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Zhang H, Han L, Qiu L, Zhao B, Gao Y, Chu Z, Dai X. Perfluorooctanoic Acid (PFOA) Exposure Compromises Fertility by Affecting Ovarian and Oocyte Development. Int J Mol Sci 2023; 25:136. [PMID: 38203307 PMCID: PMC10779064 DOI: 10.3390/ijms25010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
PFOA, a newly emerging persistent organic pollutant, is widely present in various environmental media. Previous reports have proved that PFOA exposure can accumulate in the ovary and lead to reproductive toxicity in pregnant mice. However, the potential mechanism of PFOA exposure on fertility remains unclear. In this study, we explore how PFOA compromises fertility in the zebrafish. The data show that PFOA (100 mg/L for 15 days) exposure significantly impaired fertilization and hatching capability. Based on tissue sections, we found that PFOA exposure led to ovarian damage and a decrease in the percentage of mature oocytes. Moreover, through in vitro incubation, we determined that PFOA inhibits oocyte development. We also sequenced the transcriptome of the ovary of female zebrafish and a total of 284 overlapping DEGs were obtained. Functional enrichment analysis showed that 284 overlapping DEGs function mainly in complement and coagulation cascades signaling pathways. In addition, we identified genes that may be associated with immunity, such as LOC108191474 and ZGC:173837. We found that exposure to PFOA can cause an inflammatory response that can lead to ovarian damage and delayed oocyte development.
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Affiliation(s)
| | | | | | | | | | | | - Xiaoxin Dai
- School of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China; (H.Z.); (L.H.); (L.Q.); (B.Z.); (Y.G.); (Z.C.)
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2
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Liang H, Wang XT, Ge WY, Zhang R, Liu J, Chen LL, Xi XL, Guo WH, Yin DC. Andrias Davidianus Mucus-Based Bioadhesive with Enhanced Adhesion and Wound Healing Properties. ACS APPLIED MATERIALS & INTERFACES 2023; 15:49931-49942. [PMID: 37856675 DOI: 10.1021/acsami.3c04148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The skin secretion of Andrias davidianus (SSAD) is a novel biological adhesive raw material under development. This material exhibits robust adhesion while maintaining the flexibility of the wound. It also has the potential for large-scale production, making it promising for practical application explore. Hence, in-depth research on methods to fine-tune SSAD properties is of great importance to promote its practical applications. Herein, we aim to enhance the adhesive and healing properties of SSAD by incorporating functional components. To achieve this goal, we selected 3,4-dihydroxy-l-phenylalanine and vaccarin as the functional components and mixed them with SSAD, resulting in a new bioadhesive, namely, a formulation termed "enhanced SSAD" (ESSAD). We found that the ESSAD exhibited superior adhesive properties, and its adhesive strength was improved compared with the SSAD. Moreover, ESSAD demonstrated a remarkable ability to promote wound healing. This study presents an SSAD-based bioadhesive formulation with enhanced properties, affirming the feasibility of developing SSAD-based adhesive materials with excellent performance and providing new evidence for the application of SSAD. This study also aims to show that SSAD can be mixed with other substances, and addition of effective components to SSAD can be studied to further adjust or improve its performance.
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Affiliation(s)
- Huan Liang
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xue-Ting Wang
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Wan-Yi Ge
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Rui Zhang
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jie Liu
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Liang-Liang Chen
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Xiao-Li Xi
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Wei-Hong Guo
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Da-Chuan Yin
- Key Laboratory for Space Bioscience and Space Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
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Liao J, Kang S, Zhang L, Zhang D, Xu Z, Qin Q, Wei J. Isolation and identification of a megalocytivirus strain (SKIV-TJ) from cultured spotted knifejaw (Oplegnathus punctatus) in China and its pathogenicity analysis. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109034. [PMID: 37640124 DOI: 10.1016/j.fsi.2023.109034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/26/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
The spotted knifejaw (Oplegnathus punctatus) has recently emerged as a highly economically significant farmed fish in China. However, due to increasing environmental pollution and breeding density, a range of infectious diseases, including the iridovirus pathogen, have begun to spread widely. In this study, we isolated and identified a strain of Megalocytivirus, SKIV-TJ, from cultured spotted knifejaw in Tianjin, China. We observed significant cytopathic effects (CPE) in SKIV-TJ-infected spotted knifejaw brain (SKB) cells, and electron microscopy showed numerous virus particles in the cytoplasm of SKB cells 6 days post-infection. The annotated complete genome of SKIV-TJ (GenBank accession number ON075463) contained 112,489 bp and 132 open reading frames. Based on the multigene association evolutionary tree using 26 iridovirus core genes, SKIV-TJ was found to be most closely related to Rock bream iridovirus (RBIV). Cumulative mortality of spotted knifejaw infected with SKIV-TJ reached 100% by day 9. A transcriptomic analysis were conducted and a total of 5517 differentially expressed genes were identified, including 2757 upregulated genes and 2760 downregulated genes. The upregulated genes were associated with viral infection and immune signaling pathways. Our findings provide a valuable genetic resource and a deeper understanding of the immune response to SKIV infection in spotted knifejaw.
