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Liu M, He C, Zhu T, Jia X, Zhang L, Jiang W, Chi C, Li X, Jiang G, Liu H, Zhang D. Characterizing and identifying of miRNAs involved in berberine modulating glucose metabolism of Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1667-1682. [PMID: 38963582 DOI: 10.1007/s10695-024-01362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/24/2024] [Indexed: 07/05/2024]
Abstract
The present study, as one part of a larger project that aimed to investigate the effects of dietary berberine (BBR) on fish growth and glucose regulation, mainly focused on whether miRNAs involve in BBR's modulation of glucose metabolism in fish. Blunt snout bream Megalobrama amblycephala (average weight of 20.36 ± 1.44 g) were exposed to the control diet (NCD, 30% carbohydrate), the high-carbohydrate diet (HCD, 43% carbohydrate) and the berberine diet (HCB, HCD supplemented with 50 mg/kg BBR). After 10 weeks' feeding trial, intraperitoneal injection of glucose was conducted, and then, the plasma and liver were sampled at 0 h, 1 h, 2 h, 6 h, and 12 h. The results showed the plasma glucose levels in all groups rose sharply and peaked at 1 h after glucose injection. Unlike the NCD and HCB groups, the plasma glucose in the HCD group did not decrease after 1 h, while remained high level until at 2 h. The NCD group significantly increased liver glycogen content at times 0-2 h compared to the other two groups and then liver glycogen decreased sharply until at times 6-12 h. To investigate the role of BBR that may cause the changes in plasma glucose and liver glycogen, miRNA high-throughput sequencing was performed on three groups of liver tissues at 2 h time point. Eventually, 20 and 12 differentially expressed miRNAs (DEMs) were obtained in HCD vs NCD and HCB vs HCD, respectively. Through function analyzing, we found that HCD may affect liver metabolism under glucose loading through the NF-κB pathway; and miRNAs regulated by BBR mainly play roles in adipocyte lipolysis, niacin and nicotinamide metabolism, and amino acid transmembrane transport. In the functional exploration of newly discovered novel:Chr12_18892, we found its target gene, adenylate cyclase 3 (adcy3), was widely involved in lipid decomposition, amino acid metabolism, and other pathways. Furthermore, a targeting relationship of novel:Chr12_18892 and adcy3 was confirmed by double luciferase assay. Thus, BBR may promote novel:Chr12_18892 to regulate the expression of adcy3 and participate in glucose metabolism.
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Affiliation(s)
- Mingyang Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Chang He
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Zhu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyan Jia
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibo Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Chi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hengtong Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Verleih M, Visnovska T, Nguinkal JA, Rebl A, Goldammer T, Andreassen R. The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch ( Sander lucioperca). Int J Mol Sci 2023; 25:189. [PMID: 38203361 PMCID: PMC10778745 DOI: 10.3390/ijms25010189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Micro RNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional gene expression regulators. Genes regulated in vertebrates include those affecting growth and development or stress and immune response. Pikeperch (Sander lucioperca) is a species that is increasingly being considered for farming in recirculation aquaculture systems. We characterized the pikeperch miRNA repertoire to increase the knowledge of the genomic mechanisms affecting performance and health traits by applying small RNA sequencing to different developmental stages and organs. There were 234 conserved and 8 novel miRNA genes belonging to 104 families. A total of 375 unique mature miRNAs were processed from these genes. Many mature miRNAs showed high relative abundances or were significantly more expressed at early developmental stages, like the miR-10 and miR-430 family, let-7, the miRNA clusters 106-25-93, and 17-19-92. Several miRNAs associated with immune responses (e.g., slu-mir-731-5p, slu-mir-2188-5p, and slu-mir-8159-5p) were enriched in the spleen. The mature miRNAs slu-mir-203a-3p and slu-mir-205-5p were enriched in gills. These miRNAs are similarly abundant in many vertebrates, indicating that they have shared regulatory functions. There was also a significantly increased expression of the disease-associated miR-462/miR-731 cluster in response to hypoxia stress. This first pikeperch miRNAome reference resource paves the way for future functional studies to identify miRNA-associated variations that can be utilized in marker-assisted breeding programs.
