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Kazmi SSUH, Tayyab M, Pastorino P, Barcelò D, Yaseen ZM, Grossart HP, Khan ZH, Li G. Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134574. [PMID: 38739959 DOI: 10.1016/j.jhazmat.2024.134574] [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: 02/13/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.
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Affiliation(s)
- Syed Shabi Ul Hassan Kazmi
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Muhammad Tayyab
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 Torino, Italy
| | - Damià Barcelò
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), 08034 Barcelona, Spain
| | - Zaher Mundher Yaseen
- Civil and Environmental Engineering Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, (IGB), Alte Fischerhuette 2, Neuglobsow, D-16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany
| | - Zulqarnain Haider Khan
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
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Gao Y, Huang X, Liu Y, Lv H, Yin X, Li W, Chu Z. Transcriptome analysis of large yellow croaker (Larimichthys crocea) at different growth rates. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024:10.1007/s10695-024-01367-w. [PMID: 38842792 DOI: 10.1007/s10695-024-01367-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
The unsynchronized growth of the large yellow croaker (Larimichthys crocea), which impacts growth efficiency, poses a challenge for aquaculture practitioners. In our study, juvenile stocks of large yellow croaker were sorted by size after being cultured in offshore cages for 4 months. Subsequently, individuals from both the fast-growing (FG) and slow-growing (SG) groups were sampled for analysis. High-throughput RNA-Seq was employed to identify genes and pathways that are differentially expressed during varying growth rates, which could suggest potential physiological mechanisms that influence growth rate. Our transcriptome analysis identified 382 differentially expressed genes (DEGs), comprising 145 upregulated and 237 downregulated genes in comparison to the SG group. GO and KEGG enrichment analyses indicated that these DEGs are predominantly involved in signal transduction and biochemical metabolic pathways. Quantitative PCR (qPCR) results demonstrated that cat, fasn, idh1, pgd, fgf19, igf2, and fads2 exhibited higher expression levels, whereas gadd45b and gadd45g showed lower expression compared to the slow-growing group. In conclusion, the differential growth rates of large yellow croaker are intricately associated with cellular proliferation, metabolic rates of the organism, and immune regulation. These findings offer novel insights into the molecular mechanisms and regulatory aspects of growth in large yellow croaker and enhance our understanding of growth-related genes.
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Affiliation(s)
- Yang Gao
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China.
| | - Xuming Huang
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Yanli Liu
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Huirong Lv
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
| | - Xiaolong Yin
- Zhoushan Fisheries Research Institute, Zhoushan, China
| | - Weiye Li
- Zhoushan Fisheries Research Institute, Zhoushan, China
| | - Zhangjie Chu
- Fishery School, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Street, Dinghai District, Zhoushan City, 316022, Zhejiang Province, P. R. China
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Han G, Bu D, Kong R, Huang K, Liu C. Toxic responses of environmental concentrations of bifenthrin in larval freshwater snail Bellamya aeruginosa. CHEMOSPHERE 2024; 355:141863. [PMID: 38579955 DOI: 10.1016/j.chemosphere.2024.141863] [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: 01/22/2024] [Revised: 03/04/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024]
Abstract
Bifenthrin (BF) is ubiquitous in aquatic environments, and studies have indicated that environmental concentrations of BF could cause neurotoxicity and oxidative damage in fish and decrease the abundance of aquatic insects. However, little information is available on the toxicity of BF in freshwater benthic mollusks. Bellamya aeruginosa (B. aeruginosa) is a key benthic fauna species in aquatic ecosystems, and has extremely high economic and ecological values. In this study, larval B. aeruginosa within 24 h of birth were exposed to 0, 30 or 300 ng/L of BF for 30 days, and then the toxic effects from molecular to individual levels were comprehensively evaluated in all the three treatment groups. It was found that BF at 300 ng/L caused the mortality of snails. Furthermore, BF affected snail behaviors, evidenced by reduced crawling distance and crawling speed. The hepatopancreas of snails in the two BF exposure groups showed significant pathological changes, including increase in the number of yellow granules and occurrence of hemocyte infiltration, epithelial cell thinning, and necrosis. The levels of ROS and MDA were significantly increased after exposure to 300 ng/L BF, and the activities of two antioxidant enzymes SOD and CAT were increased significantly. GSH content decreased significantly after BF exposure, indicating the occurrence of oxidative damage in snails. Transcriptomic results showed that differentially expressed genes (DEGs) were significantly enriched in pathways related to metabolism and neurotoxicity (e.g., oxidative phosphorylation and Parkinson disease), and these results were consistent with those in individual and biochemical levels above. The study indicates that environmental concentration of BF results in decreased survival rates, sluggish behavior, histopathological lesions, oxidative damage, and transcriptomic changes in the larvae of B. aeruginosa. Thus, exposure of larval snails to BF in the wild at concentrations similar to those used in this study might have adverse consequences at the population level. These findings provide a theoretical basis for further assessing the ecological risk of BF to aquatic gastropods.
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Affiliation(s)
- Guixin Han
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dianping Bu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ren Kong
- MOE Key Laboratory of Groundwater Quality and Health, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Kai Huang
- MOE Key Laboratory of Groundwater Quality and Health, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China
| | - Chunsheng Liu
- MOE Key Laboratory of Groundwater Quality and Health, School of Environmental Studies, China University of Geosciences, Wuhan, 430074, China.
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Raposo de Magalhães C, Sandoval K, Kagan F, McCormack G, Schrama D, Carrilho R, Farinha AP, Cerqueira M, Rodrigues PM. Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration. PLoS One 2024; 19:e0300472. [PMID: 38517901 PMCID: PMC10959376 DOI: 10.1371/journal.pone.0300472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
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Affiliation(s)
- Cláudia Raposo de Magalhães
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Grace McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute & School of Natural Sciences, University of Galway, Galway, Ireland
| | - Denise Schrama
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Raquel Carrilho
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Paula Farinha
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Escola Superior Agrária de Santarém, Santarém, Portugal
| | - Marco Cerqueira
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Pedro M. Rodrigues
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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Andresen AMS, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ, Fosse JH. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109357. [PMID: 38181891 DOI: 10.1016/j.fsi.2024.109357] [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: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
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Affiliation(s)
| | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
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Zhou X, Li JJ, Li S, Liu HH, Xu DD, Chi CF, Zheng LB. Transcriptomic analysis of large yellow croaker (Larimichthys crocea) reveals the suppression of the inflammatory response from Cryptocaryon irritans infection. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109258. [PMID: 38042226 DOI: 10.1016/j.fsi.2023.109258] [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: 08/11/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is the most productive marine fish in China. Cryptocaryon irritans is an extremely destructive parasite that causes great economic losses in large yellow croaker aquaculture industry. Therefore, it is very necessary to study the immune response of large yellow croaker in response to C. irritans infection. In this study, the transcriptomic profiles of large yellow croaker were sequenced and analyzed in the brain and head kidney at 72 h after C. irritans infection. Cytokines and chemokines related terms were significantly enriched based on the GO enrichment of down-regulated differentially expressed genes (DEGs) from the head kidney. Meanwhile, cytokine-cytokine receptor interaction was significantly enriched based on the KEGG enrichment of up-regulated DEGs from the brain and down-regulated DEGs from the head kidney, respectively. Moreover, the majority of inflammation-related DEGs were significantly up-regulated in the brain, but distinctly down-regulated in the head kidney. These results showed that the brain and head kidney might play different roles against C. irritans infection, and the inflammatory response of large yellow croaker may be restrained during C. irritans infection. Taken together, the transcriptomic analyses will be helpful to more comprehensively understand the immune mechanism of teleost against C. irritans infection, and provide a theoretical basis for the prevention and treatment of Cryptosporidiosis.
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Affiliation(s)
- Xu Zhou
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China
| | - Jun-Jie Li
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China
| | - Shuang Li
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China
| | - Hui-Hui Liu
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China
| | - Dong-Dong Xu
- Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhoushan, 316100, China
| | - Chang-Feng Chi
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China.
| | - Li-Bing Zheng
- National and Provincial Joint Engineering Research Centre for Marine Germplasm Resources Exploration and Utilization, School of Marine Science and Technology, Zhejiang Ocean University, 1st Haidanan Road, Changzhi Island, Lincheng, Zhoushan, 316022, China.
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Yang N, Li W, Feng W, Wang M, Liu A, Tang Y, Su S. Genomics and transcriptomics of the Chinese mitten crabs (Eriocheir sinensis). Sci Data 2023; 10:843. [PMID: 38036563 PMCID: PMC10689444 DOI: 10.1038/s41597-023-02761-4] [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: 05/24/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
To gain a deeper understanding of the genetic factors influencing the growth and development of Eriocheir sinensis, a well-known species of hairy crab found in Yangcheng Lake, this study focused on the de novo genome and full-length transcriptome information of the selected subjects. Specifically, Yangcheng Lake hairy crabs were chosen as the experimental samples. Initially, a genome analysis was performed, resulting in the identification of gene fragments with a combined length of 1266,092,319 bp. Subsequently, a transcriptome analysis was conducted on a mixture of tissues from four different sites, namely muscle, brain, eye, and heart, to further investigate the genetic characteristics at the transcriptome level. The Pacific Biosciences (Pacio) single-molecule real-time sequencing system generated a total of 36.93 G sub-fragments and 175,90041 effective inserts. This research contributes to the indirect comprehension of genetic variations underlying individual traits. Furthermore, a comparison of the obtained data with relevant literature emphasizes the advantages of this study and establishes a basis for further investigations on the Chinese mitten crab.
