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Sun M, Ye C, Wang Z, Gao X, Feng S, Hu T, Mu W. Transcriptome, histology, and enzyme activities analysis of liver in Phoxinus lagowskii to the low temperature stress and recovery. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101317. [PMID: 39241494 DOI: 10.1016/j.cbd.2024.101317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/19/2024] [Accepted: 08/22/2024] [Indexed: 09/09/2024]
Abstract
Assessing the response and resilience of fish to low temperatures over different time scales can provide valuable insights into their mechanisms of adaptation to cold conditions. Farmed Amur minnows (Phoxinus lagowskii) frequently encounter low temperatures, especially during winter. However, the specific responses of P. lagowskii to low-temperature stress remain largely unexplored. In this study, we examined serum glucose and cortisol levels, histological changes, enzymes associated with phosphate and carbohydrate metabolism, triglyceride levels, and liver transcriptomics under various conditions: control (CK), short-term cold exposure (6 days, SC), prolonged cold exposure (14 days, PC), and recovery (RY) from cold exposure at 2 °C. Liver vacuolation was observed during short-term cold exposure. Additionally, we analyzed the enzymatic activity related to carbohydrate and lipid metabolism in serum and liver. Liver transcriptomic data revealed that the PPAR signaling pathway and autophagy-related genes were enriched during short-term cold exposure. Carbohydrate metabolism-related pathways, including the AMPK and MAPK signaling pathways, were significantly enriched after prolonged cold exposure. Metabolic pathways such as fat digestion and absorption, glycine, serine, and threonine metabolism, and arginine and proline metabolism were significantly enriched in the recovery group. Rapid warming after prolonged cold stress allowed P. lagowskii to recover quickly. These findings suggest that P. lagowskii has a strong adaptive capacity for energy metabolism during prolonged cold exposure and the ability to recover rapidly from cold stress. A comprehensive examination of the histological, physiological, biochemical, and molecular responses of P. lagowskii to low temperatures is crucial for developing effective strategies for cultivating this species in challenging environments.
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Affiliation(s)
- Mingyang Sun
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Cunrun Ye
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Zhen Wang
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Xinran Gao
- China Medical University, Shenyang 110122, China
| | - Shibo Feng
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Tingting Hu
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Weijie Mu
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
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Zhou J, Yu J, Chu Q. Comparative transcriptome analysis reveals potential regulatory mechanisms of genes and immune pathways following Vibrio harveyi infection in red drum (Sciaenops ocellatus). FISH & SHELLFISH IMMUNOLOGY 2024; 146:109386. [PMID: 38242261 DOI: 10.1016/j.fsi.2024.109386] [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: 12/17/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Red drum (Sciaenops ocellatus), as an important economical marine fish, has been affected by various bacterial diseases in recent years. Vibrio harveyi cause fatal vibriosis in S. ocellatus, leading to massive mortality and causing significant setbacks in aquaculture. However, the regulatory mechanisms of S. ocellatus response to V. harveyi infection are poorly understood. In this regard, we performed transcriptomic analysis with head kidney tissues of S. ocellatus after V. harveyi infection from 12 h to 48 h to reveal genes, gene expression profiles, and pathways involved in immune and inflammation responses. Specifically, a total of 9,599, 5,728, and 7144 differentially expressed genes (DEGs) were identified after V. harveyi infection at 12 h, 24 h, and 48 h, respectively, and 1,848 shared DEGs have been identified from the above three comparison groups. Subsequent pathway analysis revealed that the shared DEGs following V. harveyi were involved in complement and coagulation cascades (C1R, C1QC, C3, C4, C5, C7, C8A, C8B, C8G, C9, CFB, CFH, and CFI), MAPK signaling pathway, chemokine signaling pathway (CCL19, CXCL8, CXCL12, CXCL14, CCR4, CCR7, and CXCR2), PPAR signaling pathway (PPAR-α, PPAR-γ and PPAR-β), and TNF signaling pathway. Finally, the expression patterns of DEGs in head kidney tissues and S. ocellatus macrophages were validated by qRT-PCR, suggesting the reliability of RNA sequencing for gene expression analysis. This dynamic transcriptome analyses provided insights into gene expression regulation and immune related pathways involved in S. ocellatus after V. harveyi infection, and provides useful information for further study on the immune defense mechanisms in S. ocellatus as well as other teleost species.
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Affiliation(s)
- Jiale Zhou
- School of Agriculture, Ludong University, Yantai, China
| | - Jingyao Yu
- School of Agriculture, Ludong University, Yantai, China
| | - Qing Chu
- School of Agriculture, Ludong University, Yantai, China.
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3
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Shang X, Xu W, Zhang Y, Sun Q, Li Z, Geng L, Teng X. Transcriptome analysis revealed the mechanism of Luciobarbus capito (L. capito) adapting high salinity: Antioxidant capacity, heat shock proteins, immunity. MARINE POLLUTION BULLETIN 2023; 192:115017. [PMID: 37172343 DOI: 10.1016/j.marpolbul.2023.115017] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/19/2023] [Accepted: 05/02/2023] [Indexed: 05/14/2023]
Abstract
Salinity has a significant influence on the physiology of freshwater aquatic organisms. However, there are few studies on the hematology and immunology of freshwater fish under high salinity. In the current study, we aimed to analyze the adaptive effect of salt stress on L. capito spleen immune function and hematology using transcriptomic analysis. We replicated a L. capito acute salinity stress model, and collected blood and spleens from freshwater and saltwater fish. It was found that salinity affected significantly the numbers of leukocytes, lymphocytes, neutrophils, and red blood cells, as well as the content of haemoglobin. Salt treatment resulted in a significant increase in the expression of HSP70, HSP90, CAT, SOD, and GPX1 genes in L. capito spleens. Transcriptomic analysis revealed a total of 546 differentially expressed genes (DEGs) in spleens, including 224 up-regulated DEGs and 322 down-regulated DEGs. In addition, GO enrichment analysis revealed immune system process, multicellular organismal process, and biological regulation of genes with the most differences in biological processes. KEGG enrichment analysis showed that the regulation of lipolysis in adipocyte, FoxO signaling pathway, Hematopoietic cell lineage signaling pathway, and HIF-1 signaling pathway were significantly enriched. L. capito adapted oxidative to high salinity through FoxO signaling pathway and immune to high salinity through Hematopoietic cell lineage signaling pathway. At the same time, we selected 10 DEGs for qRT-PCR detection, and the results showed that the qRT-PCR results were consistent with our RNA-Seq results, indicating that transcriptome sequencing was accurate and reliable. In conclusion, our results demonstrated that the improvement of antioxidant capacity, heat shock protein and immunity are involved in the molecular mechanism of L. capito adapting to high salinity. Our findings provided a rationale for further study on high salinity adaptation and related enrichment pathways.
