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Xie X, Wang D, Li B, Liang G, Chen X, Xing D, Zhao T, Zhou X, Li C. Aedes aegypti Beta-1,3-Glucan-Binding Protein Inhibits Dengue and ZIKA Virus Replication. Biomedicines 2024; 12:88. [PMID: 38255195 PMCID: PMC10812959 DOI: 10.3390/biomedicines12010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
GNBPB6, a beta-1,3-glucan-binding protein, was identified in the transcriptome of Aedes aegypti (A. aegypti) with dengue (DENV), Zika (ZIKV), and chikungunya viruses (CHIKV). In this study, we not only clarified that DENV2 and ZIKV regulate the changes in GNBPB6 expression but also identified the relationship of this gene with viral infections. The changes in GNBPB6 expression were quantified and showed a decrease in A. aegypti cells (Aag2 cells) at 2 dpi and 3 dpi and an increase at 4 dpi and 5 dpi (p < 0.05). A significant increase was observed only at 5 dpi after DENV2 infection. Subsequently, a GNBPB6 knockout (KO) cell line was constructed using the CRISPR/Cas9 system, and the DENV2 and ZIKV RNA copies, along with cell densities, were quantified and compared between the KO and wild type (WT) cells at different dpi. The result showed that DENV2 and ZIKV RNA copies were significantly increased in the KO cell line with no significant change in cell growth. Finally, DENV2 copies decreased after GNBPB6 was complemented in the KO. In conclusion, GNBPB6 knockout and complementation in Aag2 cells revealed that GNBPB6 can inhibit the replication of both DENV2 and ZIKV. These results contribute to subsequent research on mosquito-virus interactions.
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Affiliation(s)
- Xiaoxue Xie
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Di Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Bo Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, China
| | - Guorui Liang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Xiaoli Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Teng Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Xinyu Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (X.X.); (D.W.); (B.L.); (G.L.); (X.C.); (D.X.); (T.Z.)
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Zhang R, Duan Q, Luo Q, Deng L. PacBio Full-Length Transcriptome of a Tetraploid Sinocyclocheilus multipunctatus Provides Insights into the Evolution of Cavefish. Animals (Basel) 2023; 13:3399. [PMID: 37958154 PMCID: PMC10648740 DOI: 10.3390/ani13213399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Sinocyclocheilus multipunctatus is a second-class nationally protected wild animal in China. As one of the cavefish, S. multipunctatus has strong adaptability to harsh subterranean environments. In this study, we used PacBio SMRT sequencing technology to generate a first representative full-length transcriptome for S. multipunctatus. Sequence clustering analysis obtained 232,126 full-length transcripts. Among all transcripts, 40,487 were annotated in public databases, while 70,300 microsatellites, 2384 transcription factors, and 16,321 long non-coding RNAs were identified. The phylogenetic tree showed that S. multipunctatus shows a closer relationship to Carassius auratus and Cyprinus carpio, phylogenetically diverging from the common ancestor ~14.74 million years ago (Mya). We also found that between 15.6 and 17.5 Mya, S. multipunctatus also experienced an additional whole-genome duplication (WGD) event, which may have promoted the species evolution of S. multipunctatus. Meanwhile, the overall rates of evolutionary of polyploid S. multipunctatus were significantly higher than those of the other cyprinids, and 220 positively selected genes (PSGs) were identified in two sub-genomes of S. multipunctatus. These PSGs are likely to fulfill critical roles in the process of adapting to diverse cave environments. This study has the potential to facilitate future investigations into the genomic characteristics of S. multipunctatus and provide valuable insights into revealing the evolutionary history of polyploid S. multipunctatus.
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Duan Q, Luo Q, Tang Q, Deng L, Zhang R, Li Y. Comprehensive transcripts analysis based on single-molecule real-time sequencing and Illumina sequencing provides insights into the mining of Toll-like receptor family in Schizothorax lissolabiatus. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108963. [PMID: 37481099 DOI: 10.1016/j.fsi.2023.108963] [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: 04/05/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Schizothorax lissolabiatus is an economically important cold-water fish species in southwestern China. Because of water pollution and habitat destruction, the number of wild populations has dramatically decreased. In this study, we used PacBio single-molecule real-time (SMRT) sequencing and Illumina sequencing to generate the first full-length transcriptome and transcriptome, respectively. A total of 19 310 polished consensus reads (PC) were obtained, with an average length of 1379 bp and an N50 length of 1485 bp. Meanwhile, 12 253 transcripts were successfully annotated as known homologous genes. The pathway annotation indicated that the enrichment and expression of most genes were mainly related to membrane, signal transduction and binding, and immune response. Furthermore, we identified 16 Toll-like receptors (TLRs) by mining the data from the transcripts. Phylogeny analysis showed that S. lissolabiatus TLR genes (slTLRs) supported the classification of TLRs into six families as in other vertebrates. Selection pressure analyses showed that 16 slTLRs revealed purification selection at the overall evolutionary selection. Further, positive selection signals were still detected in eight slTLRs, and most of the positive selection sites were located in the leucine-rich repeat region (LRR domain) associated with the recognition of pathogenic microorganisms, indicating that the function of these slTLR genes may be affected. Tissue specific expression analysis showed all slTLRs are present in kidney, spleen and liver but the relative expression varied among tissues. In conclusion, this study not only provided a valuable resource of transcripts for further research on S. lissolabiatus, but also contributed to improve the current understanding of the evolutionary history of immune-related genes and the TLR gene family in S. lissolabiatus.
