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Shekhar MS, Katneni VK, Jangam AK, Krishnan K, Prabhudas SK, Jayaraman R, Angel JRJ, Kailasam M. Genome assembly, Full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus. Sci Data 2024; 11:796. [PMID: 39025998 PMCID: PMC11258364 DOI: 10.1038/s41597-024-03633-1] [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: 01/30/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The mangrove red snapper, Lutjanus argentimaculatus, is a marine food fish of economic and aquaculture importance. The application of genomic selection-based breeding programs for this species is limited by the absence of a reference genome and transcriptome profiles. The current study attempted to fill this void by generating genomic and transcriptomic resources for red snapper. Using PacBio long reads, and Arima Hi-C linked reads, a scaffold-level genome assembly was generated for L. argentimaculatus. The assembly is of 1.03 Gb comprising of 400 scaffolds with N50 of 33.8 Mb and was assessed to be 97.2% complete upon benchmarking with BUSCO. Full-length transcriptome generated with PacBio Iso-Sequencing strategy using six tissues (muscle, gills, liver, kidney, stomach, and gonad) contained 56,515 isoforms belonging to 18,108 unique genes with N50 length of 3,973 bp. The resources generated will have potential applications in the functional studies, conservation, broodstock management and selective breeding programmes of L. argentimaculatus.
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Affiliation(s)
- Mudagandur S Shekhar
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India.
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Karthic Krishnan
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Roja Jayaraman
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Jesudhas Raymond Jani Angel
- Crustacean Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Muniyandi Kailasam
- Finfish Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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Zhao C, Liu Y, Zhang P, Xia X, Yang Y. Alternative splicing plays a nonredundant role in greater amberjack (Seriola dumerili) in acclimation to ambient salinity fluctuations. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106549. [PMID: 38733739 DOI: 10.1016/j.marenvres.2024.106549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
Alternative splicing (AS) is an important post-transcriptional mechanism for adaptation of fish to environmental stress. Here, we performed a genome-wide investigation to AS dynamics in greater amberjack (Seriola dumerili), an economical marine teleost, in response to hypo- (10 ppt) and hyper-salinity (40 ppt) stresses. Totally, 2267-2611 differentially spliced events were identified in gills and kidney upon the exposure to undesired salinity regimes. In gills, genes involved in energy metabolism, stimulus response and epithelial cell differentiation were differentially spliced in response to salinity variation, while sodium ion transport and cellular amide metabolism were enhanced in kidney to combat the adverse impacts of salinity changes. Most of these differentially spliced genes were not differentially expressed, and AS was found to regulate different biological processes from differential gene expression, indicative of the functionally nonredundant role of AS in modulating salinity acclimation in greater amberjack. Together, our study highlights the important contribution of post-transcriptional mechanisms to the adaptation of fish to ambient salinity fluctuations and provides theoretical guidance for the conservation of marine fishery resources against increasingly environmental challenges.
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Affiliation(s)
- Chunyu Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Panpan Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Xinhui Xia
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
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Wang H, Su B, Zhang Y, Shang M, Wang J, Johnson A, Dilawar H, Bruce TJ, Dunham RA, Wang X. Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in a tank culture environment. Front Genet 2024; 15:1341555. [PMID: 38742167 PMCID: PMC11089159 DOI: 10.3389/fgene.2024.1341555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) are two economically important freshwater aquaculture species in the United States, with channel catfish contributing to nearly half of the country's aquaculture production. While differences in economic traits such as growth rate and disease resistance have been noted, the extent of transcriptomic variance across various tissues between these species remains largely unexplored. The hybridization of female channel catfish with male blue catfish has led to the development of superior hybrid catfish breeds that exhibit enhanced growth rates and improved disease resistance, which dominate more than half of the total US catfish production. While hybrid catfish have significant growth advantages in earthen ponds, channel catfish were reported to grow faster in tank culture environments. In this study, we confirmed channel fish's superiority in growth over blue catfish in 60-L tanks at 10.8 months of age (30.3 g and 11.6 g in this study, respectively; p < 0.001). In addition, we conducted RNA sequencing experiments and established transcriptomic resources for the heart, liver, intestine, mucus, and muscle of both species. The number of expressed genes varied across tissues, ranging from 5,036 in the muscle to over 20,000 in the mucus. Gene Ontology analysis has revealed the functional specificity of differentially expressed genes within their respective tissues, with significant pathway enrichment in metabolic pathways, immune activity, and stress responses. Noteworthy tissue-specific marker genes, including lrrc10, fabp2, myog, pth1a, hspa9, cyp21a2, agt, and ngtb, have been identified. This transcriptome resource is poised to support future investigations into the molecular mechanisms underlying environment-dependent heterosis and advance genetic breeding efforts of hybrid catfish.