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Affiliation(s)
- Jiaming Liao
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaozhu Kang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Luhao Zhang
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Dongzhuo Zhang
- Guangdong Winsun Biological Pharmaceutical Co., Ltd., Guangzhou, 511356, China
| | - Zhuqing Xu
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266000, China.
| | - Jingguang Wei
- College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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Wang X, Xie Y, Hu W, Wei Z, Wei X, Yuan H, Yao H, Dunxue C. Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa. Gene 2022; 842:146793. [PMID: 35952842 DOI: 10.1016/j.gene.2022.146793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
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Affiliation(s)
- Xiaodong Wang
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yongguang Xie
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Zhaoyu Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Xiuying Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hong Yuan
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hongyan Yao
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Chen Dunxue
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China.
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Four Mx Genes Identified in Andrias davidianus and Characterization of Their Response to Chinese Giant Salamander Iridovirus Infection. Animals (Basel) 2022; 12:ani12162147. [PMID: 36009736 PMCID: PMC9405346 DOI: 10.3390/ani12162147] [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: 06/01/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Amphibians, including Andrias davidianus, are declining worldwide partly due to infectious diseases. The Myxovirus resistance (Mx) gene is a typical interferon (IFN)-stimulated gene (ISG) involved in the antiviral immunity. Therefore, knowledge regarding the antiviral immunity of A. davidianus can be used for improved reproduction in captivity and protection in the wild. In this study, we amplified and characterized four different A. davidianus Mx genes (adMx) and generated temporal mRNA expression profiles in healthy and Chinese giant salamander iridovirus (GSIV) infected A. davidianus by qualitative real-time PCR (qPCR). The four adMx genes ranged in length from 2008 to 2840 bp. The sequences revealed conserved protein domains including the dynamin superfamily signature motif and the tripartite guanosine-5-triphosphate (GTP)-binding motif. Gene and deduced amino acid sequence alignment revealed relatively high sequence identity with the Mx genes and proteins of other vertebrates. In phylogenetic analysis, the adMx genes clustered together, but also clustered closely with those of fish species. The four adMx genes were broadly expressed in healthy A. davidianus, but were differentially expressed in the spleen during the GSIV infection. Our results show that the adMx genes share major structural features with their homologs, suggesting similar functions to those in other species.
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Li Y, Fan Y, Zhou Y, Jiang N, Xue M, Meng Y, Liu W, Zhang J, Lin G, Zeng L. Bcl-xL Reduces Chinese Giant Salamander Iridovirus-Induced Mitochondrial Apoptosis by Interacting with Bak and Inhibiting the p53 Pathway. Viruses 2021; 13:v13112224. [PMID: 34835028 PMCID: PMC8622046 DOI: 10.3390/v13112224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023] Open
Abstract
Chinese giant salamander iridovirus (GSIV) infection could lead to mitochondrial apoptosis in this animal, a process that involves B-cell lymphoma-2 (BCL-2) superfamily molecules. The mRNA expression level of Bcl-xL, a crucial antiapoptotic molecule in the BCL-2 family, was reduced in early infection and increased in late infection. However, the molecular mechanism remains unknown. In this study, the function and regulatory mechanisms of Chinese giant salamander (Andrias davidianus) Bcl-xL (AdBcl-xL) during GSIV infection were investigated. Western blotting assays revealed that the level of Bcl-xL protein was downregulated markedly as the infection progressed. Plasmids expressing AdBcl-xL or AdBcl-xL short interfering RNAs were separately constructed and transfected into Chinese giant salamander muscle cells. Confocal microscopy showed that overexpressed AdBcl-xL was translocated to the mitochondria after infection with GSIV. Additionally, flow cytometry analysis demonstrated that apoptotic progress was reduced in both AdBcl-xL-overexpressing cells compared with those in the control, while apoptotic progress was enhanced in cells silenced for AdBcl-xL. A lower number of copies of virus major capsid protein genes and a reduced protein synthesis were confirmed in AdBcl-xL-overexpressing cells. Moreover, AdBcl-xL could bind directly to the proapoptotic molecule AdBak with or without GSIV infection. In addition, the p53 level was inhibited and the mRNA expression levels of crucial regulatory molecules in the p53 pathway were regulated in AdBcl-xL-overexpressing cells during GSIV infection. These results suggest that AdBcl-xL plays negative roles in GSIV-induced mitochondrial apoptosis and virus replication by binding to AdBak and inhibiting p53 activation.