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Affiliation(s)
- Xinchi Shang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Rd 43 Songfa, Daoli District, Harbin 150070, China; Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Harbin 150070, Heilongjiang, China
| | - Wei Xu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Rd 43 Songfa, Daoli District, Harbin 150070, China; Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Harbin 150070, Heilongjiang, China
| | - Ying Zhang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Rd 43 Songfa, Daoli District, Harbin 150070, China
| | - Qingsong Sun
- Jilin Agricultural Science and Technology University, Key Lab of Preventive Veterinary Medicine in Jilin Province, 77 Hanlin Road, Jilin 132101,China
| | - Zhengwei Li
- D Heilongjiang Province Aquatic Animal Resources Conservation Center, China
| | - Longwu Geng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Rd 43 Songfa, Daoli District, Harbin 150070, China; Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Harbin 150070, Heilongjiang, China.
| | - Xiaohua Teng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
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Li P, Liu W, Lu W, Wang J. Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon ( Oncorhynchus keta) as determined by comparative transcriptome analysis. PeerJ 2022; 10:e13585. [PMID: 36117540 PMCID: PMC9477081 DOI: 10.7717/peerj.13585] [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: 12/06/2021] [Accepted: 05/23/2022] [Indexed: 01/17/2023] Open
Abstract
Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
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Affiliation(s)
- Peilun Li
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wei Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wanqiao Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Jilong Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
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Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments. Sci Rep 2021; 11:5064. [PMID: 33658614 PMCID: PMC7930030 DOI: 10.1038/s41598-021-84652-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023] Open
Abstract
Amur ide (Leuciscus waleckii), a Cyprinid species, is broadly distributed in Northeast Asia. Different from its freshwater counterparts, the population in Lake Dali Nor has a strong alkalinity tolerance and can adapt to extremely alkali-saline water with bicarbonate over 50 mmol/L. To uncover the genetic basis of its alkaline adaptation, three populations, including one alkali form from Lake Dali Nor (DL), one freshwater form from its adjacent sister Lake Ganggeng Nor (GG), and one freshwater form from its historical origin, namely, the Songhua River (SH), were analyzed using genome resequencing technology. A total of 679.82 Gb clean data and 38,091,163 high-quality single-nucleotide polymorphism (SNP) loci were detected in the three populations. Nucleotide diversity and population structure analysis revealed that the DL and GG populations have lower nucleotide diversities and different genetic structures than those of the SH population. Selective sweeping showed 21 genes involved in osmoregulatory regulation (DLG1, VIPR1, AKT1, and GNAI1), inflammation and immune responses (DLG1, BRINP1, CTSL, TRAF6, AKT1, STAT3, GNAI1, SEC22b, and PSME4b), and cardiorespiratory development (TRAF6, PSME4b, STAT3, AKT1, and COL9A1) to be associated with alkaline adaption of the DL population. Interestingly, selective pressure (CodeML, MEME, and FEL) methods identified two functional codon sites of VIPR1 to be under positive selection in the DL population. The subsequent 3D protein modeling confirmed that these selected sites will incur changes in protein structure and function in the DL population. In brief, this study provides molecular evidence of population divergence and alkaline adaptation, which will be very useful for revealing the genetic basis of alkaline adaptation in Amur ide.
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Cao M, Zhang M, Yang N, Fu Q, Su B, Zhang X, Li Q, Yan X, Thongda W, Li C. Full length transcriptome profiling reveals novel immune-related genes in black rockfish (Sebastes schlegelii). FISH & SHELLFISH IMMUNOLOGY 2020; 106:1078-1086. [PMID: 32947030 DOI: 10.1016/j.fsi.2020.09.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Lacking full-length transcriptome for black rockfish (Sebastes schlegelii) limits novel gene discoveries and gene structures analysis. Therefore, we constructed the full-length transcriptome of black rockfish using Single-Molecule Real-Time Sequencing technology. Totally, we produced 21.73 Gb raw reads containing 298,904 circular consensus sequence (CCS) reads. Full-length (FL) and Non-full-length (NFL) isoforms were obtained based on the presence of 5' and 3' primers as well as poly (A) tails. The results showed 70.71% reads were identified as FL isoforms. Moreover, the average length of these PacBio isoforms is 2,632 bp, which is much longer than the length of the unigenes with the average length of 589 bp which generated from Illumina platform. Meanwhile, we identified 43,068 non-redundant transcripts, 12,485 alternative splicing (AS), 6,320 polyadenylation (APA) and 499 gene fusions as well as numerous long non-coding RNAs based on mapped FL isoforms. In addition, we identified 147 and 528 immune-related genes from novel genes and unmapped transcripts. The provided dataset can be utilized to discover novel genes and construct a comprehensive transcript dataset for black rockfish.
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Affiliation(s)
- Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Min Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qi Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xu Yan
- College of Marine Science and Biological Engineering, Qingdao University of Science & Technology, Qingdao, 266011, China
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Luo H, Liu H, Zhang J, Hu B, Zhou C, Xiang M, Yang Y, Zhou M, Jing T, Li Z, Zhou X, Lv G, He W, Zeng B, Xiao S, Li Q, Ye H. Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau. Sci Rep 2020; 10:9668. [PMID: 32541658 PMCID: PMC7296019 DOI: 10.1038/s41598-020-66582-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Gymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in the Red List of China's Vertebrates. As one of the highest-altitude schizothorax fish in China, G. namensis has strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability of G. namensis are still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts of G. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes for G. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome in G. namensis by using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research of G. namensis and provide basis for further research.