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Affiliation(s)
- Haolong Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
| | - Baofeng Su
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Ying Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Timothy J. Bruce
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Rex A. Dunham
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
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Cheng X, Li F, Kumilamba G, Liao J, Cao J, Sun J, Liu Q. Transcriptome analysis in hepatopancreases reveals the response of domesticated common carp to a high-temperature environment in the agricultural heritage rice-fish system. Front Physiol 2023; 14:1294729. [PMID: 38028756 PMCID: PMC10663232 DOI: 10.3389/fphys.2023.1294729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Qingtian paddy field carp (PF-carp) is a local carp cultivated in the paddy field of Qingtian, Zhejiang. This rice-fish co-culture system has been recognized as one of the Globally Important Agriculture Heritage Systems (GIAHS). PF-carp has been acclimatized to the high-temperature environment of shallow paddy fields after several centuries of domestication. To reveal the physiological and molecular regulatory mechanisms of PF-carp, we chose to use 28°C as the control group and 34°C as the treatment group. We measured biochemical parameters in their serum and hepatopancreases and also performed transcriptome sequencing analysis. Compared with the control group, the serum levels of malondialdehyde (MDA), glucose (GLU), glutathione peroxidase (GSH-Px), catalase (CAT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) show no significant change. In addition, superoxide dismutase (SOD), GSH-Px, and CAT also show no significant change in hepatopancreases. We identified 1,253 differentially expressed genes (DEGs), and their pathway analysis revealed that heat stress affected AMPK signaling pathway, protein export, and other biological processes. It is worth noting that protein processing in the endoplasmic reticulum (ER) was the most significantly enriched pathway identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA). Significantly higher levels of HSP40, HSP70, HSP90, and other ubiquitin ligase-related genes were upregulated. In summary, heat stress did not lead to tissue damage, inflammation, oxidative stress, and ER stress in the hepatopancreases of PF-carp. This study provides valuable insights into the adaptation mechanism of this species to the high-temperature environment of paddy fields.
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Affiliation(s)
- Xiangbing Cheng
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Fangcheng Li
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Gilbert Kumilamba
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jiayi Liao
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jiangwei Cao
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jiamin Sun
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Qigen Liu
- Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
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Transcriptome Analyses Reveal Essential Roles of Alternative Splicing Regulation in Heat-Stressed Holstein Cows. Int J Mol Sci 2022; 23:ijms231810664. [PMID: 36142577 PMCID: PMC9505234 DOI: 10.3390/ijms231810664] [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: 07/28/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022] Open
Abstract
Heat stress (HS) severely impacts the productivity and welfare of dairy cows. Investigating the biological mechanisms underlying HS response is crucial for developing effective mitigation and breeding strategies. Therefore, we evaluated the changes in milk yield, physiological indicators, blood biochemical parameters, and alternative splicing (AS) patterns of lactating Holstein cows during thermoneutral (TN, N = 19) and heat-stress (HS, N = 17) conditions. There was a significant (p < 0.05) decline in milk yield as physiological indicators increased after exposure to natural HS conditions. The levels of eight out of 13 biochemical parameters of HS were also significantly altered in the presence of HS (p < 0.05). These results demonstrate that HS negatively influences various biological processes of Holstein cows. Furthermore, we investigated AS events based on the RNA-seq data from blood samples. With HS, five common types of AS events were generally increased by 6.7−38.9%. A total of 3470 AS events corresponding to 3143 unique genes were differentially alternatively spliced (DSGs) (p-adjusted < 0.05) between TN and HS groups. The functional annotation results show that the majority of DSGs are involved in mRNA splicing and spliceosomal complex, followed by enrichment in immune and metabolic processes. Eighty-seven out of 645 differentially expressed genes (DEGs) (fold change ≥ 1.5 and false discovery rate < 0.05) overlapped with DSGs. Further analyses showed that 20 of these genes were significantly enriched for the RNA splicing, RNA binding, and RNA transport. Among them, two genes (RBM25 and LUC7L3) had strong interrelation and co-expression pattern with other genes and were identified as candidate genes potentially associated with HS responses in dairy cows. In summary, AS plays a crucial role in changing the transcriptome diversity of heat-stress-related genes in multiple biological pathways and provides a different regulation mechanism from DEGs.