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Affiliation(s)
- Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Jingjing Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ge Lin
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.L.); (Y.F.); (Y.Z.); (N.J.); (M.X.); (Y.M.); (W.L.); (J.Z.); (G.L.)
- Correspondence: ; Tel.: +86-027-81785190
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7
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Jiang N, Fan Y, Zhou Y, Meng Y, Liu W, Li Y, Xue M, Robert J, Zeng L. The Immune System and the Antiviral Responses in Chinese Giant Salamander, Andrias davidianus. Front Immunol 2021; 12:718627. [PMID: 34675918 PMCID: PMC8524050 DOI: 10.3389/fimmu.2021.718627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/16/2021] [Indexed: 12/25/2022] Open
Abstract
The Chinese giant salamander, belonging to an ancient amphibian lineage, is the largest amphibian existing in the world, and is also an important animal for artificial cultivation in China. However, some aspects of the innate and adaptive immune system of the Chinese giant salamander are still unknown. The Chinese giant salamander iridovirus (GSIV), a member of the Ranavirus genus (family Iridoviridae), is a prominent pathogen causing high mortality and severe economic losses in Chinese giant salamander aquaculture. As a serious threat to amphibians worldwide, the etiology of ranaviruses has been mainly studied in model organisms, such as the Ambystoma tigrinum and Xenopus. Nevertheless, the immunity to ranavirus in Chinese giant salamander is distinct from other amphibians and less known. We review the unique immune system and antiviral responses of the Chinese giant salamander, in order to establish effective management of virus disease in Chinese giant salamander artificial cultivation.
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Affiliation(s)
- Nan Jiang
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
- Department of Microbiology and Immunology, University of Rochester Medical Center, New York, NY, United States
| | - Yuding Fan
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yong Zhou
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yan Meng
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Wenzhi Liu
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yiqun Li
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Mingyang Xue
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, New York, NY, United States
| | - Lingbing Zeng
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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Full-length transcriptome assembly of Andrias davidianus (Amphibia: Caudata) skin via hybrid sequencing. Biosci Rep 2021; 41:229267. [PMID: 34282833 PMCID: PMC8329649 DOI: 10.1042/bsr20210511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The Chinese giant salamander, Andrias davidianus, is the largest amphibian species in the world; it is thus an economically and ecologically important species. The skin of A. davidianus exhibits complex adaptive structural and functional adaptations to facilitate survival in aquatic and terrestrial ecosystems. Here, we report the first full-length amphibian transcriptome from the dorsal skin of A. davidianus, which was assembled using hybrid sequencing and the PacBio and Illumina platforms. A total of 153,038 transcripts were hybrid assembled (mean length of 2039 bp and N50 of 2172 bp), and 133,794 were annotated in at least one database (nr, Swiss-Prot, KEGG, KOGs, GO, and nt). A total of 58,732, 68,742, and 115,876 transcripts were classified into 24 KOG categories, 1903 GO term categories, and 46 KEGG pathways (level 2), respectively. A total of 207,627 protein-coding regions, 785 transcription factors, 27,237 potential long non-coding RNAs, and 8299 simple sequence repeats were also identified. The hybrid-assembled transcriptome recovered more full-length transcripts, had a higher N50 contig length, and a higher annotation rate of unique genes compared with that assembled in previous studies using next-generation sequencing. The high-quality full-length reference gene set generated in this study will help elucidate the genetic characteristics of A. davidianus skin and aid the identification of functional skin proteins.
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Gao XC, Niu SH, Huang Y, Xiong JL, Ren HT. Transcriptome Profiles in the Spleen of the Chinese Giant Salamander (Andrias davidianus) Challenged with Citrobacter freundii. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Li Y, Liu Y, Zhou Y, Liu W, Fan Y, Jiang N, Xue M, Meng Y, Zeng L. Bid is involved in apoptosis induced by Chinese giant salamander iridovirus and contributes to the viral replication in an amphibian cell line. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103935. [PMID: 33242566 DOI: 10.1016/j.dci.2020.103935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Bid is a pro-apoptotic BH3-only member of the Bcl-2 superfamily that functions to link the extrinsic apoptotic pathway and the mitochondrial amplification loop of the intrinsic pathway. In this study, the expression and functions of Chinese giant salamander (Andrias davidianus) Bid (AdBid) were investigated. The AdBid cDNA sequence contains an open reading frame (ORF) of 576 nucleotides, encoding a putative protein of 191 aa. AdBid possesses the conserved BH3 interacting domain and shared 34-52% sequence identities with other amphibian Bid. mRNA expression of AdBid was most abundant in muscle. The expression level of AdBid in Chinese giant salamander muscle, kidney and spleen significantly increased after Chinese giant salamander iridovirus (GSIV) infection. Additionally, a plasmid expressing AdBid was constructed and transfected into the Chinese giant salamander muscle cell line (GSM cells). The morphology and cytopathic effect (CPE) and apoptotic process in AdBid over-expressed GSM cells was significantly enhanced during GSIV infection compared with that in control cells. Moreover, a higher level of the virus major capsid protein (MCP) gene copies and protein synthesis was confirmed in the AdBid over-expressed cells. These results indicated that AdBid played a positive role in GSIV induced apoptosis and the viral replication. This study may contribute to the better understanding on the infection mechanism of iridovirus-induced apoptosis.