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Affiliation(s)
- Hui Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, China
| | - Jie Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
| | - Bingjie Hu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
| | - Chaowei Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Mengbin Xiang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
| | - Yuejing Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Mingrui Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Tingsen Jing
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Zhe Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
| | - Xinghua Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Guangjun Lv
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Wenping He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China
| | - Benhe Zeng
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, China
| | - Shijun Xiao
- Department of Computer Science, Wuhan University of Technology, Wuhan, 430070, China.
| | - Qinglu Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China.
| | - Hua Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University College of Animal Sciences, Chongqing, 402460, China.
- Key Laboratory of Aquatic Science of Chongqing, 400175, Chongqing, China.
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Tong C, Li M. Transcriptomic signature of rapidly evolving immune genes in a highland fish. FISH & SHELLFISH IMMUNOLOGY 2020; 97:587-592. [PMID: 31891809 DOI: 10.1016/j.fsi.2019.12.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/21/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Recent genome-wide studies have begun to elucidate the genomic basis of hypoxia, long-term cold and high saline and alkaline adaptation in highland fish, and a number of key genes contributed to its highland adaptation were identified. An increasing number of studies indicated that immune genes of Tibetan endemic fish species underwent positive selection towards functional shift, while the insight into immune gene repertoire of Tibetan highland fishes from genome-wide studies has largely lagged behind. In this study, we performed one of the first comparative genomics study in particular focusing on the signatures of immune genes in a highland fish, Gymnocypris przewalskii based on immune-relevant tissue transcriptome assemblies. We identified seven putative rapidly evolving immune genes with elevated molecular evolutionary rate (dN/dS) relative to lowland fish species. Using tissue-transcriptome data, we found most of rapidly evolving immune genes were broadly expressed in head-kidney, spleen, gills and skin tissues, which significantly enriched for complement activation and inflammatory response processes. In addition, we found a set of complement activation related genes underwent accelerated evolution and showed consistently repressed expression patterns in response to parasite Ichthyophthirius multifiliis infection. Moreover, we detected a number of immune genes involved in adaptive immune system exhibited distinct signature of upregulated expression patterns after parasite infection. Taken together, this study provided putative transcriptomic signatures of rapidly evolving immune genes, and will gain the insight into Schizothoracine fish adaptation to high-altitude extreme aquatic environments including diversified pathogen challenge.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Miao Li
- Center for Advanced Retinal and Ocular Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Feng X, Jia Y, Zhu R, Chen K, Chen Y. Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq. DNA Res 2020; 26:353-363. [PMID: 31274170 PMCID: PMC6704404 DOI: 10.1093/dnares/dsz014] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/11/2019] [Indexed: 12/26/2022] Open
Abstract
The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.
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Affiliation(s)
- Xiu Feng
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yintao Jia
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ren Zhu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kang Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yifeng Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Zhu C, Zhang L, Ding H, Pan Z. Transcriptome-wide identification and characterization of the Sox gene family and microsatellites for Corbicula fluminea. PeerJ 2019; 7:e7770. [PMID: 31660260 PMCID: PMC6814067 DOI: 10.7717/peerj.7770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022] Open
Abstract
The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled with an average length of 859 bp, and 36.7% of them were successfully annotated. Six members of Sox gene family namely SoxB1, SoxB2, SoxC, SoxD, SoxE and SoxF were identified. Based on these genes, the divergence time of C. fluminea was estimated to be around 476 million years ago. Furthermore, a total of 3,117 microsatellites were detected with a distribution density of 1:12,960 bp. Fifty of these microsatellites were randomly selected for validation, and 45 of them were successfully amplified with 31 polymorphic ones. The data obtained in this study will provide useful information for future genetic and genomic studies in C. fluminea.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Lei Zhang
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.,Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai'an City, Huai'an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an, China
| | - Huaiyu Ding
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai'an, Jiangsu, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
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11
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Yi Y, Lv Y, You X, Chen J, Bian C, Huang Y, Xu J, Deng L, Shi Q. High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database. Genomics 2019; 111:215-221. [DOI: 10.1016/j.ygeno.2018.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 01/19/2023]
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12
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Huang X, Yan H, Zhai L, Yang Z, Yi Y. Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes. PLoS One 2019; 14:e0203014. [PMID: 30860996 PMCID: PMC6414006 DOI: 10.1371/journal.pone.0203014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/16/2019] [Indexed: 01/05/2023] Open
Abstract
Rosa roxburghii Tratt (Rosaceae) has a fruit that is flavorful, economically valuable, and highly nutritious, providing numerous health benefits. Myeloblastosis (MYB) proteins play key roles in the development and fruit quality of R. roxburghii. However, there is little available genomic and transcriptomic information for R. roxburghii. Here, a normalized cDNA library was constructed from five tissues, including the stem, leaf, flower, young fruit, and mature fruit, using the Illumina HiSeq 3000 platform. De novo assembly was performed, and 470.66 million clean reads were obtained. In total, 63,727 unigenes, with an average GC content of 42.08%, were discovered, 60,406 of which were annotated. In addition, 9,354 unigenes were assigned to Gene Ontology categories, and 20,202 unigenes were assigned to 25 Eukaryotic Ortholog Groups. Additionally, 19,508 unigenes were classified into 140 pathways of the Kyoto Encyclopedia of Genes and Genomes database. Based on the transcriptome, 163 unigenes associated with MYBs were detected. Among these genes, 75 genes were significantly expressed in the various tissues, including 10 R1 MYB, 42 R2R3 MYB, one R1R2R3 MYB, three R4 MYB and 19 atypical MYB-like proteins. The expression levels of the 12 MYB genes randomly selected for quantitative real-time PCR analysis corroborated the RNA sequencing results. A total of 37,545 microsatellites were detected, with an average expressed sequence tag–simple sequence repeat frequency of 0.59 (37,545/63,727). This transcriptome data improves our understanding of the role of MYB in R. roxburghii and will be valuable for identifying genes of interest.