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Affiliation(s)
- Nan Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Wenjing Li
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou, 225309, China
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Meiyao Wang
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Aimin Liu
- Jiangsu Haorun Biological Industry Group Co., Ltd, Taizhou, 225309, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China.
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China.
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Zhang R, Duan Q, Luo Q, Deng L. PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish. Animals (Basel) 2023; 13:3399. [PMID: 37958154 PMCID: PMC10648740 DOI: 10.3390/ani13213399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.
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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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Xie GB, Liu SG, Gu GS, Lin ZY, Yu JR, Chen RB, Xie WJ, Xu HJ. LUNCRW: Prediction of potential lncRNA-disease associations based on unbalanced neighborhood constraint random walk. Anal Biochem 2023; 679:115297. [PMID: 37619903 DOI: 10.1016/j.ab.2023.115297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) are associated with various complex human diseases. They can serve as disease biomarkers and hold considerable promise for the prevention and treatment of various diseases. The traditional random walk algorithms generally exclude the effect of non-neighboring nodes on random walking. In order to overcome the issue, the neighborhood constraint (NC) approach is proposed in this study for regulating the direction of the random walk by computing the effects of both neighboring nodes and non-neighboring nodes. Then the association matrix is updated by matrix multiplication for minimizing the effect of the false negative data. The heterogeneous lncRNA-disease network is finally analyzed using an unbalanced random walk method for predicting the potential lncRNA-disease associations. The LUNCRW model is therefore developed for predicting potential lncRNA-disease associations. The area under the curve (AUC) values of the LUNCRW model in leave-one-out cross-validation and five-fold cross-validation were 0.951 and 0.9486 ± 0.0011, respectively. Data from published case studies on three diseases, including squamous cell carcinoma, hepatocellular carcinoma, and renal cell carcinoma, confirmed the predictive potential of the LUNCRW model. Altogether, the findings indicated that the performance of the LUNCRW method is superior to that of existing methods in predicting potential lncRNA-disease associations.
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Affiliation(s)
- Guo-Bo Xie
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Shi-Gang Liu
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Guo-Sheng Gu
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Zhi-Yi Lin
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Jun-Rui Yu
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Rui-Bin Chen
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Wei-Jie Xie
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
| | - Hao-Jie Xu
- School of Computer Science, Guangdong University of Technology, Guangzhou, 510000, China.
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11
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Wang Y, Liu X, Wang W, Sun G, Xu X, Feng Y, Li Z, Yang J. Investigating the Mechanism of Low-Salinity Environmental Adaptation in Sepia esculenta Larvae through Transcriptome Profiling. Animals (Basel) 2023; 13:3139. [PMID: 37835745 PMCID: PMC10571815 DOI: 10.3390/ani13193139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Sepia esculenta is an economically important mollusk distributed in the coastal waters of China. Juveniles are more susceptible to stimulation by the external environment than mature individuals. The ocean salinity fluctuates due to environmental changes. However, there is a lack of research on the salinity adaptations of S. esculenta. Therefore, in this study, we investigated the differential expression of genes in S. esculenta larvae after stimulation by low salinity. RNA samples were sequenced and 1039 differentially expressed genes (DEGs) were identified. Then, enrichment analysis was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, a protein-protein interaction network (PPI) was constructed, and the functions of key genes in S. esculenta larvae after low-salinity stimulation were explored. We suggest that low salinity leads to an excess proliferation of cells in S. esculenta larvae that, in turn, affects normal physiological activities. The results of this study can aid in the artificial incubation of S. esculenta and reduce the mortality of larvae.
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Affiliation(s)
- Yongjie Wang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Yanwei Feng
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai 264025, China
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12
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Bhardwaj S, Thakur K, Sharma AK, Sharma D, Brar B, Mahajan D, Kumar S, Kumar R. Regulation of omega-3 fatty acids production by different genes in freshwater fish species: a review. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1005-1016. [PMID: 37684550 DOI: 10.1007/s10695-023-01236-y] [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: 03/10/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
The present study aims to compare the gene expression of three different fish species (common carp, tilapia, and trout) with varying levels of fatty acids (FA). Based on transcriptome analysis and RNA sequencing, various genes and their associated metabolic pathways are identified. Pathways are categorized based on the genes they encode. Genes that were differentially expressed and their promoter's methylation patterns were revealed by RNA-seq analysis in common carp. Furthermore, fatty acid-enriched pathways, such as ARA4 and adipocytokine signaling, were also identified. Many genes and pathways may influence tilapia's growth and omega-3 content. Using the mTOR pathway, trout with differential expression were discovered to be involved in producing omega-3 fatty acids. This study revealed major pathways in fish species to produce omega-3 fatty acids.
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Affiliation(s)
- Shivani Bhardwaj
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Kushal Thakur
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Amit Kumar Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Dixit Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Bhavna Brar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Danish Mahajan
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Sunil Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India
| | - Rakesh Kumar
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, 176206, India.
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13
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Ulhaq ZS, Tse WKF. Perfluorohexanesulfonic acid (PFHxS) induces oxidative stress and causes developmental toxicities in zebrafish embryos. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131722. [PMID: 37263022 DOI: 10.1016/j.jhazmat.2023.131722] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Perfluorohexanesulfonic acid (PFHxS) is a short-chain perfluoroalkyl substance widely used to replace the banned perfluorooctanesulfonic acid (PFOS) in different industrial and household products. It has currently been identified in the environment and human bodies; nonetheless, the possible toxicities are not well-known. Zebrafish have been used as a toxicant screening model due to their fast and transparent developmental processes. In this study, zebrafish embryos were exposed to PFHxS for five days, and various experiments were performed to monitor the developmental and cellular processes. Liquid chromatography-mass spectrometry (LC/MS) analysis confirmed that PFHxS was absorbed and accumulated in the zebrafish embryos. We reported that 2.5 µM or higher PFHxS exposure induced phenotypic abnormalities, marked by developmental delay in the mid-hind brain boundary and yolk sac edema. Additionally, larvae exposed to PFHxS displayed facial malformation due to the reduction of neural crest cell expression. RNA sequencing analysis further identified 4643 differentiated expressed transcripts in 5 µM PFHxS-exposed 5-days post fertilization (5-dpf) larvae. Bioinformatics analysis revealed that glucose metabolism, lipid metabolism, as well as oxidative stress were enriched in the PFHxS-exposed larvae. To validate these findings, a series of biological experiments were conducted. PFHxS exposure led to a nearly 4-fold increase in reactive oxygen species, possibly due to hyperglycemia and impaired glutathione balance. The Oil Red O' staining and qPCR analysis strengthens the notions that lipid metabolism was disrupted, leading to lipid accumulation, lipid peroxidation, and malondialdehyde formation. All these alterations ultimately affected cell cycle events, resulting in S and G2/M cell cycle arrest. In conclusion, our study demonstrated that PFHxS could accumulate and induce various developmental toxicities in aquatic life, and such data might assist the government to accelerate the regulatory policy on PFHxS usage.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 8190395, Japan; Research Center for Pre-clinical and Clinical Medicine, National Research and Innovation Agency, Republic of Indonesia, Cibinong 16911, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 8190395, Japan.
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14
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Liu T, Amanullah S, Xu H, Gao P, Du Z, Hu X, Han M, Che Y, Zhang L, Qi G, Wang D. RNA-Seq Identified Putative Genes Conferring Photosynthesis and Root Development of Melon under Salt Stress. Genes (Basel) 2023; 14:1728. [PMID: 37761868 PMCID: PMC10530605 DOI: 10.3390/genes14091728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Melon is an important fruit crop of the Cucurbitaceae family that is being cultivated over a large area in China. Unfortunately, salt stress has crucial effects on crop plants and damages photosynthesis, membranal lipid components, and hormonal metabolism, which leads to metabolic imbalance and retarded growth. Herein, we performed RNA-seq analysis and a physiological parameter evaluation to assess the salt-induced stress impact on photosynthesis and root development activity in melon. The endogenous quantification analysis showed that the significant oxidative damage in the membranal system resulted in an increased ratio of non-bilayer/bilayer lipid (MGDG/DGDG), suggesting severe irregular stability in the photosynthetic membrane. Meanwhile, root development was slowed down by a superoxidized membrane system, and downregulated genes showed significant contributions to cell wall biosynthesis and IAA metabolism. The comparative transcriptomic analysis also exhibited that major DEGs were more common in the intrinsic membrane component, photosynthesis, and metabolism. These are all processes that are usually involved in negative responses. Further, the WGCN analysis revealed the involvement of two main network modules: the thylakoid membrane and proteins related to photosystem II. The qRT-PCR analysis exhibited that two key genes (MELO3C006053.2 and MELO3C023596.2) had significant variations in expression profiling at different time intervals of salt stress treatments (0, 6, 12, 24, and 48 h), which were also consistent with the RNA-seq results, denoting the significant accuracy of molecular dataset analysis. In summary, we performed an extensive molecular and metabolic investigation to check the salt-stress-induced physiological changes in melon and proposed that the PSII reaction centre may likely be the primary stress target.
