synthesis and membrane transport were the dominant factors involved in the adaptation of the Chinese razor clam to acute salinity increase, while lipid metabolism and signaling played only a supporting role. In addition, lncRNA/circRNA-miRNA-mRNA regulatory networks (ceRNA network) showed clearly regulatory relationships among different RNAs. Moreover, the expression of four candidate genes, including tyrosine aminotransferase (TAT), hyaluronidase 4 (HYAL4), cysteine sulfinic acid decarboxylase (CSAD), and ∆¹-pyrroline-5-carboxylate synthase (P5CS) at different challenge time were detected by qRT-PCR. The expression trend of TAT and HYAL4 was consistent with that of the ceRNA network, supporting the reliability of established network. The expression of TAT, CSAD, and P5CS were upregulated in response to increased salinity. This might be associated with increased amino acid synthesis rate, which seems to play an essential role in adaptation of the species to high salinity stress. In contrast, the expression level of HYAL4 gene decreased in response to elevated salinity level, which is associated with reduction Hyaluronan hydrolysis to help maintain water in the cell. Our findings provide a very rich reference for understanding the important role of ncRNAs in the salinity adaptation of shellfish. Moreover, the acquired information may be useful for optimization of the artificial breeding of the Chinese razor clam under aquaculture conditions. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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14 pages, 2138 KiB

Open AccessArticle

Profiling the Spatial Expression Pattern and ceRNA Network of lncRNA, miRNA, and mRNA Associated with the Development of Intermuscular Bones in Zebrafish

by Weidong Ye, Mijuan Shi, Keyi Ren, Yuhang Liu, You Duan, Yingyin Cheng, Wanting Zhang and Xiao-Qin Xia

Biology 2023, 12(1), 75; https://doi.org/10.3390/biology12010075 - 31 Dec 2022

Cited by 3 | Viewed by 2018

Abstract

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, [...] Read more.

Intermuscular bones (IBs) are small spicule-like bones in the muscular septum of fish, which affect their edible and economic value. The molecular mechanism of IB development is still uncertain. Numerous studies have shown that the ceRNA network, which is composed of mRNA, lncRNA, and miRNA, plays an important regulatory role in bone development. In this study, we compared the mRNA, lncRNA, and miRNA expression profiles in different IB development segments of zebrafish. The development of IBs includes two main processes, which are formation and growth. A series of genes implicated in the formation and growth of IBs were identified through gene differential expression analysis and expression pattern analysis. Functional enrichment analysis showed that the functions of genes implicated in the regulation of the formation and growth of IBs were quite different. Ribosome and oxidative phosphorylation signaling pathways were significantly enriched during the formation of IBs, suggesting that many proteins are required to form IBs. Several pathways known to be associated with bone development have been shown to play an important role in the growth of IBs, including calcium, ECM-receptor interaction, Wnt, TGF-β, and hedgehog signaling pathways. According to the targeting relationship and expression correlation of mRNA, lncRNA, and miRNA, the ceRNA networks associated with the growth of IBs were constructed, which comprised 33 mRNAs, 9 lncRNAs, and 7 miRNAs. This study provides new insight into the molecular mechanism of the development of IBs. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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18 pages, 2500 KiB

Open AccessArticle

Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae)

by Yosur G. Fiteha, Mohamed A. Rashed, Ramadan A. Ali, Diaa Abd El-Moneim, Fahad A. Alshanbari and Mahmoud Magdy

Biology 2023, 12(1), 40; https://doi.org/10.3390/biology12010040 - 26 Dec 2022

Viewed by 2230

Abstract

To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that [...] Read more.

To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnS^GCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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27 pages, 5271 KiB

Open AccessArticle

Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream (Sparus aurata) Production Cycle

by Fernando Naya-Català, M. Carla Piazzon, Silvia Torrecillas, Socorro Toxqui-Rodríguez, Josep À. Calduch-Giner, Ramón Fontanillas, Ariadna Sitjà-Bobadilla, Daniel Montero and Jaume Pérez-Sánchez

Biology 2022, 11(12), 1744; https://doi.org/10.3390/biology11121744 - 30 Nov 2022

Cited by 15 | Viewed by 3163

Abstract

Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5–7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t₀ [...] Read more.