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Affiliation(s)
- Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Yanan Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
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Kim A, Yoon D, Lim Y, Roh HJ, Kim S, Park CI, Kim HS, Cha HJ, Choi YH, Kim DH. Co-Expression Network Analysis of Spleen Transcriptome in Rock Bream ( Oplegnathus fasciatus) Naturally Infected with Rock Bream Iridovirus (RBIV). Int J Mol Sci 2020; 21:ijms21051707. [PMID: 32131541 PMCID: PMC7084886 DOI: 10.3390/ijms21051707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/12/2022] Open
Abstract
Rock bream iridovirus (RBIV) is a notorious agent that causes high mortality in aquaculture of rock bream (Oplegnathus fasciatus). Despite severity of this virus, no transcriptomic studies on RBIV-infected rock bream that can provide fundamental information on protective mechanism against the virus have been reported so far. This study aimed to investigate physiological mechanisms between host and RBIV through transcriptomic changes in the spleen based on RNA-seq. Depending on infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as control (0C), heavy infected fish at week 0 (0H), heavy mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and light infected fish at week 3 (3L). We explored clusters from 35,861 genes with Fragments Per Kilo-base of exon per Million mapped fragments (FPKM) values of 0.01 or more through signed co-expression network analysis using WGCNA package. Nine of 22 modules were highly correlated with viral infection (|gene significance (GS) vs. module membership (MM) |> 0.5, p-value < 0.05). Expression patterns in selected modules were divided into two: heavy infected (0H and 0MH) and control and light-infected groups (0C, 3C, and 3L). In functional analysis, genes in two positive modules (5448 unigenes) were enriched in cell cycle, DNA replication, transcription, and translation, and increased glycolysis activity. Seven negative modules (3517 unigenes) built in this study showed significant decreases in the expression of genes in lymphocyte-mediated immune system, antigen presentation, and platelet activation, whereas there was significant increased expression of endogenous apoptosis-related genes. These changes lead to RBIV proliferation and failure of host defense, and suggests the importance of blood cells such as thrombocytes and B cells in rock bream in RBIV infection. Interestingly, a hub gene, pre-mRNA processing factor 19 (PRPF19) showing high connectivity (kME), and expression of this gene using qRT-PCR was increased in rock bream blood cells shortly after RBIV was added. It might be a potential biomarker for diagnosis and vaccine studies in rock bream against RBIV. This transcriptome approach and our findings provide new insight into the understanding of global rock bream-RBIV interactions including immune and pathogenesis mechanisms.
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Affiliation(s)
- Ahran Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Dahye Yoon
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea
| | - Yunjin Lim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Hazardous Substances Analysis Division, Gwangju Regional Office of Food and Drug Safety, Gwangju 61012, Korea
| | - Heyong Jin Roh
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
| | - Suhkmann Kim
- Department of Chemistry, Center for Proteome Biophysics, and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Korea; (A.K.); (D.Y.); (S.K.)
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, Tongyeong 53064, Korea;
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea;
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan 47227, Korea;
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (Y.L.); (H.J.R.)
