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Mohindra V, Chowdhury LM, Chauhan N, Paul A, Singh RK, Kushwaha B, Maurya RK, Lal KK, Jena JK. Transcriptome Analysis Revealed Osmoregulation Related Regulatory Networks and Hub Genes in the Gills of Hilsa shad, Tenualosa ilisha, during the Migratory Osmotic Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:161-173. [PMID: 36631626 DOI: 10.1007/s10126-022-10190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Tenualosa ilisha (Hilsa shad), an anadromous fish, usually inhabits coastal and estuarine waters, and migrates to freshwater for spawning. In this study, large-scale gill transcriptome analyses from three salinity regions, i.e., fresh, brackish and marine water, revealed 3277 differentially expressed genes (DEGs), out of which 232 were found to be common between marine vs freshwater and brackish vs freshwater. These genes were mapped into 54 KEGG Pathways, and the most significant of these were focal adhesion, adherens junction, tight junction, and PI3K-Akt signaling pathways. A total of 24 osmoregulatory genes were found to be differentially expressed in different habitats. The gene members of slc16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes (cldn11 & cldn10), transmembrane tm56b, and voltage-gated potassium channel gene kcna10 were downregulated in freshwater samples, as compared to that of brackish and marine environment. Protein-protein interaction (PPI) network analysis of 232 DEGs showed 101 genes to be involved in PPI, while fn1 gene was found to be interacting with the highest number of genes (36). Twenty-five hub genes belonged to 12 functional groups, with muscle structure development with seven genes, forming the major group. These results provided valuable information about the genes, potentially involved in the molecular mechanisms regulating water homeostasis in gills, during migration for spawning and low-salinity adaptation in Hilsa shad. These genes may form the basis for the bio-marker development for adaptation to the stress levied by major environmental changes, due to hatchery/culture conditions.
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Affiliation(s)
- Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India.
| | - Labrechai Mog Chowdhury
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Nishita Chauhan
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Alisha Paul
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Rajeev Kumar Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Basdeo Kushwaha
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Rajesh Kumar Maurya
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Kuldeep K Lal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - J K Jena
- Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan-II, New Delhi, 110 012, India
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West AC, Mizoro Y, Wood SH, Ince LM, Iversen M, Jørgensen EH, Nome T, Sandve SR, Martin SAM, Loudon ASI, Hazlerigg DG. Immunologic Profiling of the Atlantic Salmon Gill by Single Nuclei Transcriptomics. Front Immunol 2021; 12:669889. [PMID: 34017342 PMCID: PMC8129531 DOI: 10.3389/fimmu.2021.669889] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/12/2021] [Indexed: 12/05/2022] Open
Abstract
Anadromous salmonids begin life adapted to the freshwater environments of their natal streams before a developmental transition, known as smoltification, transforms them into marine-adapted fish. In the wild, smoltification is a photoperiod-regulated process, involving radical remodeling of gill function to cope with the profound osmotic and immunological challenges of seawater (SW) migration. While prior work has highlighted the role of specialized "mitochondrion-rich" cells (MRCs) and accessory cells (ACs) in delivering this phenotype, recent RNA profiling experiments suggest that remodeling is far more extensive than previously appreciated. Here, we use single-nuclei RNAseq to characterize the extent of cytological changes in the gill of Atlantic salmon during smoltification and SW transfer. We identify 20 distinct cell clusters, including known, but also novel gill cell types. These data allow us to isolate cluster-specific, smoltification-associated changes in gene expression and to describe how the cellular make-up of the gill changes through smoltification. As expected, we noted an increase in the proportion of seawater mitochondrion-rich cells, however, we also identify previously unknown reduction of several immune-related cell types. Overall, our results provide fresh detail of the cellular complexity in the gill and suggest that smoltification triggers unexpected immune reprogramming.
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Affiliation(s)
- Alexander C. West
- Arctic seasonal timekeeping initiative (ASTI), Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Yasutaka Mizoro
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Shona H. Wood
- Arctic seasonal timekeeping initiative (ASTI), Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Louise M. Ince
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marianne Iversen
- Arctic seasonal timekeeping initiative (ASTI), Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Even H. Jørgensen
- Arctic seasonal timekeeping initiative (ASTI), Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Tromsø, Norway
| | - Torfinn Nome
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Simen Rød Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Life Sciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Samuel A. M. Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Andrew S. I. Loudon
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Hazlerigg
- Arctic seasonal timekeeping initiative (ASTI), Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Tromsø, Norway
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Groundwater contamination and health risk posed by industrial effluent in NCR region. ACTA ACUST UNITED AC 2021. [DOI: 10.1016/j.matpr.2021.02.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Liu Y, Wang H, Wen H, Shi Y, Zhang M, Qi X, Zhang K, Gong Q, Li J, He F, Hu Y, Li Y. First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:526-538. [PMID: 32424479 DOI: 10.1007/s10126-020-09973-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96 cM with an average marker interval of 0.33 cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haolong Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Meizhao Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xin Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kaiqiang Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingli Gong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yanbo Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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Preservative Effects of Gelatin Active Coating Containing Eugenol and Higher CO 2 Concentration Modified Atmosphere Packaging on Chinese Sea bass ( Lateolabrax maculatus) during Superchilling (-0.9 °C) Storage. Molecules 2020; 25:molecules25040871. [PMID: 32079147 PMCID: PMC7070949 DOI: 10.3390/molecules25040871] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/02/2020] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
The purpose of this research was to explore the fresh keeping effect of modified atmosphere packaging (MAP) with different gas ratios combined with gelatin active coatings containing eugenol on Chinese sea bass stored at −0.9 °C for 36 days. The results showed that MAP3 (60% CO2/10% O2/30% N2), together with gelatin active coatings containing eugenol, could prevent water loss, which maintained high field NMR, MRI, and organoleptic evaluation results. This hurdle technology could also effectively delay the bacterial reproduction, protein degradation, and alkaline accumulation, so it showed the lowest K value, total volatile basic nitrogen, free amino acids, total viable count, Pseudomonas spp., and H2S-producing bacteria, which better maintain the quality of sea bass.
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Lee SY, Lee HJ, Kim YK. Comparative transcriptome profiling of selected osmotic regulatory proteins in the gill during seawater acclimation of chum salmon (Oncorhynchus keta) fry. Sci Rep 2020; 10:1987. [PMID: 32029805 PMCID: PMC7005315 DOI: 10.1038/s41598-020-58915-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
Salmonid fishes, chum salmon (Oncorhynchus keta) have the developed adaptive strategy to withstand wide salinity changes from the early life stage. This study investigated gene expression patterns of cell membrane proteins in the gill of chum salmon fry on the transcriptome level by tracking the salinity acclimation of the fish in changing environments ranging from freshwater (0 ppt) to brackish water (17.5 ppt) to seawater (35 ppt). Using GO analysis of DEGs, the known osmoregulatory genes and their functional groups such as ion transport, transmembrane transporter activity and metal ion binding were identified. The expression patterns of membrane protein genes, including pump-mediated protein (NKA, CFTR), carrier-mediated protein (NKCC, NHE3) and channel-mediated protein (AQP) were similar to those of other salmonid fishes in the smolt or adult stages. Based on the protein-protein interaction analysis between transmembrane proteins and other related genes, we identified osmotic-related genes expressed with salinity changes and analyzed their expression patterns. The findings of this study may facilitate the disentangling of the genetic basis of chum salmon and better able an understanding of the osmophysiology of the species.
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Affiliation(s)
- Sang Yoon Lee
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Hwa Jin Lee
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Yi Kyung Kim
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung, 25457, South Korea.
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung, 25457, South Korea.
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