Fish genetically selected for growth (GS) and reference (REF) fish were fed with CTRL (15% FM, 5–7% FO) or FUTURE (7.5% FM, 10% poultry meal, 2.2% poultry oil + 2.5% DHA-algae oil) diets during a 12-months production cycle. Samples from initial (t₀; November 2019), intermediate (t₁; July 2020) and final (t₂; November 2020) sampling points were used for Illumina 16S rRNA gene amplicon sequencing of the adherent microbiota of anterior intestine (AI). Samples from the same individuals (t₁) were also used for the gene expression profiling of AI by RNA-seq, and subsequent correlation analyses with microbiota abundances. Discriminant analyses indicated the gut bacterial succession along the production cycle with the proliferation of some valuable taxa for facing seasonality and different developmental stages. An effect of genetic background was evidenced along time, decreasing through the progression of the trial, namely the gut microbiota of GS fish was less influenced by changes in diet composition. At the same time, these fish showed wider transcriptomic landmarks in the AI to cope with these changes. Our results highlighted an enhanced intestinal sphingolipid and phospholipid metabolism, epithelial turnover and intestinal motility in GS fish, which would favour their improved performance despite the lack of association with changes in gut microbiota composition. Furthermore, in GS fish, correlation analyses supported the involvement of different taxa with the down-regulated expression of pro-inflammatory markers and the boosting of markers of extracellular remodelling and response to bacterium. Altogether, these findings support the combined action of the gut microbiome and host transcriptionally mediated effects to preserve and improve gut health and function in a scenario of different growth performance and potentiality. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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9 pages, 1705 KiB

Open AccessCommunication

Transcriptomic Analysis Revealed Candidate Genes Involved in Pseudomale Sperm Abnormalities in Chinese Tongue Sole (Cynoglossus semilaevis)

by Yuxuan Sun, Ming Li, Zhongkai Cui, Mengqian Zhang, Tingting Zhang, Lu Li, Na Wang, Xiwen Xu, Min Wei and Wenteng Xu

Biology 2022, 11(12), 1716; https://doi.org/10.3390/biology11121716 - 26 Nov 2022

Cited by 4 | Viewed by 1739

Abstract

Chinese tongue sole (Cynoglossus semilaevis) has a ZZ/ZW sex determination system, but the genotypic female (ZW) can be sex-reversed into phenotypic males, namely, pseudomales. Pseudomale fish can produce only Z-type sperm but not W sperm. However, the molecular mechanism is unclear. [...] Read more.

Chinese tongue sole (Cynoglossus semilaevis) has a ZZ/ZW sex determination system, but the genotypic female (ZW) can be sex-reversed into phenotypic males, namely, pseudomales. Pseudomale fish can produce only Z-type sperm but not W sperm. However, the molecular mechanism is unclear. To screen the key genes involved in pseudomale sperm abnormalities, we analysed the transcriptomic profiles of pseudomale and male sperm. In comparison to male sperm, 592 differentially expressed genes (DEGs) were identified in pseudomale sperm, including 499 upregulated and 93 downregulated genes. KEGG analysis indicated that the FoxO signalling pathway, especially the foxo3a and foxo6-like genes, may play an important role in spermatogenesis. The DEGs were mainly distributed on sex chromosomes, with 158 downregulated genes on the Z chromosome and 41 upregulated genes on the W chromosome. A specific area (14–15 M) on the Z chromosome was identified, which enriched eight DEGs inside the ~1 M region. In addition, there were five gene alleles on the sex chromosomes, which showed the opposite transcription pattern (upregulated for the W allele, downregulated for the Z allele). This study has provided valuable data for screening candidate genes involved in the pseudomale sperm abnormality. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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15 pages, 1709 KiB