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Affiliation(s)
- Tai Liu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (S.A.); (P.G.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Huichun Xu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (S.A.); (P.G.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zhiqiang Du
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Xixi Hu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Mo Han
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Ye Che
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Ling Zhang
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Guochao Qi
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
| | - Di Wang
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing 163711, China; (T.L.); (H.X.); (Z.D.); (X.H.); (M.H.); (Y.C.); (L.Z.); (G.Q.)
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15
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Wang Y, Bao X, Wang W, Xu X, Liu X, Li Z, Yang J, Yuan T. Exploration of anti-stress mechanisms in high temperature exposed juvenile golden cuttlefish ( Sepia esculenta) based on transcriptome profiling. Front Physiol 2023; 14:1189375. [PMID: 37234426 PMCID: PMC10206265 DOI: 10.3389/fphys.2023.1189375] [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: 03/19/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Sepia esculenta is a cephalopod widely distributed in the Western Pacific Ocean, and there has been growing research interest due to its high economic and nutritional value. The limited anti-stress capacity of larvae renders challenges for their adaptation to high ambient temperatures. Exposure to high temperatures produces intense stress responses, thereby affecting survival, metabolism, immunity, and other life activities. Notably, the molecular mechanisms by which larval cuttlefish cope with high temperatures are not well understood. As such, in the present study, transcriptome sequencing of S. esculenta larvae was performed and 1,927 differentially expressed genes (DEGs) were identified. DEGs were subjected to functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The top 20 terms of biological processes in GO and 20 high-temperature stress-related pathways in KEGG functional enrichment analysis were identified. A protein-protein interaction network was constructed to investigate the interaction between temperature stress-related genes. A total of 30 key genes with a high degree of participation in KEGG signaling pathways or protein-protein interactions were identified and subsequently validated using quantitative RT-PCR. Through a comprehensive analysis of the protein-protein interaction network and KEGG signaling pathway, the functions of three hub genes (HSP90AA1, PSMD6, and PSMA5), which belong to the heat shock protein family and proteasome, were explored. The present results can facilitate further understanding of the mechanism of high temperature resistance in invertebrates and provide a reference for the S. esculenta industry in the context of global warming.
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Affiliation(s)
- Yongjie Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, China
| | - Weijun Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, China
| | - Tingzhu Yuan
- School of Agriculture, Ludong University, Yantai, China
- Marine Economy Promotion Center of Changdao County Marine Ecological Civilization Comprehensive Experimental Zone, Yantai, China
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16
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Li D, Miao J, Pan L, Zhou Y, Gao Z, Bi Y, Tang J. Integrated lipidomics and transcriptomics analysis reveal lipid metabolism disturbance in scallop (Chlamys farreri) exposure to benzo[a]pyrene. CHEMOSPHERE 2023; 331:138787. [PMID: 37119930 DOI: 10.1016/j.chemosphere.2023.138787] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
Benzo[a]pyrene (B[a]P) commonly bioaccumulates in lipid-rich tissues due to its lipophilicity and further affects lipid metabolism. The present study systematically investigated the lipid metabolism disturbance in digestive glands of scallops (Chlamys farreri) exposure to B[a]P, based on lipidomics, transcriptomics, molecular and biochemical analysis. We exposed the scallops to environmentally relevant concentrations of B[a]P for 21 days. The bioaccumulation of B[a]P, lipid content and lipid peroxidation in digestive glands were measured. Integrated lipidomics and transcriptomics analysis, the differential lipid species were identified and key genes based on the pathways in which genes and lipid species involved together were selected in scallop exposure to 10 μg/L B[a]P. The changes of lipid profile showed that triglycerides (TGs) were accumulated after 21 days exposure, while the phospholipids (PLs) decreased demonstrated membrane structures were disrupted by B[a]P. In combination with the change of gene expression, we speculated that B[a]P could induce lipids accumulation by up-regulating lipid synthesis-related genes expression, down-regulating lipolysis-related genes expression and interfering with lipid transport. Overall, this study provides new insights into the mechanisms of lipid metabolism disturbance in bivalves exposed to PAHs, and establishes a foundation for understanding the bioaccumulation mechanism of B[a]P in aquatic organisms, which is of great importance for further ecotoxicological study.
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Affiliation(s)
- Dongyu Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China.
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Zhongyuan Gao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Yaqi Bi
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Jian Tang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
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17
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Jaouani R, Roman C, Decaix J, Lagarde F, Châtel A. Effect of aging of microplastics on gene expression levels of the marine mussel Mytilus edulis: Comparison in vitro/in vivo exposures. MARINE POLLUTION BULLETIN 2023; 189:114767. [PMID: 36870134 DOI: 10.1016/j.marpolbul.2023.114767] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
In the present study, effects of aging MPs of polyethylene (PE) were investigated in the marine mussel Mytilus edulis, commonly used as bioindicator of aquatic ecosystem, using both in vitro and in vivo exposures, using concentrations found in marine waters (0.008, 10 and 100 μg.L-1). Changes in gene expression levels implicated in detoxification, immune system, cytoskeletton and cell cycle control were evaluated by quantitative RT-qPCR. Results demonstrated differential expression levels depending upon the state of plastic degradation (aged vs non-aged) and way of exposure (vitro vs vivo). This study highlighted the interest of using molecular biomarkers based on analysis of gene expression pattern in an ecotoxicological context that gives indication of relative slight changes between tested conditions as compared to other biochemical approaches (e.g. enzymatic activities). In addition, in vitro analysis could be used to generate large amount of data as regards to the toxicological effects of MPs.
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Affiliation(s)
- Rihab Jaouani
- Biology of Organisms Stress Health Environment (BIOSSE), Université Catholique de l'Ouest, Angers, France; Institut des Molécules et des Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans Cedex, France
| | - Coraline Roman
- Biology of Organisms Stress Health Environment (BIOSSE), Université Catholique de l'Ouest, Angers, France
| | - Justine Decaix
- Biology of Organisms Stress Health Environment (BIOSSE), Université Catholique de l'Ouest, Angers, France
| | - Fabienne Lagarde
- Institut des Molécules et des Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans Cedex, France
| | - Amélie Châtel
- Biology of Organisms Stress Health Environment (BIOSSE), Université Catholique de l'Ouest, Angers, France.
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18
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Jiang T, Liang YS, Gu Y, Yao FC, Liu YF, Zhang KX, Song FB, Sun JL, Luo J. Different reoxygenation rates induce different metabolic, apoptotic and immune responses in Golden Pompano (Trachinotus blochii) after hypoxic stress. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108640. [PMID: 36871632 DOI: 10.1016/j.fsi.2023.108640] [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: 11/29/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Dissolved oxygen (DO) is essential for teleosts, and fluctuating environmental factors can result in hypoxic stress in the golden pompano (Trachinotus blochii). However, it is unknown whether different recovery speeds of DO concentration after hypoxia induce stress in T. blochii. In this study, T. blochii was subjected to hypoxic conditions (1.9 ± 0.2 mg/L) for 12 h followed by 12 h of reoxygenation at two different speeds (30 mg/L per hour and 1.7 mg/L per hour increasing). The gradual reoxygenation group (GRG), experienced DO recovery (1.9 ± 0.2 to 6.8 ± 0.2 mg/L) within 3 h, and the rapid reoxygenation group (RRG), experienced DO recovery (1.9 ± 0.2 to 6.8 ± 0.2 mg/L) within 10 min. Physiological and biochemical parameters of metabolism (glucose, glycegon, lactic acid (LD), lactate dehydrogenase (LDH), pyruvic acid (PA), phosphofructokinase (PFKA), and hexokinase (HK), triglyceride (TG), lipoprotein lipase (LPL), carnitine palmitoyltransferase 1 (CPT-1)) and transcriptome sequencing (RNA-seq of liver) were monitored to identify the effects of the two reoxygenation speeds. Increased LD content and increased activity of LDH, PA, PFKA, and HK suggested enhanced anaerobic glycolysis under hypoxic stress. LD and LDH levels remained significantly elevated during reoxygenation, indicating that the effects of hypoxia were not immediately alleviated during reoxygenation. The expressions of PGM2, PFKA, GAPDH, and PK were increased in the RRG, which suggests that glycolysis was enhanced. The same pattern was not observed in the GRG. Additionally, In the RRG, reoxygenation may promote glycolysis to guarantee energy supply. However, the GRG may through the lipid metabolism such as steroid biosynthesis at the later stage of reoxygenation. In the aspect of apoptosis, differentially expressed genes (DEGs) in the RRG were enriched in the p53 signaling pathway, which promoted cell apoptosis, while DEGs in the GRG seem to activate cell apoptosis at early stage of reoxygenation but was restrained latterly. DEGs in both the RRG and the GRG were enriched in the NF-kappa B and JAK-STAT signaling pathways, the RRG may induce cell survival by regulating the expression of IL-12B, COX2, and Bcl-XL, while in the GRG it may induce by regulating the expression of IL-8. Moreover, DEGs in the RRG were also enriched in the Toll-like receptor signaling pathway. This research revealed that at different velocity of reoxygenation after hypoxic stress, T. blochii would represent different metabolic, apoptotic and immune strategies, and this conclusion would provide new insight into the response to hypoxia and reoxygenation in teleosts.