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Affiliation(s)
- Qian Duan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Qi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Qian Tang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Lei Deng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
| | - Yanping Li
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China.
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Sun L, Cheng L, Fu H, Wang R, Gu Y, Qiu Y, Sun K, Xu H, Lei P. A strategy for nitrogen conversion in aquaculture water based on poly-γ-glutamic acid synthesis. Int J Biol Macromol 2023; 229:1036-1043. [PMID: 36603727 DOI: 10.1016/j.ijbiomac.2022.12.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Ammonia and nitrite are nitrogenous pollutants in aquaculture effluents, which pose a major threat to the health of aquatic animals. In this study, we developed a nitrogen conversion strategy based on synthesis of poly-γ-glutamic acid (γ-PGA) by Bacillus subtilis NX-2. The nitrogen removal efficiency of NX-2 was closely related to synthesizing γ-PGA, and was positively correlated with the inoculum level. The degradation rates of ammonia nitrogen and nitrite at 104 CFU/mL were 84.42 % and 62.56 %, respectively. Through adaptive laboratory evolution (ALE) experiment, we obtained a strain named ALE 5 M with ammonia degradation rate of 98.03 % and nitrite of 93.62 % at the inoculum level of 104 CFU/mL. Transcriptome analysis showed that the strain was more likely to produce γ-PGA after ALE. By enzyme activity and qPCR analysis, we confirmed that ALE 5 M degraded ammonia nitrogen through γ-PGA synthesis, which provided a new way for nitrogen removal in aquaculture water.
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Affiliation(s)
- Liang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Lifangyu Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Heng Fu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yian Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ke Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Peng Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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Wang X, Bao M, Xu N, Sun R, Dai W, Sun K, Wang H, Feng J. Full-Length Transcriptome of Myotis pilosus as a Reference Resource and Mining of Auditory and Immune Related Genes. Int J Mol Sci 2022; 24:ijms24010062. [PMID: 36613506 PMCID: PMC9820712 DOI: 10.3390/ijms24010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Rickett's big-footed bat, Myotis pilosus, which belongs to the family Vespertilionida, is the only known piscivorous bat in East Asia. Accurate whole genome and transcriptome annotations are essential for the study of bat biological evolution. The lack of a whole genome for M. pilosus has limited our understanding of the molecular mechanisms underlying the species' evolution, echolocation, and immune response. In the present work, we sequenced the entire transcriptome using error-corrected PacBio single-molecule real-time (SMRT) data. Then, a total of 40 GB of subreads were generated, including 29,991 full-length non-chimeric (FLNC) sequences. After correction by Illumina short reads and de-redundancy, we obtained 26,717 error-corrected isoforms with an average length of 3018.91 bp and an N50 length of 3447 bp. A total of 1528 alternative splicing (AS) events were detected by transcriptome structural analysis. Furthermore, 1032 putative transcription factors (TFs) were identified, with additional identification of several long non-coding RNAs (lncRNAs) with high confidence. Moreover, several key genes, including PRL-2, DPP4, Glul, and ND1 were also identified as being associated with metabolism, immunity, nervous system processes, and auditory perception. A multitude of pattern recognition receptors was identified, including NLR, RLR, SRCR, the antiviral molecule IRF3, and the IFN receptor subunit IFNAR1. High-quality reference genomes at the transcriptome level may be used to quantify gene or transcript expression, evaluate alternative splicing levels, identify novel transcripts, and enhance genome annotation in bats.
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Affiliation(s)
- Xue Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Mingyue Bao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Ningning Xu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Ruyi Sun
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (H.W.); (J.F.)
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Correspondence: (H.W.); (J.F.)
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Zhou K, Chen Z, Du X, Huang Y, Qin J, Wen L, Pan X, Lin Y. SMRT Sequencing Reveals Candidate Genes and Pathways With Medicinal Value in Cipangopaludina chinensis. Front Genet 2022; 13:881952. [PMID: 35783279 PMCID: PMC9243326 DOI: 10.3389/fgene.2022.881952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/26/2022] [Indexed: 12/03/2022] Open
Abstract
Cipangopaludina chinensis is an economically important aquatic snail with high medicinal value. However, molecular biology research on C. chinensis is limited by the lack of a reference genome, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. chinensis. Herein, we conducted the first full-length transcriptome analysis of C. chinensis using PacBio single-molecule real-time (SMRT) sequencing technology. We identified a total of 26,312 unigenes with an average length of 2,572 bp, of which the largest number of zf-c2h2 transcription factor families (120,18.24%) were found, and also observed that the majority of the 8,058 SSRs contained 4-7 repeat units, which provided data for subsequent work on snail genetics Subsequently, 91.86% (24,169) of the genes were successfully annotated to the four major databases, while the highest homology was observed with Pomacea canaliculata. Functional annotation revealed that the majority of transcripts were enriched in metabolism, signal transduction and Immune-related pathways, and several candidate genes involved in drug metabolism and immune response were identified (e.g., CYP1A1, CYP2J, CYP2U1, GST, ,PIK3, PDE3A, PRKAG). This study lays a foundation for future molecular biology research and provides a reference for studying genes associated with the medicinal value of C. chinensis.
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Affiliation(s)
| | | | | | | | | | | | | | - Yong Lin
- *Correspondence: Xianhui Pan, ; Yong Lin,
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