- Correspondence: ; Tel.: +82-51-629-5945
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Li Y, Jiang N, Fan Y, Zhou Y, Liu W, Xue M, Meng Y, Zeng L. Chinese Giant Salamander ( Andrias davidianus) Iridovirus Infection Leads to Apoptotic Cell Death through Mitochondrial Damage, Caspases Activation, and Expression of Apoptotic-Related Genes. Int J Mol Sci 2019; 20:ijms20246149. [PMID: 31817556 PMCID: PMC6940751 DOI: 10.3390/ijms20246149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Chinese giant salamander iridovirus (GSIV) is the causative pathogen of Chinese giant salamander (Andrias davidianus) iridovirosis, leading to severe infectious disease and huge economic losses. However, the infection mechanism by GSIV is far from clear. In this study, a Chinese giant salamander muscle (GSM) cell line is used to investigate the mechanism of cell death during GSIV infection. Microscopy observation and DNA ladder analysis revealed that DNA fragmentation happens during GSIV infection. Flow cytometry analysis showed that apoptotic cells in GSIV-infected cells were significantly higher than that in control cells. Caspase 8, 9, and 3 were activated in GSIV-infected cells compared with the uninfected cells. Consistently, mitochondria membrane potential (MMP) was significantly reduced, and cytochrome c was released into cytosol during GSIV infection. p53 expression increased at an early stage of GSIV infection and then slightly decreased late in infection. Furthermore, mRNA expression levels of pro-apoptotic genes participating in the extrinsic and intrinsic pathway were significantly up-regulated during GSIV infection, while those of anti-apoptotic genes were restrained in early infection and then rose in late infection. These results collectively indicate that GSIV induces GSM apoptotic cell death involving mitochondrial damage, caspases activation, p53 expression, and pro-apoptotic molecules up-regulation.
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Geng X, Guo J, Zang X, Chang C, Shang H, Wei H, Xu C. Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus). Sci Rep 2019; 9:16415. [PMID: 31712686 PMCID: PMC6848178 DOI: 10.1038/s41598-019-50909-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus, CGS) is the largest extant amphibian species in the world. Global quantitative proteome analysis of multiple tissues would indicate tissue-specific physiological processes and clarify the function of each protein from a whole-organism perspective. This study performed proteome analysis of eleven tissues collected from adult CGSs using iTRAQ coupled with LC-MS/MS technology. Based on the predicted protein database from previously obtained CGS transcriptome data, 2153 proteins were identified for subsequent analysis. A weighted gene co-expression network analysis (WGCNA) clustered 2153 proteins into 17 co-expressed modules, which will be useful for predicting the functions of unannotated proteins. The protein levels of molecular complexes with housekeeping functions, such as ribosomes, spliceosomes and mitochondrial respiratory chain complexes, were tightly regulated in different tissues of the CGS, as they are in mammalian tissues. Transcription regulator, pathway and bio-functional analysis of tissue-specific proteins showed that highly expressed proteins largely reflected the physiological functions of specific tissues. Our data, as an initial atlas of protein expression of an amphibian species, will be useful for further molecular biology research on CGS.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.,Henan Key Laboratory of immunology and targeted therapy, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Cuifang Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Wei
- The Engineering Technology Research Center for Germ-free and Genome-editing animal, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.
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Yong Huang, Chen H, Gao X, Sun X. Identification and Сharacteristics of Conserved miRNA in Testis Tissue from Chinese Giant Salamander (Andrias davidianus) by Deep Sequencing. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201902016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Jiang N, Fan Y, Zhou Y, Wang W, Ma J, Zeng L. Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii). Sci Rep 2018; 8:17925. [PMID: 30560883 PMCID: PMC6298973 DOI: 10.1038/s41598-018-36376-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
The hybrid sturgeon (Huso dauricus × Acipenser schrenckii) is an economically important species in China. With the increasing aquaculture of hybrid sturgeon, the bacterial diseases are a great concern of the industry. In this study, de novo sequencing was used to compare the difference in transcriptome in spleen of the infected and mock infected sturgeon with Aeromonas hydrophila. Among 187,244 unigenes obtained, 87,887 unigenes were annotated and 1,147 unigenes were associated with immune responses genes. Comparative expression analysis indicated that 2,723 differently expressed genes between the infected and mock-infected group were identified, including 1,420 up-regulated and 1,303 down-regulated genes. 283 differently expressed anti-bacterial immune related genes were scrutinized, including 168 up-regulated and 115 down-regulated genes. Ten of the differently expressed genes were further validated by qRT-PCR. In this study, toll like receptors (TLRs) pathway, NF-kappa B pathway, class A scavenger receptor pathway, phagocytosis pathway, mannose receptor pathway and complement pathway were shown to be up-regulated in Aeromonas hydrophila infected hybrid sturgeon. Additionally, 65,040 potential SSRs and 2,133,505 candidate SNPs were identified from the hybrid sturgeon spleen transcriptome. This study could provide an insight of host immune genes associated with bacterial infection in hybrid sturgeon.
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Affiliation(s)
- Nan Jiang
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China
| | - Yuding Fan
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China
| | - Yong Zhou
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China
| | - Weiling Wang
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China
| | - Jie Ma
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China
| | - Lingbing Zeng
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, P. R. China.