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Affiliation(s)
- Tian Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Ye Song Liang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Yue Gu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Fu Cheng Yao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Yi Fan Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Kai Xi Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Fei Biao Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Jun Long Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China.
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19
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Integration of Transcriptomics and Non-Targeted Metabolomics Reveals the Underlying Mechanism of Skeletal Muscle Development in Duck during Embryonic Stage. Int J Mol Sci 2023; 24:ijms24065214. [PMID: 36982289 PMCID: PMC10049352 DOI: 10.3390/ijms24065214] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Skeletal muscle is an important economic trait in duck breeding; however, little is known about the molecular mechanisms of its embryonic development. Here, the transcriptomes and metabolomes of breast muscle of Pekin duck from 15 (E15_BM), 21 (E21_BM), and 27 (E27_BM) days of incubation were compared and analyzed. The metabolome results showed that the differentially accumulated metabolites (DAMs), including the up-regulated metabolites, l-glutamic acid, n-acetyl-1-aspartylglutamic acid, l-2-aminoadipic acid, 3-hydroxybutyric acid, bilirubin, and the significantly down-regulated metabolites, palmitic acid, 4-guanidinobutanoate, myristic acid, 3-dehydroxycarnitine, and s-adenosylmethioninamine, were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of cofactors, protein digestion and absorption, and histidine metabolism, suggesting that these pathways may play important roles in the muscle development of duck during the embryonic stage. Moreover, a total of 2142 (1552 up-regulated and 590 down-regulated), 4873 (3810 up-regulated and 1063 down-regulated), and 2401 (1606 up-regulated and 795 down-regulated) DEGs were identified from E15_BM vs. E21_BM, E15_BM vs. E27_BM and E21_BM vs. E27_BM in the transcriptome, respectively. The significantly enriched GO terms from biological processes were positive regulation of cell proliferation, regulation of cell cycle, actin filament organization, and regulation of actin cytoskeleton organization, which were associated with muscle or cell growth and development. Seven significant pathways, highly enriched by FYN, PTK2, PXN, CRK, CRKL, PAK, RHOA, ROCK, INSR, PDPK1, and ARHGEF, were focal adhesion, regulation of actin cytoskeleton, wnt signaling pathway, insulin signaling pathway, extracellular matrix (ECM)-receptor interaction, cell cycle, and adherens junction, which participated in regulating the development of skeletal muscle in Pekin duck during the embryonic stage. KEGG pathway analysis of the integrated transcriptome and metabolome indicated that the pathways, including arginine and proline metabolism, protein digestion and absorption, and histidine metabolism, were involved in regulating skeletal muscle development in embryonic Pekin duck. These findings suggested that the candidate genes and metabolites involved in crucial biological pathways may regulate muscle development in the Pekin duck at the embryonic stage, and increased our understanding of the molecular mechanisms underlying the avian muscle development.
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Wang J, Chen G, Yu X, Zhou X, Zhang Y, Wu Y, Tong J. Transcriptome analyses reveal differentially expressed genes associated with development of the palatal organ in bighead carp (Hypophthalmichthys nobilis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY PART D: GENOMICS AND PROTEOMICS 2023; 46:101072. [PMID: 36990038 DOI: 10.1016/j.cbd.2023.101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/12/2023] [Accepted: 03/11/2023] [Indexed: 03/28/2023]
Abstract
The palatal organ is a filter-feeding related organ and occupies a considerable proportion of the head of bighead carp (Hypophthalmichthys nobilis), a large cyprinid fish intensive aquaculture in Asia. In this study, we performed RNA-seq of the palatal organ during growth periods of two (M2), six (M6) and 15 (M15) months of age after hatching. The numbers of differentially expressed genes (DEGs) were 1384, 481 and 1837 for M2 VS M6, M6 VS M15 and M2 VS M15 respectively. The following signaling pathways of energy metabolism and cytoskeleton function were enriched, including ECM-receptor interaction, Cardiac muscle contraction, Steroid biosynthesis and PPAR signaling pathway. Several members of collagen family (col1a1, col2a1, col6a2, col6a3, col9a2), Laminin gamma 1 (lamc1), integrin alpha 1 (itga1), Fatty acid binding protein 2 (fads2) and lipoprotein lipase (lpl), and Protein tyrosine kinase 7 (Ptk7) are candidate genes for growth and development of basic tissues of the palatal organ. Furthermore, taste-related genes such as fgfrl1, fgf8a, fsta and notch1a were also identified, which may be involved in the development of taste buds of the palatal organ. The transcriptome data obtained in this study provide insights into the understanding functions and development mechanisms of palatal organ, and potential candidate genes that may be related to the genetic modulation of head size of bighead carp.
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Affiliation(s)
- Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geng Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaoyu Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yanhong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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21
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Recent advances in predicting lncRNA-disease associations based on computational methods. Drug Discov Today 2023; 28:103432. [PMID: 36370992 DOI: 10.1016/j.drudis.2022.103432] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/19/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
Abstract
Mutations in and dysregulation of long non-coding RNAs (lncRNAs) are closely associated with the development of various human complex diseases, but only a few lncRNAs have been experimentally confirmed to be associated with human diseases. Predicting new potential lncRNA-disease associations (LDAs) will help us to understand the pathogenesis of human diseases and to detect disease markers, as well as in disease diagnosis, prevention and treatment. Computational methods can effectively narrow down the screening scope of biological experiments, thereby reducing the duration and cost of such experiments. In this review, we outline recent advances in computational methods for predicting LDAs, focusing on LDA databases, lncRNA/disease similarity calculations, and advanced computational models. In addition, we analyze the limitations of various computational models and discuss future challenges and directions for development.
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22
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Chiari Y, Howard L, Moreno N, Relyea S, Dunnigan J, Boyer MC, Kardos M, Glaberman S, Luikart G. Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Mol Ecol Resour 2023; 23:803-817. [PMID: 36704853 DOI: 10.1111/1755-0998.13757] [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: 01/19/2021] [Revised: 12/14/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.
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Affiliation(s)
- Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Leif Howard
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Nickolas Moreno
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Scott Relyea
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | - James Dunnigan
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
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23
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He Z, Shou C, Han Z. Transcriptome Analysis of Marbled Rockfish Sebastiscus marmoratus under Salinity Stress. Animals (Basel) 2023; 13:ani13030400. [PMID: 36766289 PMCID: PMC9913653 DOI: 10.3390/ani13030400] [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: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‱, 479 and 520 differential genes were obtained for 35‱ and 10‱, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.
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24
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Priscilla L, Malathi E, Moses Inbaraj R. Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India. Gen Comp Endocrinol 2023; 331:114118. [PMID: 36037874 DOI: 10.1016/j.ygcen.2022.114118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.
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Affiliation(s)
- Lyndsay Priscilla
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India; Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India
| | - E Malathi
- Department of Zoology, Queen Mary's College (Autonomous), Affiliated to the University of Madras, Chennai 600004, Tamil Nadu, India
| | - R Moses Inbaraj
- Endocrinology Unit, Department of Zoology, Madras Christian College, Affiliated to the University of Madras, Chennai, India.
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25
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Morphological and Molecular Functional Evidence of the Pharyngeal Sac in the Digestive Tract of Silver Pomfret, Pampus argenteus. Int J Mol Sci 2023; 24:ijms24021663. [PMID: 36675173 PMCID: PMC9866116 DOI: 10.3390/ijms24021663] [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: 11/11/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
The pharyngeal sac is a comparatively rare organ in the digestive tract among teleost fishes. However, our understanding of this remarkable organ in the silver pomfret (Pampus argenteus) is limited. In the present study, we examined the various morphological and histological characteristics of the pharyngeal sac using histochemical techniques and electron microscopy. The pharyngeal sac showed unique characteristics such as well-developed muscular walls, weakly keratinized epithelium, numerous goblet cells, and needle-like processes on the papillae. The porous cavity of the papillae contained numerous adipocytes and was tightly enveloped by type I collagen fibers. These structures might provide mechanical protection and excellent biomechanical properties for grinding and shredding prey. A comparison of gene expression levels between the pharyngeal sac and esophagus using RNA-seq showed that phenotype-associated genes (epithelial genes and muscle genes) were upregulated, whereas genes related to nutrient digestion and absorption were downregulated in the pharyngeal sac. These results support the role of the pharyngeal sac in shredding and predigesting food. Overall, these findings provide a clearer understanding of the pharyngeal sac morphology and explain the morphological adaptations of the digestive tract for feeding on gelatinous prey. To our knowledge, this is the first report on pharyngeal sac gene expression in P. argenteus.
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Yue GH, Tay YX, Wong J, Shen Y, Xia J. Aquaculture species diversification in China. AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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27
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Alsoufi MA, Liu Y, Cao C, Zhao J, Kang J, Li M, Wang K, He Y, Ge C. Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits. Genes (Basel) 2022; 14:95. [PMID: 36672833 PMCID: PMC9859260 DOI: 10.3390/genes14010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.