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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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Sudhagar A, El-Matbouli M, Kumar G. Genome-wide alternative splicing profile in the posterior kidney of brown trout (Salmo trutta) during proliferative kidney disease. BMC Genomics 2022; 23:446. [PMID: 35710345 PMCID: PMC9204890 DOI: 10.1186/s12864-022-08685-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/08/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The cnidarian myxozoan parasite Tetracapsuloides bryosalmonae causes chronic proliferative kidney disease (PKD) in salmonids. This parasite is a serious threat to wild and cultured salmonids. T. bryosalmonae undergoes intra-luminal sporogonic development in the kidney of brown trout (Salmo trutta) and the viable spores are released via urine. We investigated the alternative splicing pattern in the posterior kidney of brown trout during PKD. RESULTS RNA-seq data were generated from the posterior kidney of brown trout collected at 12 weeks post-exposure to T. bryosalmonae. Subsequently, this data was mapped to the brown trout genome. About 153 significant differently expressed alternatively spliced (DEAS) genes, (delta PSI = 5%, FDR P-value < 0.05) were identified from 19,722 alternatively spliced events. Among the DEAS genes, the least and most abundant alternative splicing types were alternative 5' splice site (5.23%) and exon skipping (70.59%), respectively. The DEAS genes were significantly enriched for sodium-potassium transporter activity and ion homeostasis (ahcyl1, atp1a3a, atp1a1a.1, and atp1a1a.5). The protein-protein interaction network analysis enriched two local network clusters namely cation transporting ATPase C-terminus and Sodium/potassium ATPase beta chain cluster, and mixed inclusion of Ion homeostasis and EF-hand domain cluster. Furthermore, the human disease-related salmonella infection pathway was significantly enriched in the protein-protein interaction network. CONCLUSION This study provides the first baseline information about alternative splicing in brown trout during PKD. The generated data lay a foundation for further functional molecular studies in PKD - brown trout infection model. The information generated from the present study can help to develop therapeutic strategies for PKD in the future.
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Affiliation(s)
- Arun Sudhagar
- Clinical Division of Fish Medicine, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Peninsular and Marine Fish Genetic Resources Centre, ICAR - National Bureau of Fish Genetic Resources, Kochi, Kerala, 682 018, India
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
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Thorstensen MJ, Turko AJ, Heath DD, Jeffries KM, Pitcher TE. Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern. J Exp Biol 2022; 225:275812. [DOI: 10.1242/jeb.244162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022]
Abstract
Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesised to be an important cause of population declines. We tested the hypothesis that gene expression-splicing interactions contribute to the thermal stress response. Wild fish exposed to acute thermal stress were compared with both handling controls and fish sampled directly from a river. Liver tissue was sampled to study the transcriptomic stress response. With a gene set enrichment analysis, we found that thermally stressed fish showed a transcriptional response related to transcription regulation and responses to unfolded proteins, and alternatively spliced genes related to gene expression regulation and metabolism. One splicing factor, prpf38b, was upregulated in the thermally stressed group compared to the other treatments. This splicing factor may have a role in the Jun/AP-1 cellular stress response, a pathway with wide-ranging and context-dependent effects. Given large gene interaction networks and the context-dependent nature of transcriptional responses, our results highlight the importance of understanding interactions between gene expression and splicing for understanding transcriptomic responses to thermal stress. Our results also reveal transcriptional pathways that can inform conservation breeding, translocation, and reintroduction programs for redside dace and other imperilled species by identifying appropriate source populations.