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16
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Jiang N, Fan Y, Zhou Y, Liu W, Robert J, Zeng L. Rag1 and rag2 gene expressions identify lymphopoietic tissues in juvenile and adult Chinese giant salamander (Andrias davidianus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:24-35. [PMID: 29800626 DOI: 10.1016/j.dci.2018.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/21/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Rag1 and rag2 are two closely linked recombination activating genes required for V(D)J recombination of antigen receptors in immature lymphocytes, whose expression can serve as marker to identify the lymphopoietic tissues. To study the development of lymphopoietic tissues in Chinese giant salamander (Andrias davidianus), the Chinese giant salamander rag1 and rag2 coding sequences were cloned and determined. High transcript levels of rag1 and rag2 were co-detected in the thymus before 14 months of age, whereas levels were lower in spleen, liver and kidney at all stage of development. The spatial expression patterns of rag1 and rag2 were studied in combination with igY and tcrβ gene expression using in situ hybridization. Significant transcript signals for rag1, rag2, tcrβ and igY were detected not only in the thymus and spleen but also the liver and kidney of juvenile and adult Chinese giant salamanders, which suggests that cells of lymphocyte lineage are present in multiple tissues of the Chinese giant salamander. This implies that lymphopoiesis may take place in these tissues. The tissue morphology of thymus suggested that the branched thymic primordium developed into mature organ with the development of thymocyte from juvenile to adult. These results not only confirm that as expected the thymus and spleen are primordial lymphopoietic tissues but also suggest that the liver and kidney provide site of lymphocyte differentiation in Chinese giant salamander.
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Affiliation(s)
- Nan Jiang
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yuding Fan
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yong Zhou
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Wenzhi Liu
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, New York 14642, USA.
| | - Lingbing Zeng
- Division of Fish Disease, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
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17
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Hu Q, Meng Y, Wang D, Tian H, Xiao H. Characterization and function of the T-box 1 gene in Chinese giant salamander Andrias davidianus. Genomics 2018; 111:1351-1359. [PMID: 30244141 DOI: 10.1016/j.ygeno.2018.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/07/2018] [Accepted: 09/14/2018] [Indexed: 11/25/2022]
Abstract
We characterized the Andrias davidianus T-box 1 (Tbx1) gene. Tbx1 expression was high in testis and low in other examined tissues. Immunohistochemistry detected tbx1 expression in somatic and germ cells 62 days post-hatching (dph), prior to gonad differentiation. At 210 dph, after gonad differentiation, tbx1 was expressed in spermatogonia and testis somatic cells and in granulosa cells in ovary. Tbx1 expression was up-regulated in ovary after high temperature treatment. In the neomale, tbx1 expression showed a similar profile to normal males, and vice-versa for genetic male. Over-expression of tbx1 in females after injection of TBX1 protein down-regulated the female-biased genes cyp19a and foxl2 and up-regulated the male-biased amh gene. When tbx1 was knocked down by tbx1/siRNA, cyp19a and foxl2 expression was up-regulated, and expression of amh, cyp26a, dmrt1, and wt1 was down-regulated. Results suggest that tbx1 influenced sex-related gene expression and participates in regulation of A. davidianus testis development.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Dan Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
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Meng Y, Tian H, Hu Q, Liang H, Zeng L, Xiao H. MicroRNA repertoire and comparative analysis of Andrias davidianus infected with ranavirus using deep sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:108-114. [PMID: 29626489 DOI: 10.1016/j.dci.2018.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Andrias davidianus is a large and economically important amphibian in China. Ranavirus infection causes serious losses in A. davidianus farming industry. MicroRNA mediated host-pathogen interactions are important in antiviral defense. In this study, five small-RNA libraries from ranavirus infected and non-infected A. davidianus spleens were sequenced using high throughput sequencing. The miRNA expression pattern, potential functions, and target genes were investigated. In total, 1356 known and 431 novel miRNAs were discovered. GO and KEGG analysis revealed that certain miRNA target genes are associated with apoptotic, signal pathway, and immune response categories. Analysis identified 82 downregulated and 9 upregulated differentially expressed miRNAs, whose putative target genes are involved in pattern-recognition receptor signaling pathways and immune response. These findings suggested miRNAs play key roles in A. davidianus's response to ranavirus and could provide a reference for further miRNA functional identification, leading to novel approaches to improve A. davidianus ranavirus resistance.
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Affiliation(s)
- Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China
| | - Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hubei, 430223, China.