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Affiliation(s)
- Xiaolong Huang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- * E-mail: (HY); (YY)
| | - Lisheng Zhai
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zhengting Yang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang, China
- * E-mail: (HY); (YY)
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13
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Chen J, Li Y, Wang W, Xia L, Wang Z, Hou S, Huang J, Lu Y. Transcriptome analysis of immune-related gene expression in hybrid snakehead (Channa maculata ♀ × Channa argus ♂) after challenge with Nocardia seriolae. FISH & SHELLFISH IMMUNOLOGY 2018; 81:476-484. [PMID: 30048684 DOI: 10.1016/j.fsi.2018.07.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/05/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Hybrid snakehead fish (Channa maculata ♀ × Channa argus ♂), a new species used in freshwater aquaculture in China, is the common host of an epizootic bacterial infection by Nocardia seriolae. However, the information on the functions and mechanisms of hybrid snakehead immune pathways with the N. seriolae infection is limited. Thus, the peripheral blood lymphocytes from hybrid snakehead were used for transcriptome analysis to understand the host immune response after challenge with N. seriolae. A total of 49,839,332 and 50,059,283 raw reads were obtained from the N. seriolae-challenged group (Ns group) and phosphate-buffered saline control group (Ctr group), respectively. The 75.50% and 74.25% reads from the Ns and Ctr groups were matched to reference genomic sequence after cleaning the raw reads, respectively. Additionally, there were 2892 significant differentially expressed genes (DEGs) among the 17,196 expressed genes between the Ns and Ctr groups, including 1387 upregulated and 1505 downregulated genes. All the DEGs were classified into three gene ontology categories, and 2502 DEGs had significant matches, which were allocated to 246 Kyoto Encyclopedia of Genes and Genomes pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways. Moreover, the regulation of several observed effective genes was confirmed by real-time quantitative polymerase chain reaction. Altogether, this study offers deep-sequence data of hybrid snakehead peripheral blood lymphocyte via transcriptome analysis and lays the foundation for further study on the immunogenetics of hybrid snakehead. Moreover, it provides insights into the pathogenic mechanism of N. seriolae, facilitating the prevention and treatment of fish nocardiosis.
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Affiliation(s)
- Jianlin Chen
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Yanqun Li
- Fisheries College of Guangdong Ocean University, Zhanjiang, China
| | - Wenji Wang
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Liqun Xia
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
| | - Zhiwen Wang
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Suying Hou
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Jiahui Huang
- Fisheries College of Guangdong Ocean University, Zhanjiang, China
| | - Yishan Lu
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China; Fisheries College of Guangdong Ocean University, Zhanjiang, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
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14
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Cai L, Li J, Yu L, Wei Y, Miao Z, Chen M, Huang R. Characterization of transcriptional responses mediated by benzo[a]pyrene stress in a new marine fish model of goby, Mugilogobius chulae. Genes Genomics 2018; 41:113-123. [PMID: 30242742 DOI: 10.1007/s13258-018-0743-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Benzo[a]pyrene (BaP) is one of the most studied targets among polycyclic aromatic hydrocarbons (PAHs). Because of the complexity of the toxicity mechanism in BaP, little is known about the molecular mechanism at the level of transcription of BaP in marine fishes. The primary objective of this study was to investigate the molecular basis of the effects of BaP on marine fish, using Mugilogobius chulae (Smith 1932) as the model. A closed colony of M. chulae was used for the BaP toxicity test. Two fish liver samples per replicate from each group were excised and blended into one sample by pooling an equal amount of liver tissue. Total RNA of all samples was extracted separately. Equal quantities of total RNA from the three replicates of the two groups were pooled for sequencing. The sequencing cDNA libraries were sequenced using Illumina HiSeq 2000 system. Differentially expressed genes were detected with the DEGSeq R package. In total, 52,364,032 and 53,771,748 clean nucleotide reads were obtained in the control and BaP-exposed libraries, respectively, with N50 lengths of 1277 and 1288 bp, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a significant enrichment of genes related to detoxification, transportation, and lipid metabolism. We also identified, for the first time, an association between endoplasmic reticulum dysfunction and lipid metabolism resulting from BaP exposure. Using quantitative real-time PCR, some effective molecular biomarkers for monitoring of BaP-polluted seawater were identified. The results demonstrate that BaP enhanced the expression of genes involved in detoxification in M. chulae and inhibited that of genes related to lipid metabolism, possibly by suppressing the expression of numerous ER-related genes involved in fat digestion and absorption.
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Affiliation(s)
- Lei Cai
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Jianjun Li
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Lujun Yu
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Yuanzheng Wei
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Zongyu Miao
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Meili Chen
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China
| | - Ren Huang
- Key Laboratory of Guangdong Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, No. 11, Fengxin Road, Huangpu District, Guangzhou, 510663, Guangdong, People's Republic of China.
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15
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Ye H, Zhang Z, Zhou C, Zhu C, Yang Y, Xiang M, Zhou X, Zhou J, Luo H. De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes and microsatellite markers. RSC Adv 2018; 8:13945-13953. [PMID: 35539357 PMCID: PMC9079874 DOI: 10.1039/c8ra00619a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/09/2018] [Indexed: 11/30/2022] Open
Abstract
Schizothorax waltoni (S. waltoni) is one kind of the subfamily Schizothoracinae and an indigenous economic tetraploid fish to Tibet in China. It is rated as a vulnerable species in the Red List of China's Vertebrates, owing to overexploitation and biological invasion. S. waltoni plays an important role in ecology and local fishery economy, but little information is known about genetic diversity, local adaptation, immune system and so on. Functional gene identification and molecular marker development are the first and essential step for the following biological function and genetics studies. For this purpose, the transcriptome from pooled tissues of three adult S. waltoni was sequenced and analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83 103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66 975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58 934, 87.99%) were successfully annotated by 7 public databases, and 15 KEGG pathways of immune-related genes were identified for the following functional research. Furthermore, 19 497 putative simple sequence repeats (SSRs) of 1-6 bp unit length were detected from 14 690 unigenes (21.93%) with an average distribution density of 1 : 3.28 kb. We identified 3590 unigenes (5.36%) containing more than one SSR, providing abundant potential polymorphic markers in functional genes. This is the first reported high-throughput transcriptome analysis of S. waltoni, and it would provide valuable genetic resources for the functional genes involved in multiple biological processes, including the immune system, genetic conservation, and molecular marker-assisted breeding of S. waltoni.