Open AccessArticle

Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome

by Daniel G. Silva, Célia P. F. Domingues, João F. Figueiredo, Francisco Dionisio, Ana Botelho and Teresa Nogueira

Biology 2022, 11(11), 1681; https://doi.org/10.3390/biology11111681 - 21 Nov 2022

Cited by 4 | Viewed by 2340

Abstract

It is recognized that the spread of antibiotic resistance (AR) genes among aquatic environments, including aquaculture and the human environment, can have detrimental effects on human and animal health and the ecosystem. Thus, when transmitted to the human microbiome or pathogens, resistance genes [...] Read more.

It is recognized that the spread of antibiotic resistance (AR) genes among aquatic environments, including aquaculture and the human environment, can have detrimental effects on human and animal health and the ecosystem. Thus, when transmitted to the human microbiome or pathogens, resistance genes risk human health by compromising the eventual treatment of infections with antibiotic therapy. This study aimed to define the resistance profile of aquaculture farms and their potential risk for spreading. Twenty-four sediments from oyster and gilthead sea bream aquaculture farms located in three Portuguese river estuaries (17 sediments from Sado, 4 from Aveiro, and 3 from Lima) were studied by comparative metagenomic analysis. The computation of the diversity of genes conferring resistance per antibiotic class revealed a significant increase in aminoglycosides, beta-lactams, disinfectants, quinolones, and tetracyclines counts. In all geographic locations under study, the most diverse AR genes confer resistance to the macrolides, tetracyclines and oxazolidinones classes, all of which are medically important for human and animal therapies, as well as resistance to disinfectants. The diversity of mobile genetic elements correlated with the number of AR genes such as tetracyclines, suggesting that AR could be easily mobilized among bacterial genomes and microbiomes. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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15 pages, 2680 KiB

Open AccessArticle

Integrated mRNA and miRNA Expression Profile Analysis of Female and Male Gonads in Acrossocheilus fasciatus

by Wenbo Wei, Jiamei He, Muhammad Amjad Yaqoob, Lang Gui, Jianfeng Ren, Jiale Li and Mingyou Li

Biology 2022, 11(9), 1296; https://doi.org/10.3390/biology11091296 - 31 Aug 2022

Cited by 5 | Viewed by 2249

Abstract

MicroRNAs (miRNAs) are regarded as key regulators in gonadal development and sex determination in diverse organisms. However, the functions of miRNAs in gonads of Acrossocheilus fasciatus, an economically important freshwater species in the south of China, are still unclear. Here, high-throughput sequencing [...] Read more.

MicroRNAs (miRNAs) are regarded as key regulators in gonadal development and sex determination in diverse organisms. However, the functions of miRNAs in gonads of Acrossocheilus fasciatus, an economically important freshwater species in the south of China, are still unclear. Here, high-throughput sequencing was performed to investigate the mRNA and miRNAs on gonads of A. fasciatus. In total, 49,447 unigenes were obtained, including 11,635 differentially expressed genes (DEGs), among which 4147 upregulated genes and 7488 downregulated genes in the testis compared to the ovary, while 300 (237 known, and 63 novel) miRNAs with 36 differentially expressed miRNAs (DEMs) were identified, from which 17 upregulated and 19 downregulated DEMs. GO and KEGG enrichment analysis were performed to analyze the potential biological functions of DEGs and DEMs. Using qRT-PCR, 9 sex-related genes and 9 miRNAs were selected to verify the sequencing data. By dual-luciferase reporter assay, miR-22a-5p and miR-22b-5p interaction with piwil1, and miR-10d-5p interaction with piwil2 were identified. These findings could provide a reference for miRNA-regulated sex control of A. fasciatus and may reveal new insights into aquaculture and breeding concepts. Full article

(This article belongs to the Special Issue Omics Technologies Applied to Aquaculture Research)

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