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Affiliation(s)
- Matt J. Thorstensen
- 1 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Andy J. Turko
- 2 Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON L8S 4L8, Canada
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Daniel D. Heath
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Ken M. Jeffries
- 1 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Trevor E. Pitcher
- 3 Department of Integrative Biology & Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
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Trieu-Duc V, Oshima K, Matsumura K, Iwasaki Y, Chiu MT, Nikaido M, Okada N. Alternative splicing plays key roles in response to stress across different stages of fighting in the fish Betta splendens. BMC Genomics 2022; 22:920. [PMID: 35637454 PMCID: PMC9150285 DOI: 10.1186/s12864-022-08609-2] [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: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Background Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens, across different stages of fighting interactions, fighting opponents suffer from various stressors, especially from the great demand for oxygen. Using RNA sequencing, we profiled differential alternative splicing (DAS) events in the brains of fish collected before fighting, during fighting, and after fighting to study the involvement of alternative splicing (AS) in the response to stress during the fight. Results We found that fighting interactions induced the greatest increase in AS in the ‘during-fighting’ fish, followed by that of the ‘after-fighting’ fish. Intron retention (IR) was the most enriched type among all the basic AS events. DAS genes were mainly associated with synapse assembly, ion transport, and regulation of protein secretion. We further observed that IR events significantly differentiated between winners and losers for 19 genes, which were associated with messenger RNA biogenesis, DNA repair, and transcription machinery. These genes share many common features, including shorter intron length and higher GC content. Conclusions This study is the first comprehensive view of AS induced by fighting interactions in a fish species across different stages of those interactions, especially with respect to IR events in winners and losers. Together, these findings facilitate future investigations into transcriptome complexity and AS regulation in response to stress under the context of aggression in vertebrates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08609-2.
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Affiliation(s)
- Vu Trieu-Duc
- School of Pharmacy, Kitasato University, Tokyo, Japan.,Life Sciences and Biotechnology Department, Tokyo Institute of Technology, Tokyo, Japan.,Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Yuri Iwasaki
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Ming-Tzu Chiu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masato Nikaido
- Life Sciences and Biotechnology Department, Tokyo Institute of Technology, Tokyo, Japan
| | - Norihiro Okada
- School of Pharmacy, Kitasato University, Tokyo, Japan. .,Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. .,Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.
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Chan SKN, Suresh S, Munday P, Ravasi T, Bernal MA, Schunter C. The alternative splicing landscape of a coral reef fish during a marine heatwave. Ecol Evol 2022; 12:e8738. [PMID: 35342554 PMCID: PMC8933327 DOI: 10.1002/ece3.8738] [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: 11/11/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n = 40) genes during the onset of the heatwave (i.e., 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding, and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n = 26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.
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Affiliation(s)
- Stanley Kin Nok Chan
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Sneha Suresh
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Phillip Munday
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
| | - Moisés A. Bernal
- Department of Biological SciencesCollege of Science and MathematicsAuburn UniversityAuburnAlabamaUSA
| | - Celia Schunter
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
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12
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Huang S, Dou J, Li Z, Hu L, Yu Y, Wang Y. Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. Genes (Basel) 2022; 13:genes13020358. [PMID: 35205403 PMCID: PMC8871965 DOI: 10.3390/genes13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.
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Affiliation(s)
- Shangzhen Huang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Jinhuan Dou
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 100193, China
- Correspondence: (J.D.); (Y.W.)
| | - Zhongshu Li
- Agricultural College, Yanbian University, Yanji 133002, China;
| | - Lirong Hu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Yachun Wang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
- Correspondence: (J.D.); (Y.W.)