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Affiliation(s)
- Hua Ye
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Zhengshi Zhang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Chaowei Zhou
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Chengke Zhu
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Yuejing Yang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Mengbin Xiang
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Xinghua Zhou
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
| | - Jian Zhou
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences Chengdu 611731 China
| | - Hui Luo
- College of Animal Science, Southwest University Chongqing 402460 China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing 400175 China
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16
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Cai Y, Wang S, Guo W, Xie Z, Zheng Y, Cao Z, Zhou Y. Transcriptome analysis provides insights into the immune responsive pathways and genes in the head kidney of tiger grouper (Epinephelus fuscoguttatus) fed with Spatholobus suberectus, Phellodendron amurense, or Eclipta prostrata. FISH & SHELLFISH IMMUNOLOGY 2018; 73:100-111. [PMID: 29222026 DOI: 10.1016/j.fsi.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
The tiger grouper, Epinephelus fuscoguttatus, is an economically important fish in Southeast Asia but has been plagued by several diseases. Spatholobus suberectus (S), Phellodendron amurense (P), and Eclipta prostrate (E) are three commonly used Chinese medicinal herbs. Although previous pharmacological and clinical studies indicated that S, P, and E possess a variety of beneficial functions in mammals, little is known about their functions in farmed fish and the underlying molecular mechanism of their actions. Challenge tests in this study showed that after 14 days of diet supplement, all these herbs could effectively enhance the disease resistance of E. fuscoguttatus against Vibrio harveyi. However, the non-specific immune parameters of the herb-supplemented groups were not significantly different from the control group. To further explore the molecular mechanism of herbal immune-regulating effects on E. fuscoguttatus, transcriptome sequencing and RNA-Seq technique were applied on E. fuscoguttatus kidney. De novo transcriptome assembly of E. fuscoguttatus kidney yield 80,014 unigenes, among which, 44,901 (56.12%) were annotated with at least one of the public databases (Nr, Nt, Swiss-Prot, KEGG, COG, GO). Among these, 22,738, 11,700 and 27,457 unigenes were assigned to 57, 25 and 258 categories of GO, COG and KEGG databases, respectively. Using Solexa/Illumina's DGE platform, a total of 231, 186 and 144 putative differentially expressed genes (DEGs) were detected in P, E and S group compared with the control group. GO analysis indicated that in P and E, down-regulated DEGs were dominant in almost every GO term; whereas in S, up-regulated DEGs were more dominant. KEGG pathway analysis revealed that putative DEGs in all three herb groups were obviously enriched in the pathways related to infective diseases and immune system. We also identified a number of immune relative genes and pathways (TLR5, IL8 and MAPK pathway, for instance) associated with P, E and S's regulatory effects on E. fuscoguttatus. This study will enrich the E. fuscoguttatus transcriptome database, contribute to a better understanding of the molecular mechanisms associated with the immunoregulatory activities of Chinese medicinal herbs on teleost and provide valuable information on the prevention of grouper Vibrio diseases using Chinese medicinal herbs.
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Affiliation(s)
- Yan Cai
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, PR China
| | - Shifeng Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China.
| | - Weiliang Guo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China
| | - Yu Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China
| | - Zhenjie Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, PR China.
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17
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Sudhagar A, Kumar G, El-Matbouli M. Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review. Int J Mol Sci 2018; 19:ijms19010245. [PMID: 29342931 PMCID: PMC5796193 DOI: 10.3390/ijms19010245] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, with the advent of next-generation sequencing along with the development of various bioinformatics tools, RNA sequencing (RNA-Seq)-based transcriptome analysis has become much more affordable in the field of biological research. This technique has even opened up avenues to explore the transcriptome of non-model organisms for which a reference genome is not available. This has made fish health researchers march towards this technology to understand pathogenic processes and immune reactions in fish during the event of infection. Recent studies using this technology have altered and updated the previous understanding of many diseases in fish. RNA-Seq has been employed in the understanding of fish pathogens like bacteria, virus, parasites, and oomycetes. Also, it has been helpful in unraveling the immune mechanisms in fish. Additionally, RNA-Seq technology has made its way for future works, such as genetic linkage mapping, quantitative trait analysis, disease-resistant strain or broodstock selection, and the development of effective vaccines and therapies. Until now, there are no reviews that comprehensively summarize the studies which made use of RNA-Seq to explore the mechanisms of infection of pathogens and the defense strategies of fish hosts. This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.
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Affiliation(s)
- Arun Sudhagar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
- Central Institute of Fisheries Education, Rohtak Centre, Haryana 124411, India.
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna 1210, Austria.
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18
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Tong C, Tian F, Zhao K. Genomic signature of highland adaptation in fish: a case study in Tibetan Schizothoracinae species. BMC Genomics 2017; 18:948. [PMID: 29207953 PMCID: PMC5718033 DOI: 10.1186/s12864-017-4352-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 11/28/2017] [Indexed: 12/13/2022] Open
Abstract
Background Genome-wide studies on highland adaptation mechanism in terrestrial animal have been widely reported with few available for aquatic animals. Tibetan Schizothoracinae species are ideal model systems to study speciation and adaptation of fish. The Schizothoracine fish, Gymnocypris przewalskii ganzihonensis had underwent the ecological niche shift from salt water to freshwater, and also experienced a recent split from Gymnocypris przewalskii przewalskii. In addition, G. p. ganzihonensis inhabited harsh aquatic environment including low temperature and hypoxia as well as other Schizothoracinae species, its genetic mechanism of highland adaptation have yet to be determined. Results Our study used comparative genomic analysis based on the transcriptomic data of G. p. ganzihonensis and other four fish genome datasets to investigate the genetic basis of highland adaptation in Schizothoracine fish. We found that Schizothoracine fish lineage on the terminal branch had an elevated dN/dS ratio than its ancestral branch. A total of 202 gene ontology (GO) categories involved into transport, energy metabolism and immune response had accelerated evolutionary rates than zebrafish. Interestingly, we also identified 162 genes showing signature of positive selection (PSG) involved into energy metabolism, transport and immune response in G. p. ganzihonesis. While, we failed to find any PSG related to hypoxia response as previous studies. Conclusions Comparative genomic analysis based on G. p. ganzihonensis transcriptome data revealed significant genomic signature of accelerated evolution ongoing within Tibetan Schizothoracinae species lineage. Molecular evolution analysis suggested that genes involved in energy metabolism, transport and immune response functions in Schizothoracine fish underwent positive selection, especially in innate immunity including toll-like receptor signaling pathway genes. Taken together, our result as a case study in Schizothoracinae species provides novel insights in understanding the aquatic animal adaptation to extreme environment on the Tibetan Plateau, and also provides valuable genomic resource for further functional verification studies. Electronic supplementary material The online version of this article (10.1186/s12864-017-4352-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6018, USA.