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Ke F, Gui JF, Chen ZY, Li T, Lei CK, Wang ZH, Zhang QY. Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander. BMC Genomics 2018; 19:211. [PMID: 29558886 PMCID: PMC5861657 DOI: 10.1186/s12864-018-4596-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Background Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio with a genome of 105.79 kb and Andrias davidianus ranavirus (ADRV), from diseased Chinese giant salamander (CGS) with a genome of 106.73 kb, contains 99% homologous genes. Results To uncover the differences in virus replication and host responses under interspecies infection, we analyzed transcriptomes of CGS challenged with RGV and ADRV in different time points (1d, 7d) for the first time. A total of 128,533 unigenes were obtained from 820,858,128 clean reads. Transcriptome analysis revealed stronger gene expression of RGV than ADRV at 1 d post infection (dpi), which was supported by infection in vitro. RGV replicated faster and had higher titers than ADRV in cultured CGS cell line. RT-qPCR revealed the RGV genes including the immediate early gene (RGV-89R) had higher expression level than that of ADRV at 1 dpi. It further verified the acute infection of RGV in interspecies infection. The number of differentially expressed genes and enriched pathways from RGV were lower than that from ADRV, which reflected the variant host responses at transcriptional level. No obvious changes of key components in pathway “Antigen processing and presentation” were detected for RGV at 1 dpi. Contrarily, ADRV infection down-regulated the expression levels of MHC I and CD8. The divergent host immune responses revealed the differences between interspecies and natural infection, which may resulted in different fates of the two viruses. Altogether, these results revealed the differences in transcriptome responses among ranavirus interspecies infection of amphibian and new insights in DNA virus-host interactions in interspecies infection. Conclusion The DNA virus (RGV) not only expressed self-genes and replicated quickly after entry into host under interspecies infection, but also avoided the over-activation of host responses. The strategy could gain time for the survival of interspecies pathogen, and may provide opportunity for its adaptive evolution and interspecies transmission. Electronic supplementary material The online version of this article (10.1186/s12864-018-4596-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhong-Yuan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Cun-Ke Lei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zi-Hao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Huang Y, Xiong JL, Gao XC, Sun XH. Transcriptome analysis of the Chinese giant salamander ( Andrias davidianus) using RNA-sequencing. GENOMICS DATA 2017; 14:126-131. [PMID: 29159068 PMCID: PMC5675895 DOI: 10.1016/j.gdata.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/21/2017] [Accepted: 10/21/2017] [Indexed: 12/21/2022]
Abstract
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. Of these, 6323 unigenes were annotated in all database and 39,672 unigenes were annotated in at least one database. Blasted with KEGG pathway, 10,958 unigenes were annotated, and it was divided into 343 categories according to different pathways. In addition, we also identified 29,790 SSRs. This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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Geng X, Li W, Shang H, Gou Q, Zhang F, Zang X, Zeng B, Li J, Wang Y, Ma J, Guo J, Jian J, Chen B, Qiao Z, Zhou M, Wei H, Fang X, Xu C. A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. Gigascience 2017; 6:1-7. [PMID: 28204480 PMCID: PMC5467019 DOI: 10.1093/gigascience/gix006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/07/2017] [Indexed: 01/11/2023] Open
Abstract
Background Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled. Results We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog. Conclusions These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | | | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Qiang Gou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jiang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Wang
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Ji Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | | | - Bing Chen
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Zhigang Qiao
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Minghui Zhou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | | | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
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22
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Chen R, Du J, Ma L, Wang LQ, Xie SS, Yang CM, Lan XY, Pan CY, Dong WZ. Comparative microRNAome analysis of the testis and ovary of the Chinese giant salamander. Reproduction 2017. [PMID: 28630098 DOI: 10.1530/rep-17-0109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of the important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data. We found that many miRNAs and other small RNAs such as piRNA and tsRNA were abundant in CGS tissue. A total of 757 and 756 unique miRNAs were annotated as miRNA candidates in the ovary and testis respectively. We identified 145 miRNAs in CGS ovary and 155 miRNAs in CGS testis that were homologous to those in Xenopus laevis ovary and testis respectively. Forty-five miRNAs were more highly expressed in ovary than in testis and 21 miRNAs were more highly expressed in testis than in ovary. The expression profiles of the selected miRNAs (miR-451, miR-10c, miR-101, miR-202, miR-7a and miR-499) had their own different roles in other eight tissues and different development stages of testis and ovary, suggesting that these miRNAs play vital regulatory roles in sexual differentiation, gametogenesis and development in CGS. To our knowledge, this is the first study to reveal miRNA profiles that are related to male and female CGS gonads and provide insights into sex differences in miRNA expression in CGS.