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Affiliation(s)
- Marieke Verleih
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0424 Oslo, Norway
| | - Julien A. Nguinkal
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tom Goldammer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
- Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet—Oslo Metropolitan University, 0167 Oslo, Norway;
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Arick MA, Grover CE, Hsu CY, Magbanua Z, Pechanova O, Miller ER, Thrash A, Youngblood RC, Ezzell L, Alam MS, Benzie JAH, Hamilton MG, Karsi A, Lawrence ML, Peterson DG. A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination. G3 (BETHESDA, MD.) 2023; 13:6987299. [PMID: 36639248 PMCID: PMC9997561 DOI: 10.1093/g3journal/jkad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]
Abstract
Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.
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Affiliation(s)
- Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Zenaida Magbanua
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Olga Pechanova
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Adam Thrash
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Lauren Ezzell
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Md Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - John A H Benzie
- WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia
| | | | - Attila Karsi
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Mark L Lawrence
- Global Center for Aquatic Health and Food Security, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
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Comparative Analysis of miRNA-mRNA Regulation in the Testes of Gobiocypris rarus following 17α-Methyltestosterone Exposure. Int J Mol Sci 2023; 24:ijms24044239. [PMID: 36835651 PMCID: PMC9968023 DOI: 10.3390/ijms24044239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
17α-Methyltestosterone (17MT), a synthetic organic compound commonly found in sewage waters, can affect reproduction in aquatic animals, such as tilapia and yellow catfish. In the present study, male Gobiocypris rarus were exposed to 25, 50, and 100 ng/L of 17α-methyltestosterone (17MT) for 7 days. We first analyzed miRNA- and RNA-seq results to determine miRNA-target gene pairs and then developed miRNA-mRNA interactive networks after 17MT administration. Total weights, total lengths, and body lengths were not significantly different between the test groups and control groups. The paraffin slice method was applied to testes of G. rarus in the MT exposure and control groups. We found that there were more mature sperm (S) and fewer secondary spermatocytes (SSs) and spermatogonia (SGs) in the testes of control groups. As 17MT concentration increased, fewer and fewer mature sperm (S) were observed in the testes of male G. rarus. The results showed that FSH, 11-KT, and E2 were significantly higher in individuals exposed to 25 ng/L 17MT compared with the control groups. VTG, FSH, LH, 11-KT, and E2 were significantly lower in the 50 ng/L 17MT exposure groups compared to the control groups. VTG, FSH, LH, 11-KT, E2, and T were significantly lower in the groups exposed to 100 ng/L 17MT. High-throughput sequencing revealed 73,449 unigenes, 1205 known mature miRNAs, and 939 novel miRNAs in the gonads of G. rarus. With miRNA-seq, 49 (MT25-M vs. Con-M), 66 (MT50-M vs. Con-M), and 49 (MT100-M vs. Con-M) DEMs were identified in the treatment groups. Five mature miRNAs (miR-122-x, miR-574-x, miR-430-y, lin-4-x, and miR-7-y), as well as seven differentially expressed genes (soat2, inhbb, ihhb, gatm, faxdc2, ebp, and cyp1a1), which may be associated with testicular development, metabolism, apoptosis, and disease response, were assayed using qRT-PCR. Furthermore, miR-122-x (related to lipid metabolism), miR-430-y (embryonic development), lin-4-x (apoptosis), and miR-7-y (disease) were differentially expressed in the testes of 17MT-exposed G. rarus. This study highlights the role of miRNA-mRNA pairs in the regulation of testicular development and immune response to disease and will facilitate future studies on the miRNA-RNA-associated regulation of teleost reproduction.