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
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19
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Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish. PLoS One 2017; 12:e0186433. [PMID: 29045433 PMCID: PMC5646821 DOI: 10.1371/journal.pone.0186433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/29/2017] [Indexed: 11/19/2022] Open
Abstract
Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways. Interestingly, we identified two candidate genes contributed to normal skeletal development. The altered expression of these gene groups could potentially be associated with the developmental issues of deformity and induced larval death. Our results have three important implications: first, these findings provide strong evidences to support our hypothesis that G. przewalskii possess ability to build heat-tolerance against the controversial issue. Second, this study shows that transcriptional and post-transcriptional regulations are extensively involved in thermal acclimation. Third, the integrated mRNA and microRNA transcriptome analyses provide a large number of valuable genetic resources for future studies on environmental stress response in G. przewalskii and as a case study in Tibetan Schizothoracine fish.
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20
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Sun S, Xuan F, Ge X, Zhu J, Zhang W. Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala). Sci Rep 2017; 7:12846. [PMID: 28993687 PMCID: PMC5634510 DOI: 10.1038/s41598-017-12537-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/12/2017] [Indexed: 12/24/2022] Open
Abstract
Adaptation to hypoxia is a complex process involving various pathways and regulation mechanisms. A better understanding of the genetic influence on these mechanisms could permit selection for hypoxia-sensitive fish. To aid this understanding, an integrated analysis of miRNA and mRNA expression was performed in Megalobrama amblycephala under four acute hypoxia and reoxygenation stages. A number of significantly differentially-expressed miRNAs and genes associated with oxidative stress were identified, and their functional characteristics were revealed by GO function and KEGG pathway analysis. They were found to be involved in HIF-1 pathways known to affect energy metabolism and apoptosis. MiRNA-mRNA interaction pairs were detected from comparison of expression between the four different stages. The function annotation results also showed that many miRNA-mRNA interaction pairs were likely to be involved in regulating hypoxia stress. As a unique resource for gene expression and regulation during hypoxia and reoxygenation, this study could provide a starting point for further studies to better understand the genetic background of hypoxia stress.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China
| | - Fujun Xuan
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province, 224002, P.R. China
| | - Xianping Ge
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Wuxiao Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, P.R. China
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Petit J, David L, Dirks R, Wiegertjes GF. Genomic and transcriptomic approaches to study immunology in cyprinids: What is next? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:48-62. [PMID: 28257855 DOI: 10.1016/j.dci.2017.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 02/24/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding.
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Affiliation(s)
- Jules Petit
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Lior David
- Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ron Dirks
- ZF-screens B.V., J.H, Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.
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22
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Salinas I, Magadán S. Omics in fish mucosal immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:99-108. [PMID: 28235585 DOI: 10.1016/j.dci.2017.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 05/22/2023]
Abstract
The mucosal immune system of fish is a complex network of immune cells and molecules that are constantly surveilling the environment and protecting the host from infection. A number of "omics" tools are now available and utilized to understand the complexity of mucosal immune systems in non-traditional animal models. This review summarizes recent advances in the implementation of "omics" tools pertaining to the four mucosa-associated lymphoid tissues in teleosts. Genomics, transcriptomics, proteomics, and "omics" in microbiome research require interdisciplinary collaboration and careful experimental design. The data-rich datasets generated are proving really useful at discovering new innate immune players in fish mucosal secretions, identifying novel markers of specific mucosal immune responses, unraveling the diversity of the B and T cell repertoires and characterizing the diversity of the microbial communities present in teleost mucosal surfaces. Bioinformatics, data analysis and storage platforms should be developed to facilitate rapid processing of large datasets, especially when mammalian tools such as bioinformatics analysis software are not available in fishes.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Susana Magadán
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM 87131, USA; Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra 36310, Spain.
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23
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Qi D, Xia M, Chao Y, Zhao Y, Wu R. Identification, molecular evolution of toll-like receptors in a Tibetan schizothoracine fish (Gymnocypris eckloni) and their expression profiles in response to acute hypoxia. FISH & SHELLFISH IMMUNOLOGY 2017; 68:102-113. [PMID: 28698123 DOI: 10.1016/j.fsi.2017.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Hypoxia plays an important role in regulating a variety of physiological responses as well as in pathological situations, but to date the roles of Toll-like receptors (TLRs) in fish in response to hypoxia are still poorly understood. Here, we sequenced the transcriptome of G. eckloni and identified the members of TLR family by scanning transcriptome, and then investigated the expression profiles of a complete set of TLRs in G. eckloni in response to acute hypoxia (4 h at DO = 0.3 ± 0.1 mg/L). The de novo-assembled transcriptome consisted of a total of 162,235 transcripts, further clustered into 110,231 unigenes. Based on the transcriptome, a total of 18 TLRs were identified in G. eckloni, and of them three TLRs (TLR5, TLR8 and TLR22) possessed two distinct paralogous genes. The duplicated genes of TLR22 were discovered for the first time in cyprinid fish, but did not origin from a recent duplication event. Of them TLR22b may be specific for schizothoracine fish, at least for G. eckloni. Phylogenetic analysis supported the classification of TLRs into six families as in other vertebrates but was partly different from the previous study. The sliding window analysis showed strong signals of positive selection in TLR2, TLR 4, TLR 5a, TLR 7, TLR 19, TLR 20, TLR 21, TLR 22a and TLR 22b, but most codons under positive selection were located in the putative LRR regions. The mRNA expression of most TLRs in head kidney, spleen and gill decreased significantly or remained unchanged under acute hypoxia, whereas acute hypoxia increased expressions of TLR2 and TLR3 in head kidney, of TLR8a, TLR12 and TLR19 in spleen, and of TLR1 in gill, suggesting tissues-specific expressions of TLRs play important roles in mediating innate immune responses for host defense against tissue damages or physiological changes induced by hypoxia.