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Affiliation(s)
- Mohammed Abdulwahid Alsoufi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Department of Animal Production, Faculty of Agriculture, Sana’a University, Alwehdah Street, Sana’a P.O. Box 19509, Yemen
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changwei Cao
- Department of Food Science and Engineering, College of Biological Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jinbo Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengyuan Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yang He
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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28
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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29
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Wang X, Xie Y, Hu W, Wei Z, Wei X, Yuan H, Yao H, Dunxue C. Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa. Gene 2022; 842:146793. [PMID: 35952842 DOI: 10.1016/j.gene.2022.146793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
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Affiliation(s)
- Xiaodong Wang
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yongguang Xie
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Zhaoyu Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Xiuying Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hong Yuan
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hongyan Yao
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Chen Dunxue
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China.
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30
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Yang H, Huang Y, Li Z, Guo Y, Li S, Huang H, Yang X, Li G, Chen H. Effects of Dietary Supplementation with Aurantiochytrium sp. on Zebrafish Growth as Determined by Transcriptomics. Animals (Basel) 2022; 12:ani12202794. [PMID: 36290180 PMCID: PMC9597791 DOI: 10.3390/ani12202794] [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: 09/04/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
The marine protist Aurantiochytrium produces several bioactive chemicals, including EPA (eicosapentaenoic acid), DHA (docosahexaenoic acid), and other critical fish fatty acids. It has the potential to improve growth and fatty acid profiles in aquatic taxa. This study evaluated zebrafish growth performance in response to diets containing 1% to 3% Aurantiochytrium sp. crude extract (TE) and single extract for 56 days. Growth performance was best in the 1% TE group, and therefore, this concentration was used for further analyses of the influence of Aurantiochytrium sp. Levels of hepatic lipase, glucose-6-phosphate dehydrogenase, acetyl-CoA oxidase, glutathione peroxidase, and superoxide dismutase increased significantly in response to 1% TE, while malic enzyme activity, carnitine lipid acylase, acetyl-CoA carboxylase, fatty acid synthase, and malondialdehyde levels decreased. These findings suggest that Aurantiochytrium sp. extract can modulate lipase activity, improve lipid synthesis, and decrease oxidative damage caused by lipid peroxidation. Transcriptome analysis revealed 310 genes that were differentially expressed between the 1% TE group and the control group, including 185 up-regulated genes and 125 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses of the differentially expressed genes revealed that Aurantiochytrium sp. extracts may influence liver metabolism, cell proliferation, motility, and signal transduction in zebrafish.
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Affiliation(s)
- Hao Yang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
| | - Yanlin Huang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhiyuan Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuwen Guo
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
- Correspondence: (H.H.); (H.C.); Tel.: +86-18876860068 (H.H.); +86-18820706692 (H.C.); Fax: +86-898-88651861 (H.H.); +86-759-2382459 (H.C.)
| | - Xuewei Yang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Huapu Chen
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
- Correspondence: (H.H.); (H.C.); Tel.: +86-18876860068 (H.H.); +86-18820706692 (H.C.); Fax: +86-898-88651861 (H.H.); +86-759-2382459 (H.C.)
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Wang Y, Weng Y, Lv L, Wang D, Yang G, Jin Y, Wang Q. Transgenerational effects of co-exposure to cadmium and carbofuran on zebrafish based on biochemical and transcriptomic analyses. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129644. [PMID: 35882171 DOI: 10.1016/j.jhazmat.2022.129644] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/02/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The combined toxicity of heavy metals and pesticides to aquatic organisms is still largely unexplored. In this study, we investigated the combined impacts of cadmium (Cd) and carbofuran (CAR) on female zebrafish (F0 generation) and their following F1 generation. Results showed that mixtures of Cd and CAR induced acute synergistic effects on both zebrafish adults of the F0 generation and embryos of the F1 generation. Combined exposure to Cd and CAR could obviously alter the hepatic VTG level of females, and the individual exposures increased the relative mRNA levels of vtg1 and vtg2. Through maternal transmission, co-exposure of Cd and CAR caused toxicity to 4-day-old larvae of the F1 generation, evidenced by the significant changes in T4 and VTG levels, CYP450 activity, and the relative transcriptional levels of genes related to the hormone, oxidative stress, and apoptosis. These effects were also reflected by the global gene expression pattern to 7-day-old larvae of F1 generation using the transcriptomic analysis, and they could also affect energy metabolism. Our results provided a more comprehensive insight into the transgenerational toxic impacts of heavy metal and pesticide mixtures. These findings highlighted that it was highly necessary to consider transgenerational exposures in the ecological risk assessment of chemical mixtures.
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Affiliation(s)
- Yanhua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - You Weng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Dou Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Guiling Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Zhejiang, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China.
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32
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Abdelzaher H, Tawfik SM, Nour A, Abdelkader S, Elbalkiny ST, Abdelkader M, Abbas WA, Abdelnaser A. Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty. Front Public Health 2022; 10:973000. [PMID: 36211706 PMCID: PMC9533016 DOI: 10.3389/fpubh.2022.973000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Climate change is an anthropogenic phenomenon that is alarming scientists and non-scientists alike. The emission of greenhouse gases is causing the temperature of the earth to rise and this increase is accompanied by a multitude of climate change-induced environmental exposures with potential health impacts. Tracking human exposure has been a major research interest of scientists worldwide. This has led to the development of exposome studies that examine internal and external individual exposures over their lifetime and correlate them to health. The monitoring of health has also benefited from significant technological advances in the field of "omics" technologies that analyze physiological changes on the nucleic acid, protein, and metabolism levels, among others. In this review, we discuss various climate change-induced environmental exposures and their potential health implications. We also highlight the potential integration of the technological advancements in the fields of exposome tracking, climate monitoring, and omics technologies shedding light on important questions that need to be answered.
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Affiliation(s)
| | | | | | | | | | | | | | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
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33
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Li Z, Jiang B, Zhong Z, Cao J, Li H, Wang C, Li A. Skin transcriptomic analysis and immune-related gene expression of golden pompano (Trachinotus ovatus) after Amyloodinium ocellatum infection. FISH & SHELLFISH IMMUNOLOGY 2022; 128:188-195. [PMID: 35870749 DOI: 10.1016/j.fsi.2022.07.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Amyloodiniosis is a severe disease of marine and brackish water fish caused by Amyloodinium ocellatum. Golden pompano (Trachinotus ovatus) is often repeatedly infected by A. ocellatum, leading to extensive mortality. However, little is known about the immune response mechanisms of the T. ovatus following reinfection with A. ocellatum. In this study, an extensive analysis at the transcriptome level of T. ovatus skin was carried out at 24 h post-infection by A. ocellatum. During the transcriptomic analysis, 1367 differentially expressed genes (DEGs) in the skin of T. ovatus under A. ocellatum infection and control conditions were obtained. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotated analyses, the DEGs were significantly enriched in the immune-related pathways. To better understand the immune-related gene expression dynamics, a quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was used to assess the primary and secondary infection groups of T. ovatus at different stages (3 h, 12 h, 24 h, 48 h and, 72 h post-infection) of infection with A.ocellatum. The results showed that innate immunity-related genes [interleukin (IL-8), chemokine ligand 3 (CCL3), toll-like receptor 7 (TLR7), and G-type lysosome (LZM g)] and adaptive immunity-related gene [major histocompatibility complex (MHC) alpha antigen I and MHC alpha antigen II] expression levels in the primary and secondary infection groups were significantly increased compared to the control group. The expression of MHC I and MHC II was more rapidly upregulated in the secondary infection group compared with the primary infection group after A.ocellatum infection. However, no significant differences of A.ocellatum load were observed in primary and secondary infection groups. In addition, the serum of the primary infection group had significantly higher concentrations of triglyceride (TG), higher alanine transaminase (ALT), aspartate transaminase (AST), and lactate dehydrogenase (LDH) activities than the control group. This study contributes to understanding the defense mechanisms in fish skin against ectoparasite infection.
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Affiliation(s)
- Zhicheng Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Biao Jiang
- Innovative Institute of Animal Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510222, Guangdong, China
| | - Zhihong Zhong
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Jizhen Cao
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Han Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Chenxi Wang
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Anxing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China.
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McLimans CJ, Shelledy K, Conrad W, Prendergast K, Le AN, Grant CJ, Buonaccorsi VP. Potential biomarkers of endocrine and habitat disruption identified via RNA-Seq in Salvelinus fontinalis with proximity to fracking operations in Pennsylvania headwater stream ecosystems. ECOTOXICOLOGY (LONDON, ENGLAND) 2022; 31:1044-1055. [PMID: 35834075 DOI: 10.1007/s10646-022-02564-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Unconventional natural gas development (fracking) has been a rapidly expanding technique used for the extraction of natural gas from the Marcellus Shale formation in Pennsylvania. There remains a knowledge gap regarding the ecological impacts of fracking, especially regarding the long-term health of native Brook trout (Salvelinus fontinalis) populations. During the summer of 2015, Brook trout were sampled from twelve streams located in forested, northwestern Pennsylvania in order to evaluate the impacts of fracking on Brook trout. Four stream sites were undisturbed (no fracking activity), three had a developed well pad without fracking activity, and five had active fracking with natural gas production. Liver tissue was isolated from two to five fish per stream and underwent RNA-Seq analysis to identify differentially expressed genes between ecosystems with differing fracking status. Data were analyzed individually and with samples pooled within-stream to account for hierarchical data structure and variation in sample coverage within streams. Differentially expressed and differentially alternatively spliced genes had functions related to lipid and steroid metabolism, mRNA processing, RNA polymerase and protein regulation. Unique to our study, genes related to xenobiotic and stress responses were found as well as potential markers for endocrine disruption and saline adaptation that were identified in watersheds with active fracking activity. These results support the utility of RNA-Seq to assess trout health and suggest detrimental impacts of fracking on sensitive trout populations.