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13
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Genome-Wide Analysis of Alternative Splicing (AS) Mechanism Provides Insights into Salinity Adaptation in the Livers of Three Euryhaline Teleosts, including Scophthalmus maximus, Cynoglossus semilaevis and Oncorhynchus mykiss. BIOLOGY 2022; 11:biology11020222. [PMID: 35205090 PMCID: PMC8869236 DOI: 10.3390/biology11020222] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Alternative splicing (AS) is a key post-transcriptional regulatory mechanism that acts an important regulator in response to environmental stimuli in organisms. In the present study, 18 RNA-Seq datasets were utilized to investigate the potential roles of AS in response to different salinity environments in the livers of three euryhaline teleosts, including turbot (Scophthalmus maximus), tongue sole (Cynoglossus semilaevis) and steelhead trout (Oncorhynchus mykiss). The results indicated that different salinity environments changed the splicing patterns of numerous RNA splicing regulators, which might affect the splicing decisions of many downstream target genes in response to salinity changes. This study provides preliminary evidence for the important roles of AS events in salinity adaptation in teleosts. Abstract Salinity is an important environmental factor that directly affects the survival of aquatic organisms, including fish. However, the underlying molecular mechanism of salinity adaptation at post-transcriptional regulation levels is still poorly understood in fish. In the present study, 18 RNA-Seq datasets were utilized to investigate the potential roles of alternative splicing (AS) in response to different salinity environments in the livers of three euryhaline teleosts, including turbot (Scophthalmus maximus), tongue sole (Cynoglossus semilaevis) and steelhead trout (Oncorhynchus mykiss). A total of 10,826, 10,741 and 10,112 AS events were identified in the livers of the three species. The characteristics of these AS events were systematically investigated. Furthermore, a total of 940, 590 and 553 differentially alternative splicing (DAS) events were determined and characterized in the livers of turbot, tongue sole and steelhead trout, respectively, between low- and high-salinity environments. Functional enrichment analysis indicated that these DAS genes in the livers of three species were commonly enriched in some GO terms and KEGG pathways associated with RNA processing. The most common DAS genes work as RNA-binding proteins and play crucial roles in the regulation of RNA splicing. The study provides new insights into uncovering the molecular mechanisms of salinity adaptation in teleosts.
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Xiao Q, Huang Z, Shen Y, Gan Y, Wang Y, Gong S, Lu Y, Luo X, You W, Ke C. Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone. BMC Genomics 2021; 22:650. [PMID: 34496767 PMCID: PMC8428104 DOI: 10.1186/s12864-021-07954-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive. RESULTS Heterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone. CONCLUSION More alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.
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Affiliation(s)
- Qizhen Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yang Gan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yi Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Shihai Gong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yisha Lu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen, 361102, People's Republic of China.
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15
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RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish. BMC Genomics 2021; 22:273. [PMID: 33858341 PMCID: PMC8048188 DOI: 10.1186/s12864-021-07592-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/05/2021] [Indexed: 01/03/2023] Open
Abstract
Background Messenger RNA sequencing is becoming more common in studies of non-model species and is most often used for gene expression-based investigations. However, the method holds potential for numerous other applications as well—including analyses of alternative splicing, population structure, and signatures of selection. To maximize the utility of mRNA data sets, distinct analyses may be combined such as by exploring dynamics between gene expression with signatures of selection in the context of population structure. Here, we compare two published data sets describing two populations of a minnow species endemic to the San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus): a microsatellite data set showing population structure, and an mRNA whole transcriptome data set obtained after the two populations were exposed to a salinity challenge. We compared measures of population structure and genetic variation using single nucleotide polymorphisms (SNPs) called from mRNA from the whole transcriptome sequencing study with those patterns determined from microsatellites. For investigating plasticity and evolution, intra- and inter-population transcriptome plasticity was investigated with differential gene expression, differential exon usage, and gene expression variation. Outlier SNP analysis was also performed on the mRNA data set and signatures of selection and phenotypic plasticity were investigated on an individual-gene basis. Results We found that mRNA sequencing revealed patterns of population structure consistent with those found with microsatellites, but with lower magnitudes of genetic variation and population differentiation consistent with widespread purifying selection expected when using mRNA. In addition, within individual genes, phenotypic plasticity or signatures of selection were found in almost mutual exclusion (except heatr6, nfu1, slc22a6, sya, and mmp13). Conclusions These results show that an mRNA sequencing data set may have multiple uses, including describing population structure and for investigating the mechanistic interplay of evolution and plasticity in adaptation. MRNA sequencing thus complements traditional sequencing methods used for population genetics, in addition to its utility for describing phenotypic plasticity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07592-4.