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Affiliation(s)
- Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China.
| | - Mingzhe Xia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Yongli Zhao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
| | - Rongrong Wu
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining 810016, China
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24
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Transcriptome Analysis Reveals Increases in Visceral Lipogenesis and Storage and Activation of the Antigen Processing and Presentation Pathway during the Mouth-Opening Stage in Zebrafish Larvae. Int J Mol Sci 2017; 18:ijms18081634. [PMID: 28758957 PMCID: PMC5578024 DOI: 10.3390/ijms18081634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
The larval phase of the fish life cycle has the highest mortality, particularly during the transition from endogenous to exogenous feeding. However, the transcriptional events underlying these processes have not been fully characterized. To understand the molecular mechanisms underlying mouth-opening acclimation, RNA-seq was used to investigate the transcriptional profiles of the endogenous feeding, mixed feeding and exogenous feeding stages of zebrafish larvae. Differential expression analysis showed 2172 up-regulated and 2313 down-regulated genes during this stage. Genes associated with the assimilation of exogenous nutrients such as the arachidonic acid metabolism, linoleic acid metabolism, fat digestion and absorption, and lipogenesis were activated significantly, whereas dissimilation including the cell cycle, homologous recombination, and fatty acid metabolism were inhibited, indicating a physiological switch for energy storage occurred during the mouth-opening stage. Moreover, the immune recognition involved in the antigen processing and presentation pathway was activated and nutritional supply seemed to be required in this event confirmed by qPCR. These results suggested the energy utilization during the mouth-opening stage is more tended to be reserved or used for some important demands, such as activity regulation, immune defense, and lipid deposition, instead of rapid growth. The findings of this study are important for understanding the physiological switches during the mouth-opening stage.
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Tong C, Tian F, Zhang C, Zhao K. The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau. PLoS One 2017; 12:e0174534. [PMID: 28358922 PMCID: PMC5373569 DOI: 10.1371/journal.pone.0174534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/11/2017] [Indexed: 12/12/2022] Open
Abstract
Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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26
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Zhu C, Pan Z, Wang H, Chang G, Wu N, Ding H. De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis. PLoS One 2017; 12:e0171966. [PMID: 28196101 PMCID: PMC5308828 DOI: 10.1371/journal.pone.0171966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/28/2017] [Indexed: 11/30/2022] Open
Abstract
The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved. 96.2% of these unigenes were annotated in 9 public databases, and 16 segments of growth-related genes were identified for future studies. In addition, 28,493 unigenes were assigned to 61 subcategories of Gene Ontology (GO), and 10,483 unigenes were assigned to 25 categories of Cluster of Orthologous Group (COG). Moreover, 14,943 unigenes were classified into 225 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 30,666 microsatellites were detected from 17,627 unigenes with an average distribution density of 1:2405 bp. This transcriptome data set will be valuable for researches on discovery, expression and evolution on genes of interest. Meanwhile, the identified microsatellites would be useful tools for genetic and genomic studies in S. sinensis.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
- * E-mail:
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Hui Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Guoliang Chang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Nan Wu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Huaiyu Ding
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
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Ferraresso S, Bonaldo A, Parma L, Buonocore F, Scapigliati G, Gatta PP, Bargelloni L. Ontogenetic onset of immune-relevant genes in the common sole (Solea solea). FISH & SHELLFISH IMMUNOLOGY 2016; 57:278-292. [PMID: 27554393 DOI: 10.1016/j.fsi.2016.08.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/25/2016] [Accepted: 08/19/2016] [Indexed: 06/06/2023]
Abstract
Fish are free-living organisms since initial stages of development and are exposed to numerous pathogens before their lymphoid organs have matured and adaptive immunity has developed. Susceptibility to diseases and juvenile mortality represent key critical factors for aquaculture. In this context, the characterization of the appearance kinetics of the immune system key members will be useful in understanding the ability of a particular species in generating immune protection against invading pathogens at different developmental stages. The present study characterized, for the first time, the transcriptional onset of un-explored relevant genes of both innate and adaptive immune system during the Solea solea ontogenesis. Gene expression profiles of immune relevant genes was investigated, by means of DNA microarray, in ten developmental stages, from hatching (1 day post-hatching, dph) to accomplishment of the juvenile form (33 dph). The obtained results revealed that transcripts encoding relevant members of innate immune repertoire, such as lysozyme, AMPs (hepcidin, β-defensin), PPRs and complement components are generally characterized by high expression levels at first stages (i.e. hatch and first feeding) indicating protection from environmental pathogens even at early development. Transcription of adaptive immune genes (i.e. Class I and class II MHC, TCRs) differs from that of the innate immune system. Their onset coincides with metamorphosis and larvae-to-juvenile transition, and likely overlaps with the appearance and maturation of the main lymphoid organs. Finally, data collected suggest that at the end of metamorphosis S. solea cell-mediated immune system hasn't still undergone full maturation.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Alessio Bonaldo
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Luca Parma
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Via San Camillo de Lellis s.n.c., 01100 Viterbo, Italy.
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, Tuscia University, Via San Camillo de Lellis s.n.c., 01100 Viterbo, Italy.
| | - Pier Paolo Gatta
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy.
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
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Dang Y, Xu X, Shen Y, Hu M, Zhang M, Li L, Lv L, Li J. Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila. PLoS One 2016; 11:e0157413. [PMID: 27383749 PMCID: PMC4934786 DOI: 10.1371/journal.pone.0157413] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/27/2016] [Indexed: 02/02/2023] Open
Abstract
The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.