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Fan Z, Wang L, Li C, Wu D, Li J, Zhang H, Xiong S, Miao L, Ge X, Li Z. Integration of microRNA and mRNA analyses depicts the potential roles of Momordica charantia saponin administration in insulin resistance of juvenile common carp ( Cyprinus carpio) fed with a high-starch diet. Front Mol Biosci 2023; 10:1054949. [PMID: 37091861 PMCID: PMC10113649 DOI: 10.3389/fmolb.2023.1054949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
Background: The regulation of target gene mRNA mediated by microRNA may play an important role in glucose metabolism in fish. Previous research findings of our research group revealed that Momordica charantia saponin (MS) administration in a high-starch diet could improve insulin resistance of common carp through renovating insulin signaling pathways, whose fundamental mechanisms have remained unknown by far. To reveal this potential mechanism, we aimed to investigate the difference in miRNA and mRNA expression profiles between common carp fed with high-starch diets containing MS (HS_MS1 and HS_MS2) and common carp fed with high-starch (HS) diets. Results: Through miRNA deep-sequencing, 10 significantly differentially expressed miRNAs in HC and HS_MS1, including one upregulated and nine downregulated miRNAs, were identified, whereas 10 significantly differentially expressed miRNAs in HC and HS_MS2, including four upregulated and six downregulated miRNAs, were identified. These miRNAs may not only be involved in the regulation of insulin signaling pathways and insulin resistance in common carp but also be the markers for liver insulin resistance in MS therapy for the remission of insulin resistance. This study identified 10 potential known miRNAs, namely, ccr-miR-10b, ccr-miR-122, ccr-miR-143, ccr-miR-146a, ccr-miR-155, ccr-miR-16c, ccr-miR-200a, ccr-miR-29a, ccr-miR-34, and ccr-miR-375, as candidates participating in modulating the liver insulin resistance. According to the biopathway enrichment analysis of the 252 target genes using the KEGG classical biopathway database, the relative expression levels of gsk3bb, pik3r1, and pik3r3b were analyzed using RNA-seq. Compared to the HC group, a significant decrease in the relative expression levels of pik3r1 and pik3r3b was observed in HS_MS1 and HS_MS2 groups (p < 0.05). This study raised a presumption of the presence of ccr-miR-29a targeting pik3r1 or ccr-miR-143 targeting pik3r3 playing likely roles in Momordica charantia saponins remitting the liver insulin resistance. Conclusion: The findings will further deepen the understanding of the carbohydrate metabolism of common carp and provide an important scientific basis for the application of Momordica saponins as functional nutrients to alleviate insulin resistance of fish in fish culture.
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Affiliation(s)
- Ze Fan
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Liansheng Wang
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- *Correspondence: Liansheng Wang, ; Haitao Zhang,
| | - Chenhui Li
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Di Wu
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Jinnan Li
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Haitao Zhang
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture and Rural Affairs, Guangdong Evergreen Feed Industry Co., Ltd., Zhanjiang, China
- *Correspondence: Liansheng Wang, ; Haitao Zhang,
| | - Siwei Xiong
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Tianjin Agricultural University, Tianjin, China
| | - Linghong Miao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Xianping Ge
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Zhengwei Li
- Heilongjiang Aquatic Animal Resource Conservation Center, Heilongjiang, China
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Sundaray JK, Dixit S, Rather A, Rasal KD, Sahoo L. Aquaculture omics: An update on the current status of research and data analysis. Mar Genomics 2022; 64:100967. [PMID: 35779450 DOI: 10.1016/j.margen.2022.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
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Affiliation(s)
- Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Ashraf Rather
- Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu and Kashmir, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
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Shwe A, Krasnov A, Visnovska T, Ramberg S, Østbye TKK, Andreassen R. Expression Analysis in Atlantic Salmon Liver Reveals miRNAs Associated with Smoltification and Seawater Adaptation. BIOLOGY 2022; 11:biology11050688. [PMID: 35625416 PMCID: PMC9138835 DOI: 10.3390/biology11050688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Smoltification is a developmental process that preadapts Atlantic salmon for a life in seawater. Suboptimal smoltification and poor timing of transfer to seawater is associated with increased mortality. MicroRNAs (miRNAs) are small non-coding genes. They regulate gene expression post-transcriptionally as part of the miRNA induce silencing complex (miRISC) where they guide miRISC to