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Affiliation(s)
| | | | - William Conrad
- Department of Biology, Juniata College, Huntingdon, PA, USA
| | | | - Anh N Le
- Department of Biology, Juniata College, Huntingdon, PA, USA
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Tan S, Wang W, Jie W, Liu J. FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species. Comput Struct Biotechnol J 2022; 20:3676-3684. [PMID: 35891795 PMCID: PMC9293738 DOI: 10.1016/j.csbj.2022.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.
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Affiliation(s)
- Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wencai Jie
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinding Liu
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, 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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Lv Y, Amanullah S, Liu S, Zhang C, Liu H, Zhu Z, Zhang X, Gao P, Luan F. Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon ( Cucumis melo L.). Int J Mol Sci 2022; 23:ijms23126721. [PMID: 35743161 PMCID: PMC9224399 DOI: 10.3390/ijms23126721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
Stigma color is an important morphological trait in many flowering plants. Visual observations in different field experiments have shown that a green stigma in melons is more attractive to natural pollinators than a yellow one. In the current study, we evaluated the characterization of two contrasted melon lines (MR-1 with a green stigma and M4-7 with a yellow stigma). Endogenous quantification showed that the chlorophyll and carotenoid content in the MR-1 stigmas was higher compared to the M4-7 stigmas. The primary differences in the chloroplast ultrastructure at different developmental stages depicted that the stigmas of both melon lines were mainly enriched with granum, plastoglobulus, and starch grains. Further, comparative transcriptomic analysis was performed to identify the candidate pathways and genes regulating melon stigma color during key developmental stages (S1–S3). The obtained results indicated similar biological processes involved in the three stages, but major differences were observed in light reactions and chloroplast pathways. The weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) uncovered a “black” network module (655 out of 5302 genes), mainly corresponding to light reactions, light harvesting, the chlorophyll metabolic process, and the chlorophyll biosynthetic process, and exhibited a significant contribution to stigma color. Overall, the expression of five key genes of the chlorophyll synthesis pathway—CAO (MELO03C010624), CHLH (MELO03C007233), CRD (MELO03C026802), HEMA (MELO03C011113), POR (MELO03C016714)—were checked at different stages of stigma development in both melon lines using quantitative real time polymerase chain reaction (qRT-PCR). The results exhibited that the expression of these genes gradually increased during the stigma development of the MR-1 line but decreased in the M4-7 line at S2. In addition, the expression trends in different stages were the same as RNA-seq, indicating data accuracy. To sum up, our research reveals an in-depth molecular mechanism of stigma coloration and suggests that chlorophyll and related biological activity play an important role in differentiating melon stigma color.
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Affiliation(s)
- Yuanzuo Lv
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Chen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xian Zhang
- Horticulture College of Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (P.G.); (F.L.)
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; (Y.L.); (S.A.); (S.L.); (C.Z.); (H.L.); (Z.Z.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (P.G.); (F.L.)
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Zhao H, Wang Q, Zhao H, Chen C. Transcriptome profiles revealed high- and low-salinity water altered gill homeostasis in half-smooth tongue sole (Cynoglossus semilaevis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100989. [PMID: 35421665 DOI: 10.1016/j.cbd.2022.100989] [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: 01/24/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Salinity is an important environmental factor that affects fish growth, development, and reproduction. As euryhaline fish, half-smooth tongue sole (Cynoglossus semilaevis) are a suitable species for deciphering the salinity adaptation mechanism of fish; however, the molecular mechanisms underlying low- and high-salinity responses remain unclear. In this study, RNA-seq was applied to characterize the genes and regulatory pathways involved in C. semilaevis gill responses to high- (32 ppt), low- (8 ppt), and control-salinity (24 ppt) water. Gills were rich in mitochondria-rich cells (MRCs) in high salinity. Compared with control, 2137 and 218 differentially expressed genes (DEGs) were identified in low and high salinity, respectively. The enriched functions of most DEGs were metabolism, ion transport, regulation of cell cycle, and immune response. The DEGs involved in oxidative phosphorylation, citrate cycle, and fatty acid metabolism were down-regulated in low salinity. For ion transport, high and low salinity significantly altered the expressions of prlr, ca12, and cftr. In cell cycle arrest and cellular repair, gadd45b, igfbp5, and igfbp2 were significantly upregulated in high and low salinity. For immune response, il10, il34, il12b, and crp increased in high and low salinity. Our findings suggested that alterations in material and energy metabolism, ions transport, cell cycle arrest, cellular repair, and immune response, are required to maintain C. semilaevis gill homeostasis under high and low salinity. This study provides insight into the divergence of C. semilaevis osmoregulation mechanisms acclimating to high and low salinity, which will serve as reference for the healthy culture of C. semilaevis.
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Affiliation(s)
- Huiyan Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Qingkui Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China.
| | - Honghao Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Chengxun Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
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Zhong L, Liu H, Zhang H, Zhang W, Li M, Huang Y, Yao J, Huang X, Geng Y, Chen D, Ouyang P, Yang S, Luo W, Yin L. High Starch in Diet Leads to Disruption of Hepatic Glycogen Metabolism and Liver Fibrosis in Largemouth Bass (Micropterus salmoides), Which is Mediated by the PI3K/Akt Signaling Pathway. Front Physiol 2022; 13:880513. [PMID: 35677086 PMCID: PMC9168315 DOI: 10.3389/fphys.2022.880513] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
Due to its special flavour and cheapness, starch is a source of nutrition for humans and most animals, some of whom even prefer to consume large amounts of starchy foods. However, the use of starch by carnivorous fish is limited and excessive starch intake can lead to liver damage, but the mechanism of damage is not clear. Therefore, in this study, two isonitrogenous and isolipid semi-pure diets, Z diet (0% starch) and G diet (22% starch), were formulated, respectively. The largemouth bass (M. salmoides) cultured in fiberglass tanks were randomly divided into two groups and fed the two diets for 45 days. Blood and liver were collected on day 30 and 45 for enzymology, histopathology, ultramicropathology, flow cytometry, and transcriptomics to investigate the damage of high starch on the liver of largemouth bass and its damage mechanism. The results showed that the high starch not affect the growth performance of largemouth bass. However, high starch caused a whitening of the liver and an increase in hepatopancreas index (HSI), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in the serum. Histopathological observations showed that high starch led to severe vacuolisation, congestion, and moderate to severe necrotizing hepatitis in the liver. The high starch intake led to a significant increase in postprandial blood glucose and insulin in serum of largemouth bass, promoting the synthesis and accumulation of large amounts of hepatic glycogen in the liver, leading to the loss of hepatocyte organelles and inducing liver fibrosis. Meanwhile, high starch induced the production of oxidative stress and promoted apoptosis and necrosis of hepatocytes. Transcriptome analysis revealed that there were 10,927 and 2,656 unique genes in the G and Z groups, respectively. KEGG enrichment analysis showed that 19 pathways were significantly enriched, including those related to glucose metabolism and cell survival. Network mapping based on enrichment pathways and differential expressing genes showed the emergence of a regulatory network dominated by PI3K/Akt signaling pathway. This indicated that the PI3K/Akt signalling pathway plays a very important role in this process, regulating the liver injury caused by high starch. Our results provide a reference for the mechanism of liver injury caused by high starch, and the PI3K/Akt signalling pathway could be a potential therapeutic target for liver injury caused by high starch.