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Affiliation(s)
- Yunfei Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Xiaoyan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Moyan Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Meng Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Lisen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Liqun Lv
- National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, PR China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
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Luo H, Xiao S, Ye H, Zhang Z, Lv C, Zheng S, Wang Z, Wang X. Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti. PLoS One 2016; 11:e0152572. [PMID: 27019203 PMCID: PMC4809619 DOI: 10.1371/journal.pone.0152572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/16/2016] [Indexed: 12/21/2022] Open
Abstract
Schizothorax prenanti (S. prenanti) is mainly distributed in the upstream regions of the Yangtze River and its tributaries in China. This species is indigenous and commercially important. However, in recent years, wild populations and aquacultures have faced the serious challenges of germplasm variation loss and an increased susceptibility to a range of pathogens. Currently, the genetics and immune mechanisms of S. prenanti are unknown, partly due to a lack of genome and transcriptome information. Here, we sought to identify genes related to immune functions and to identify molecular markers to study the function of these genes and for trait mapping. To this end, the transcriptome from spleen tissues of S. prenanti was analyzed and sequenced. Using paired-end reads from the Illumina Hiseq2500 platform, 48,517 transcripts were isolated from the spleen transcriptome. These transcripts could be clustered into 37,785 unigenes with an N50 length of 2,539 bp. The majority of the unigenes (35,653, 94.4%) were successfully annotated using non-redundant nucleotide sequence analysis (nt), and the non-redundant protein (nr), Swiss-Prot, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. KEGG pathway assignment identified more than 500 immune-related genes. Furthermore, 7,545 putative simple sequence repeats (SSRs), 857,535 single nucleotide polymorphisms (SNPs), and 53,481 insertion/deletion (InDels) were detected from the transcriptome. This is the first reported high-throughput transcriptome analysis of S. prenanti, and it provides valuable genetic resources for the investigation of immune mechanisms, conservation of germplasm, and molecular marker-assisted breeding of S. prenanti.
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Affiliation(s)
- Hui Luo
- College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China
| | - Shijun Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Hua Ye
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Zhengshi Zhang
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Changhuan Lv
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Shuming Zheng
- Fisheries Breeding and Healthy Cultivation Research Centre, Southwest University, Chongqing, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, P.R. China, Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Xiaoqing Wang
- College of Animal Science & Technology, Hunan Agricultural University, Changsha, Hunan, China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, Hunan, China
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Tong C, Tian F, Tang Y, Feng C, Guan L, Zhang C, Zhao K. Positive Darwinian selection within interferon regulatory factor genes of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau. FISH & SHELLFISH IMMUNOLOGY 2016; 50:34-42. [PMID: 26774494 DOI: 10.1016/j.fsi.2016.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/06/2016] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
Tibetan Plateau (TP) had experienced phased uplift, resulting in inhospitable environment of low temperature, hypoxia and high ultraviolet radiation for Tibetan wildlife. Many organisms can well adapt to TP, it is of ecological and evolutionary interest to untangle how organisms adapt to extreme environment on TP through evolution. Previous studies mainly focused on hypoxia and metabolism related genes, but we know little about the evolutionary history of immune genes in Tibetan wildlife. In this study, we first identified 10 interferon regulatory factor (IRF) genes from Tibetan naked carp Gymnocypris przewalskii. Within this gene family, IRF3, IRF5, IRF7 and IRF8 contained positive selection sites. Evidences indicated that positive selection may lead to IRF genes functional alternations, presumably driving genes towards adaptation to the environmental changes. Taken together, our results suggested 4 candidate genes as interesting targets for further experimental confirmation of their functional variations and contributions to high altitude adaptation in Tibet fish.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenguang Feng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lihong Guan
- Department of Life Science and Technology, Xinxiang Medical University, Xinxiang, 453003, China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China; Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
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Lee X, Yi Y, Weng S, Zeng J, Zhang H, He J, Dong C. Transcriptomic analysis of koi (Cyprinus carpio) spleen tissue upon cyprinid herpesvirus 3 (CyHV3) infection using next generation sequencing. FISH & SHELLFISH IMMUNOLOGY 2016; 49:213-24. [PMID: 26690666 DOI: 10.1016/j.fsi.2015.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 05/18/2023]
Abstract
Cyprinid Herpesvirus 3 (CyHV-3) can infect and specifically cause a huge economic loss in both common carp (Cyprinus carpio) and its ornamental koi variety. The molecular mechanisms underlying CyHV-3 infection are not well understood. In this study, koi spleen tissues of both mock and CyHV-3 infection groups were collected, and high-throughput sequencing technology was used to analyze the differentially expressed genes (DEGs) at the transcriptome level. A total of 105,356,188 clean reads from two libraries were obtained. After the de novo assembly of the transcripts, 129,314 unigenes were generated. Of these unigenes, 70,655 unigenes were matched to the known proteins in the database, while 2190 unigenes were predicted by ESTScan software. Comparing the infection group to the mock group, a total of 23,029 significantly differentially expressed unigenes were identified, including 10,493 up-regulated DEGs and 12,536 down-regulated DEGs. GO (Gene Ontology) annotation and functional enrichment analysis indicated that all of the DEGs were annotated into GO terms in three main GO categories: biological process, cellular component and molecular function. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the DEGs showed that a total of 12,002 DEG unigenes were annotated into 256 pathways classified into 6 main categories. Additionally, 20 differentially expressed genes were validated by quantitative real-time PCR. As the first report of a transcriptome analysis of koi carp with CyHV-3 infection, the data presented here provide knowledge of the innate immune response against CyHV-3 in koi carp and useful data for further research of the molecular mechanism of CyHV-3 infection.
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Affiliation(s)
- Xuezhu Lee
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yang Yi
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shaoping Weng
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jie Zeng
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hetong Zhang
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jianguo He
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
| | - Chuanfu Dong
- State Key Laboratory for Bio-control / MOE Key Laboratory of Aquatic Food Safety, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou 510275, PR China.
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