particular mRNAs (target genes). The aim of this study was to identify Atlantic salmon miRNAs expressed in liver that are associated with smoltification and adaptation to seawater as well as to predict their target genes. In total, 62 guide miRNAs were identified, and by their expression patterns they were clustered into three groups. Target gene predictions followed by gene enrichment analysis of the predicted targets indicated that the guide miRNAs were involved in post-transcriptional regulation of important smoltification associated biological processes. Some of these were energy metabolism, protein metabolism and transport, circadian rhythm, stress and immune response. Together, the results indicate that certain miRNAs are involved in the regulation of many of the important changes occurring in the liver during this developmental transition. Abstract Optimal smoltification is crucial for normal development, growth, and health of farmed Atlantic salmon in seawater. Here, we characterize miRNA expression in liver to reveal whether miRNAs regulate gene expression during this developmental transition. Expression changes of miRNAs and mRNAs was studied by small-RNA sequencing and microarray analysis, respectively. This revealed 62 differentially expressed guide miRNAs (gDE-miRNAs) that could be divided into three groups with characteristic dynamic expression patterns. Three of miRNA families are known as highly expressed in liver. A rare arm shift was observed during smoltification in the Atlantic salmon-specific novel-ssa-miR-16. The gDE-miRNAs were predicted to target 2804 of the genes revealing expression changes in the microarray analysis. Enrichment analysis revealed that targets were significantly enriched in smoltification-associated biological process groups. These included lipid and cholesterol synthesis, carbohydrate metabolism, protein metabolism and protein transport, immune system genes, circadian rhythm and stress response. The results indicate that gDE-miRNAs may regulate many of the changes associated with this developmental transition in liver. The results pave the way for validation of the predicted target genes and further study of gDE-miRNA and their targets by functional assays.
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Affiliation(s)
- Alice Shwe
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway; (A.S.); (S.R.)
| | - Aleksei Krasnov
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), 1430 Ås, Norway; (A.K.); (T.-K.K.Ø.)
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0372 Oslo, Norway;
| | - Sigmund Ramberg
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway; (A.S.); (S.R.)
| | - Tone-Kari K. Østbye
- Nofima (Norwegian Institute of Food, Fisheries and Aquaculture Research), 1430 Ås, Norway; (A.K.); (T.-K.K.Ø.)
| | - Rune Andreassen
- Department of Life Science and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, Norway; (A.S.); (S.R.)
- Correspondence:
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Starch in aquafeeds: the benefits of a high amylose to amylopectin ratio and resistant starch content in diets for the carnivorous fish, largemouth bass ( Micropterus salmoides). Br J Nutr 2020; 124:1145-1155. [PMID: 32624026 DOI: 10.1017/s0007114520002214] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Aquafeeds for carnivorous species face a nutritional-technological conundrum: containing sufficient starch to meet specific manufacturing requirements for binding, extrusion and expansion, but ideally containing as little starch as possible owing to their limited ability to utilise carbohydrates. The present study evaluated the effects of dietary starch with different amylose to amylopectin ratios and resistant starch contents on growth performance, hepatic glycogen accumulation and glucose metabolism of an important cultured carnivorous finfish, largemouth bass (Micropterus salmoides). A common starch source (α-cassava starch (CS)) was tested as is or after being enzymatically de-branched at three different inclusion levels in diets for largemouth bass. Results showed that the increased dietary starch levels compromised performance and high dietary α-CS content led to obvious liver damage. However, the growth performances of fish fed the diets with de-branched starch (DS) were improved, and no manifest liver damages were observed even at the higher inclusion level. The increasing dietary starch contents significantly increased hepatic glycogen accumulation, but not when DS was used. High dietary starch content, without regard to starch sources, had no effect on the expression of glucose metabolism-related genes, except for down-regulation of insulin receptor expression. However, the use of dietary DS promoted the expression of genes involved in the insulin pathway and glycolysis. In conclusion, this study showed that the use of starch sources with a high amylose to amylopectin ratio and resistant starch in the feed for cultured carnivorous finfish could alleviate the hepatic glycogen deposition through regulating the insulin pathway and glycolysis.
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