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Affiliation(s)
- Liang Zhong
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongli Liu
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Haiqi Zhang
- Zhejiang Institute of Freshwater Fisheries, Hangzhou, China
| | - Weidong Zhang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghao Li
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ya Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiayun Yao
- Zhejiang Institute of Freshwater Fisheries, Hangzhou, China
- *Correspondence: Jiayun Yao, ; Xiaoli Huang,
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jiayun Yao, ; Xiaoli Huang,
| | - Yi Geng
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chendu, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ping Ouyang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chendu, China
| | - Shiyong Yang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lizi Yin
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chendu, China
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Dynamics of sexual development in teleosts with a note on Mugil cephalus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Yan W, Qiao Y, He J, Qu J, Liu Y, Zhang Q, Wang X. Molecular Mechanism Based on Histopathology, Antioxidant System and Transcriptomic Profiles in Heat Stress Response in the Gills of Japanese Flounder. Int J Mol Sci 2022; 23:ijms23063286. [PMID: 35328705 PMCID: PMC8955770 DOI: 10.3390/ijms23063286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
As an economically important flatfish in Asia, Japanese flounder is threatened by continuously rising temperatures due to global warming. To understand the molecular responses of this species to temperature stress, adult Japanese flounder individuals were treated with two kinds of heat stress—a gradual temperature rise (GTR) and an abrupt temperature rise (ATR)—in aquaria under experimental conditions. Changes in histopathology, programmed cell death levels and the oxidative stress status of gills were investigated. Histopathology showed that the damage caused by ATR stress was more serious. TUNEL signals confirmed this result, showing more programmed cell death in the ATR group. In addition, reactive oxygen species (ROS) levels and the 8-O-hDG contents of both the GTR and ATR groups increased significantly, and the total superoxide dismutase (T-SOD) activities and total antioxidant capacity (T-AOC) levels decreased in the two stressed groups, which showed damage to antioxidant systems. Meanwhile, RNA-seq was utilized to illustrate the molecular mechanisms underyling gill damage. Compared to the control group of 18 °C, 507 differentially expressed genes (DEGs) were screened in the GTR group; 341 were up-regulated and 166 were down-regulated, and pathway enrichment analysis indicated that they were involved in regulation and adaptation, including chaperone and folding catalyst pathways, the mitogen-activated protein kinase signaling (MAPK) pathway and DNA replication protein pathways. After ATR stress, 1070 DEGs were identified, 627 were up-regulated and 423 were down-regulated, and most DEGs were involved in chaperone and folding catalyst and DNA-related pathways, such as DNA replication proteins and nucleotide excision repair. The annotation of DEGs showed the great importance of heat shock proteins (HSPs) in protecting Japanese flounder from heat stress injury; 12 hsp genes were found after GTR, while 5 hsp genes were found after ATR. In summary, our study records gill dysfunction after heat stress, with different response patterns observed in the two experimental designs; chaperones were activated to defend heat stress after GTR, while replication was almost abandoned due to the severe damage consequent on ATR stress.
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Affiliation(s)
| | | | | | | | | | | | - Xubo Wang
- Correspondence: ; Tel.: +86-532-82031986; Fax: +86-532-82031802
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42
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Stanley TR, Guisbert KSK, Perez SM, Oneka M, Kernin I, Higgins NR, Lobo A, Subasi MM, Carroll DJ, Turingan RG, Guisbert E. Stress response gene family expansions correlate with invasive potential in teleost fish. J Exp Biol 2022; 225:274389. [PMID: 35258619 PMCID: PMC8987736 DOI: 10.1242/jeb.243263] [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: 08/02/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022]
Abstract
The bluegill sunfish Lepomis macrochirus and the closely related redear sunfish Lepomis microlophus have important ecological and recreational value and are widely used for research and aquaculture. While both species have been introduced outside of their native ranges, only the bluegill is considered invasive. Here, we report de novo transcriptome assemblies for these fish as a resource for sunfish biology. Comparative analyses of the transcriptomes revealed an unexpected, bluegill-specific expansion in the HSP70 and HSP90 molecular chaperone gene families. These expansions were not unique to the bluegill as expansions in HSP70s and HSP90s were identified in the genomes of other teleost fish using the NCBI RefSeq database. To determine whether gene family expansions are specific for thermal stress responses, GST and SOD gene families that are associated with oxidative stress responses were also analyzed. Species-specific expansions were also observed for these gene families in distinct fish species. Validating our approach, previously described expansions in the MHC gene family were also identified. Intriguingly, the number of HSP70 paralogs was positively correlated with thermotolerance range for each species, suggesting that these expansions can impact organismal physiology. Furthermore, fish that are considered invasive contained a higher average number of HSP70 paralogs than non-invasive fish. Invasive fish also had higher average numbers of HSP90, MHC and GST paralogs, but not SOD paralogs. Taken together, we propose that expansions in key cellular stress response gene families represent novel genetic signatures that correlate with invasive potential.
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Affiliation(s)
- Taylor R Stanley
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Karen S Kim Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Sabrina M Perez
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Morgan Oneka
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Isabela Kernin
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Nicole R Higgins
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Alexandra Lobo
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Munevver M Subasi
- Department of Mathematical Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - David J Carroll
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Ralph G Turingan
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
| | - Eric Guisbert
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL 32937, USA
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Rericha Y, Cao D, Truong L, Simonich MT, Field JA, Tanguay RL. Sulfonamide functional head on short-chain perfluorinated substance drives developmental toxicity. iScience 2022; 25:103789. [PMID: 35146398 PMCID: PMC8819378 DOI: 10.1016/j.isci.2022.103789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 01/09/2023] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are ubiquitously detected in environmental and biological samples and cause adverse health effects. Studies have predominately focused on long-chain PFAS, with far fewer addressing short-chain alternatives. This study leveraged embryonic zebrafish to investigate developmental toxicity of a short-chain series: perfluorobutane sulfonate (PFBS), perfluoropentanoic acid (PFPeA), perfluorobutane sulfonamide (FBSA), and 4:2 fluorotelomer sulfonic acid (4:2 FTS). Following static exposures at 8 h postfertilization (hpf) to each chemical (1-100 μM), morphological and behavioral endpoints were assessed at 24 and 120 hpf. Only FBSA induced abnormal morphology, while exposure to all chemicals caused aberrant larval behavior. RNA sequencing at 48 hpf following 47 μM exposures revealed only FBSA significantly disrupted normal gene expression. Measured tissue concentrations were FBSA > PFBS > 4:2 FTS > PFPeA. This study demonstrates functional head groups impact bioactivity and bioconcentration.
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Affiliation(s)
- Yvonne Rericha
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Dunping Cao
- Department of Chemistry, College of Science, Oregon State University, Corvallis, OR 97333, USA
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Michael T Simonich
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Jennifer A Field
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA.,Sinnhuber Aquatic Research Laboratory, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97333, USA
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44
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Amino Acids and IGF1 Regulation of Fish Muscle Growth Revealed by Transcriptome and microRNAome Integrative Analyses of Pacu ( Piaractus mesopotamicus) Myotubes. Int J Mol Sci 2022; 23:ijms23031180. [PMID: 35163102 PMCID: PMC8835699 DOI: 10.3390/ijms23031180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
Amino acids (AA) and IGF1 have been demonstrated to play essential roles in protein synthesis and fish muscle growth. The myoblast cell culture is useful for studying muscle regulation, and omics data have contributed enormously to understanding its molecular biology. However, to our knowledge, no study has performed the large-scale sequencing of fish-cultured muscle cells stimulated with pro-growth signals. In this work, we obtained the transcriptome and microRNAome of pacu (Piaractus mesopotamicus)-cultured myotubes treated with AA or IGF1. We identified 1228 and 534 genes differentially expressed by AA and IGF1. An enrichment analysis showed that AA treatment induced chromosomal changes, mitosis, and muscle differentiation, while IGF1 modulated IGF/PI3K signaling, metabolic alteration, and matrix structure. In addition, potential molecular markers were similarly modulated by both treatments. Muscle-miRNAs (miR-1, -133, -206 and -499) were up-regulated, especially in AA samples, and we identified molecular networks with omics integration. Two pairs of genes and miRNAs demonstrated a high-level relationship, and involvement in myogenesis and muscle growth: marcksb and miR-29b in AA, and mmp14b and miR-338-5p in IGF1. Our work helps to elucidate fish muscle physiology and metabolism, highlights potential molecular markers, and creates a perspective for improvements in aquaculture and in in vitro meat production.