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Affiliation(s)
- Rui Chen
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Jian Du
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Lin Ma
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Li-Qing Wang
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Sheng-Song Xie
- Key Lab of Agricultural Animal GeneticsBreeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Chang-Ming Yang
- Animal Husbandry and Veterinary Station of Chenggu CountyHanzhong, China
| | - Xian-Yong Lan
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Chuan-Ying Pan
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
| | - Wu-Zi Dong
- College of Animal Science and TechnologyNorthwest A& F University, Yangling, China
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23
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Molecular characterization, expression and evolutionary analysis of 3 cathepsin genes (CTSH, CTSL and CTSS) from Chinese giant salamander (Andrias davidianus). GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Huang Y, Gao XC, Xiong JL, Ren HT, Sun XH. Sequencing and de novo transcriptome assembly of the Chinese giant salamander ( Andrias davidianus). GENOMICS DATA 2017; 12:109-110. [PMID: 28413781 PMCID: PMC5384290 DOI: 10.1016/j.gdata.2017.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/21/2017] [Accepted: 03/26/2017] [Indexed: 11/28/2022]
Abstract
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690 bp and N50 of 1263 bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
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25
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Wei J, Liu B, Fan S, Li H, Chen M, Zhang B, Su J, Meng Z, Yu D. Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis. FISH & SHELLFISH IMMUNOLOGY 2017; 62:247-256. [PMID: 28126621 DOI: 10.1016/j.fsi.2017.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/18/2017] [Accepted: 01/20/2017] [Indexed: 06/06/2023]
Abstract
The pearl oyster Pinctada fucata is commonly cultured for marine pearls in China. To culture pearls, a mantle piece from a donor pearl oyster is grafted with a nucleus into a receptor. This transplanted mantle piece may be rejected by the immune system of the recipient oyster, thus reducing the success of transplantation. However, there have been limited studies about the oyster's immune defense against allograft. In this study, hemocyte transcriptome analysis was performed to detect the immune responses to allograft in P. fucata at 0 h and 48 h after a transplant. The sequencing reaction produced 92.5 million reads that were mapped against the reference genome sequences of P. fucata. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify all immune-related differentially expressed genes (DEGs). Compared with patterns at 0 h, a total of 798 DEGs were identified, including 410 up-regulated and 388 down-regulated genes at 48 h. The expression levels of interleukin receptor and toll-like receptor in hemocytes were increased significantly 48 h post-transplant, indicating that the oyster immune response was induced. Finally, altered levels of 18 randomly selected immune-related DEGs were confirmed by quantitative real-time PCR (qRT-PCR). Our results provide the basis for further analysis of the immune rejection of allotransplantation.
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Affiliation(s)
- Jinfen Wei
- Qinzhou University, Qinzhou 535011, China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Sigang Fan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Haimei Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Mingqiang Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Bo Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Jiaqi Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Zihao Meng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Dahui Yu
- Qinzhou University, Qinzhou 535011, China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou 510300, China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
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26
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Zhao L, Tu J, Zhang Y, Wang J, Yang L, Wang W, Wu Z, Meng Q, Lin L. Transcriptomic analysis of the head kidney of Topmouth culter (Culter alburnus) infected with Flavobacterium columnare with an emphasis on phagosome pathway. FISH & SHELLFISH IMMUNOLOGY 2016; 57:413-418. [PMID: 27601296 DOI: 10.1016/j.fsi.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/03/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Flavobacterium columnare (FC) has caused worldwide fish columnaris disease with high mortality and great economic losses in cultured fish, including Topmouth culter (Culter alburnus). However, the knowledge about the host factors involved in FC infection is little known. In this study, the transcriptomic profiles of the head kidney from Topmouth culter with or without FC infection were obtained using HiSeq™ 2500 (Illumina). Totally 79,641 unigenes with high quality were obtained. Among them, 4037 differently expressed genes, including 1217 up-regulated and 2820 down-regulated genes, were identified and enriched using databases of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differently expressed genes were mainly associated with pathways such as immune response, carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Since phagocytosis is a central mechanism of innate immune response by host cells to defense against infectious agents, genes related to the phagosome pathway were scrutinized and 9 differently expressed phagosome-related genes were identified including 3 up-regulated and 6 down-regulated genes. Five of them were further validated by quantitative real-time polymerase chain reaction (qRT-PCR). This transcriptomic analysis of host genes in response to FC infection provides data towards understanding the infection mechanisms and will shed a new light on the prevention of columnaris.
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Affiliation(s)
- Lijuan Zhao
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China; Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yulei Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jinfu Wang
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China
| | - Ling Yang
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China
| | - Weimin Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zaohe Wu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Qinglei Meng
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China.
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China.
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27
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Zhu R, Du HJ, Li SY, Li YD, Ni H, Yu XJ, Yang YY, Fan YD, Jiang N, Zeng LB, Wang XG. De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis). FISH & SHELLFISH IMMUNOLOGY 2016; 55:699-716. [PMID: 27368537 DOI: 10.1016/j.fsi.2016.06.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.
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Affiliation(s)
- Rong Zhu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - He-Jun Du
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, Hubei 443100, China
| | - Shun-Yi Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ya-Dong Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Hong Ni
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xue-Jing Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yan-Yan Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yu-Ding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Ling-Bing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.
| | - Xing-Guo Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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