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16
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Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed ( Brassica napus L.) Infected with Sclerotinia sclerotiorum. Genes (Basel) 2020; 11:genes11070784. [PMID: 32668742 PMCID: PMC7397149 DOI: 10.3390/genes11070784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022] Open
Abstract
Alternative splicing (AS) is a post-transcriptional level of gene expression regulation that increases transcriptome and proteome diversity. How the AS landscape of rapeseed (Brassica napus L.) changes in response to the fungal pathogen Sclerotinia sclerotiorum is unknown. Here, we analyzed 18 RNA-seq libraries of mock-inoculated and S. sclerotiorum-inoculated susceptible and tolerant B. napus plants. We found that infection increased AS, with intron retention being the main AS event. To determine the key genes functioning in the AS response, we performed a differential AS (DAS) analysis. We identified 79 DAS genes, including those encoding splicing factors, defense response proteins, crucial transcription factors and enzymes. We generated coexpression networks based on the splicing isoforms, rather than the genes, to explore the genes’ diverse functions. Using this weighted gene coexpression network analysis alongside a gene ontology enrichment analysis, we identified 11 modules putatively involved in the pathogen defense response. Within these regulatory modules, six DAS genes (ascorbate peroxidase 1, ser/arg-rich protein 34a, unknown function 1138, nitrilase 2, v-atpase f, and amino acid transporter 1) were considered to encode key isoforms involved in the defense response. This study provides insight into the post-transcriptional response of B. napus to S. sclerotiorum infection.
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17
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Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia. Front Genet 2020; 11:244. [PMID: 32256528 PMCID: PMC7093569 DOI: 10.3389/fgene.2020.00244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.
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Affiliation(s)
| | | | | | | | | | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Hu F, Fan J, Wu C, Zhu M, Zhou Y, Wang S, Zhang C, Tao M, Zhao R, Tang C, Luo K, Qin Q, Ma M, Chen B, Wang J, Zhou A, Bai L, Liu S. Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:515-525. [PMID: 31203477 PMCID: PMC6679832 DOI: 10.1007/s10126-019-09899-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 50 chromosomes [corrected]. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1-91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma.
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Affiliation(s)
- Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Jingjing Fan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Ming Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yunfan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Jinpu Wang
- Hunan Province Livestock and Fisheries Bureau, Changsha, 410081, China
| | - Aiguo Zhou
- Chenzhou Animal Husbandry-Veterinary & Fisheries Bureau, Changsha, 410081, China
| | - Liangxiong Bai
- Mangshan Forestry Resources Administration Bureau, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:248-255. [PMID: 30952021 DOI: 10.1016/j.cbd.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/24/2019] [Accepted: 03/24/2019] [Indexed: 11/21/2022]
Abstract
Polyadenylation plays important roles in gene expression regulation in eukaryotes, which typically involves cleavage and poly(A) tail addition at the polyadenylation site (PAS) of the pre-mature mRNA. Many eukaryotic genes contain more than one PASs, termed as alternative polyadenylation (APA). As a crucial post-transcriptional regulation, polyadenylation affects various aspects of RNA metabolism such as mRNA stability, translocation, and translation. However, polyadenylation has been rarely studied in teleosts. Here we conducted polyadenylation analysis in channel catfish, a commercially important aquaculture species around the world. Using RNA-Seq data, we identified 20,320 PASs which were classified into 14,500 clusters by merging adjacent PASs. Most of the PASs were found in 3' UTRs, followed by intron regions based on the annotation of channel catfish reference genome. No apparent difference in PAS distribution was observed between the sense and antisense strand of the channel catfish genome. The sequence analysis of nucleotide composition and motif around PASs yielded a highly similar profile among various organisms, suggesting the conservation and importance of polyadenylation in evolution. Using APA genes with more than two PASs, gene ontology enrichment revealed genes particularly involved in RNA binding. Reactome pathway analysis showed the enrichment of the innate immune system, especially neutrophil degranulation.
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