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Yang T, Liu J, Li X, Amanullah S, Lu X, Zhang M, Zhang Y, Luan F, Liu H, Wang X. Transcriptomic Analysis of Fusarium oxysporum Stress-Induced Pathosystem and Screening of Fom-2 Interaction Factors in Contrasted Melon Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:961586. [PMID: 35937314 PMCID: PMC9354789 DOI: 10.3389/fpls.2022.961586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 05/03/2023]
Abstract
Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused by fusarium oxysporum. In this study, transcriptome sequencing and Yeast Two-Hybrid (Y2H) methods were used for quantification of differentially expressed genes (DEGs) involved in fusarium oxysporum (f. sp. melonis race 1) stress-induced mechanisms in contrasted melon varieties (M4-45 "susceptible" and MR-1 "resistant"). The interaction factors of Fom-2 resistance genes were also explored in response to the plant-pathogen infection mechanism. Transcriptomic analysis exhibited total 1,904 new genes; however, candidate DEGs analysis revealed a total of 144 specific genes (50 upregulated and 94 downregulated) for M4-45 variety and 104 specific genes (71 upregulated and 33 downregulated) for MR-1 variety, respectively. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway depicted some candidate DEGs, including Phenylalanine metabolism, phenylpropane biosynthesis, plants-pathogen interaction, and signal transduction of plant hormones, which were mainly involved in disease resistance metabolic pathways. The weighted gene co-expression network analysis (WGCNA) analysis revealed a strong correlation module and exhibited the disease resistance-related genes encoding course proteins, transcription factors, protein kinase, benzene propane biosynthesis path, plants-pathogen interaction pathway, and glutathione S-transferase. Meanwhile, the resistance-related specific genes expression was relatively abundant in MR-1 compared to the M4-45, and cell wall-associated receptor kinases (MELO3C008452 and MELO3C008453), heat shock protein (Cucumis_melo_newGene_172), defensin-like protein (Cucumis_melo_newGene_5490), and disease resistance response protein (MELO3C016325), activator response protein (MELO3C021623), leucine-rich repeat receptor protein kinase (MELO3C024412), lactyl glutathione ligase (Cucumis_melo_newGene_36), and unknown protein (MELO3C007588) were persisted by exhibiting the upregulated expressions. At the transcription level, the interaction factors between the candidate genes in response to the fusarium oxysporum induced stress, and Y2H screening signified the main contribution of MYB transcription factors (MELO3C009678 and MELO3C014597), BZIP (MELO3C011839 and MELO3C019349), unknown proteins, and key enzymes in the ubiquitination process (4XM334FK014). The candidate genes were further verified in exogenously treated melon plants with f. oxysporum (Fom-2, Race 1), Abscisic acid (ABA), Methyl Jasmonite (MeJA), and Salicylic acid (SA), using the fluorescence quantitative polymerase chain reaction (qRT-PCR) analysis. The overall expression results indicated that the SA signal pathway is involved in effective regulation of the Fom-2 gene activity.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jiajun Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xiaomei Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xueyan Lu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Mingchong Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yanhang Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- *Correspondence: Hongyu Liu,
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- Xuezheng Wang,
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Li R, Peng X, Wu Y, Lv W, Xie H, Ishii Y, Zhang C. Exposure to PM 2.5 during pregnancy causes lung inflammation in the offspring: Mechanism of action of mogrosides. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 228:112955. [PMID: 34781127 DOI: 10.1016/j.ecoenv.2021.112955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/16/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Epidemiological and toxicological studies have demonstrated that exposure to fine particulate matter (PM2.5) during pregnancy is harmful to the tissues of the offspring. However, the mechanism by which PM2.5 exposure causes lung damage in the offspring or potential dietary therapy for this condition remains unclear. Mogrosides (MGs) are derived from the traditional plant Siraitia grosvenorii and are used medicinally, where they can moisten the lungs and relieve coughing. In this study, pregnant rats were exposed to PM2.5 by intratracheal instillation and treated with MGs by gavage to model the effect of PM2.5 in the offspring and the interventional effect of MGs on lung tissue. We then used transcriptomics, metabolomics, and RT-qPCR as tools to look for metabolite and genetic changes in the offspring. We found that when compared to the control group, the mRNA levels of the inflammatory mediator Pla2g2d and the metabolites lysophosphatidylcholines (LysoPCs) and arachidonic acid (AA) were up-regulated in the lung tissues of PM2.5 group. In contrast, these inflammatory changes were restored after treatment with MGs during pregnancy. In addition, the levels of AA, LPC 15:0 and LPC 18:0 were elevated in the PM2.5 group compared with control group. This increase was inhibited by co-administration of MGs. The change of PGA1 was adverse. In conclusion, even a relatively low exposure to PM2.5 in rats during pregnancy produces inflammation in the lungs of the male offspring, and an intervention with MGs could significantly alleviate this effect. Furthermore, Pla2g2d may represent a potential target for MGs resulting in the improvement of PM2.5-induced lung injury.
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Affiliation(s)
- Renshi Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xuewei Peng
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yanliang Wu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Weichao Lv
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haifeng Xie
- Research and Development Department, Chengdu Biopurify Phytochemicals Ltd., Chengdu 611130, China
| | - Yuji Ishii
- Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Chaofeng Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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47
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Toufiq M, Huang SSY, Boughorbel S, Alfaki M, Rinchai D, Saraiva LR, Chaussabel D, Garand M. SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. THE JOURNAL OF IMMUNOLOGY 2021; 207:2195-2202. [PMID: 34663591 DOI: 10.4049/jimmunol.2100697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/30/2021] [Indexed: 11/19/2022]
Abstract
Sepsis develops after a dysregulated host inflammatory response to a systemic infection. Identification of sepsis biomarkers has been challenging because of the multifactorial causes of disease susceptibility and progression. Public transcriptomic data are a valuable resource for mechanistic discoveries and cross-studies concordance of heterogeneous diseases. Nonetheless, the approach requires structured methodologies and effective visualization tools for meaningful data interpretation. Currently, no such database exists for sepsis or systemic inflammatory diseases in human. Hence we curated SysInflam HuDB (http://sepsis.gxbsidra.org/dm3/geneBrowser/list), a unique collection of human blood transcriptomic datasets associated with systemic inflammatory responses to sepsis. The transcriptome collection and the associated clinical metadata are integrated onto a user-friendly and Web-based interface that allows the simultaneous exploration, visualization, and interpretation of multiple datasets stemming from different study designs. To date, the collection encompasses 62 datasets and 5719 individual profiles. Concordance of gene expression changes with the associated literature was assessed, and additional analyses are presented to showcase database utility. Combined with custom data visualization at the group and individual levels, SysInflam HuDB facilitates the identification of specific human blood gene signatures in response to infection (e.g., patients with sepsis versus healthy control subjects) and the delineation of major genetic drivers associated with inflammation onset and progression under various conditions.
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Affiliation(s)
| | - Susie Shih Yin Huang
- Sidra Medicine, Doha, Qatar.,Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO; and
| | | | | | | | - Luis R Saraiva
- Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Alipoor B, Nikouei S, Rezaeinejad F, Malakooti-Dehkordi SN, Sabati Z, Ghasemi H. Long non-coding RNAs in metabolic disorders: pathogenetic relevance and potential biomarkers and therapeutic targets. J Endocrinol Invest 2021; 44:2015-2041. [PMID: 33792864 DOI: 10.1007/s40618-021-01559-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND It has been suggested that dysregulation of long non-coding RNAs (lncRNAs) could be associated with the incidence and development of metabolic disorders. AIM Accordingly, this narrative review described the molecular mechanisms of lncRNAs in the development of metabolic diseases including insulin resistance, diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), cirrhosis, and coronary artery diseases (CAD). Furthermore, we investigated the up-to-date findings on the association of deregulated lncRNAs in the metabolic disorders, and potential use of lncRNAs as biomarkers and therapeutic targets. CONCLUSION LncRNAs/miRNA/regulatory proteins axis plays a crucial role in progression of metabolic disorders and may be used in development of therapeutic and diagnostic approaches.
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Affiliation(s)
- B Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - S Nikouei
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | - F Rezaeinejad
- Department of Biochemistry, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Z Sabati
- MSc student of Hematology, Student Research Committee, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - H Ghasemi
- Abadan Faculty of Medical Sciences, Abadan, Iran.
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49
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Zhong Z, Ao L, Wang Y, Wang S, Zhao L, Ma S, Jiang Y. Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1565-1583. [PMID: 34415453 DOI: 10.1007/s10695-021-00977-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Pearlscale angelfish Centropyge vrolikii is a kind of protogynous hermaphrodite fish with a natural sexual reversion. Under appropriate social conditions, a female fish can transform into a male fish spontaneously. It is an important prerequisite for artificial breeding to understand the process of its gonadal development and sexual reversion. Gonadal development is regulated by many sex-related genes. In this study, we used unreferenced RNA-Seq technology to sequence the ovary at the perinucleolus stage (OII), ovary at the yolk vesicle stage (OIV),IV and testis (T), respectively; screened the gonadal differential expression genes (DEGs); and analyzed the expression of these genes in different developmental stages of ovary and different sex gonads. The results showed that a total of 142,589 all-unigene samples were assembled, and gene annotation was performed by COG, GO, KEGG, KOG, Pfam, Swissprot, eggNOG, and NR functional database. Comparative analysis revealed that there were 1919 genes that were up-regulated and 1289 genes were down-regulated in comparison to OIV vs OII, while there were 3653 genes that were up-regulated and 2874 genes were down-regulated in comparison of OIV vs T, there were 3345 genes that were up-regulated and 2995 genes were down-regulated in comparison of the OII vs the T. At the same time, the results verified by RT-qPCR were consistent with the variation trend of transcriptome data. Among the results, amh, sox9b, dmrt1, dmrt2, cyp11a, cyp17a, and cyp19a were significantly expressed in the testes, while sox3, sox4, sox11, sox17, and hsd3b7 were significantly expressed in the ovaries. And, the expression of the amh, sox9b, dmrt2, and dmrt1 were low in the OII and OIV, while significantly increased during the ovotestis in the hermaphroditic period (OT), and finally reached the highest level in pure testis after sex reversal. The expression of sox3, sox4, hsd3b7, sox11, and sox17 was significantly reduced during the hermaphroditic period (OT). These results suggested that these genes may play an important role in the process of sex reversal. This study is helpful to further understand the molecular regulation mechanism of gonadal development and sexual reversion in Pearlscale angelfish and also provide important clues for future studies.
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Affiliation(s)
- Zhaowei Zhong
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Lulu Ao
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China
| | - Shuhong Wang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China
| | - Liping Zhao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Senwei Ma
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yonghua Jiang
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, 361021, China.
- National Demonstration Center for Experimental Aquatic Science and Technology Education, Jimei University), Xiamen, 361021, China.
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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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