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Li X, Lin Y, Li W, Cheng Y, Zhang J, Qiu J, Fu Y. Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila. Int J Mol Sci 2024; 25:6438. [PMID: 38928143 PMCID: PMC11204273 DOI: 10.3390/ijms25126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.
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Affiliation(s)
- Xike Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yue Lin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Wenjuan Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuejuan Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junling Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junqiang Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.L.); (W.L.); (Y.C.); (J.Z.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
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Garcia Neto PG, Titon SCM, Muxel SM, Titon B, Figueiredo ACD, Floreste FR, Lima AS, Assis VR, Gomes FR. Immune and endocrine alterations at the early stage of inflammatory assemblage in toads after stimulation with heat-killed bacteria (Aeromonas hydrophila). Comp Biochem Physiol A Mol Integr Physiol 2024; 291:111606. [PMID: 38354902 DOI: 10.1016/j.cbpa.2024.111606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
The red-leg syndrome in amphibians is a condition commonly associated with the bacteria Aeromonas hydrophila and has led to population declines. However, there is little information concerning the inflammatory assemblage in infected anurans. We evaluated immune and endocrine alterations induced by stimulation with heat-killed A. hydrophila injected in Rhinella diptycha toads. Control animals were not manipulated, while the others were separated into groups that received intraperitoneal injection of 300 μl of saline or heat-killed bacteria: groups A1 (3 × 107 cells), A2 (3 × 108 cells), and A3 (3 × 109 cells). Animals were bled and euthanized six hours post-injection. We evaluated neutrophil: lymphocyte ratio (NLR), plasma bacterial killing ability (BKA), testosterone (T), melatonin (MEL), and corticosterone (CORT) plasma levels. Heat-killed A. hydrophila increased CORT and NLR, and decreased MEL, especially at higher concentrations. There was no effect of treatment on T and BKA. We then selected the saline and A3 groups to conduct mRNA expression of several genes including glucocorticoid receptor (GR), toll-like receptor-4 (TLR-4), interferon-γ (IFN-γ), interleukin (IL)-1β, IL-6, and IL-10. We found higher expression of IL-6, IL-1β, IL-10, and IFN-γ in group A3 compared to the saline group. These results indicate the beginning of an inflammatory assemblage, notably at the two highest concentrations of bacteria, and give a better understanding of how anurans respond to an infection within an integrated perspective, evaluating different physiological aspects. Future studies should investigate later phases of the immune response to elucidate more about the inflammation in amphibians challenged with A. hydrophila.
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Affiliation(s)
- Patrício G Garcia Neto
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil.
| | - Stefanny C M Titon
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Sandra M Muxel
- Laboratório de Neuroimunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes n° 1730, Cidade Universitária, São Paulo, SP CEP 05508-000, Brazil.
| | - Braz Titon
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Aymam C de Figueiredo
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Felipe R Floreste
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Alan S Lima
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Vania R Assis
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil; Global Health and Interdisciplinary Disease Research Center and Center for Genomics, College of Public Health, Interdisciplinary Research Building (IDRB), 3720 Spectrum Boulevard. Tampa, FL 33612-9415, United States. https://twitter.com/VaniaRAssis1
| | - Fernando R Gomes
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão - Travessa 14 - n° 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil.
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Wang L, Wang B, Hu C, Wang C, Gao C, Jiang H, Yan Y. Influences of chronic copper exposure on intestinal histology, antioxidative and immune status, and transcriptomic response in freshwater grouper (Acrossocheilus fasciatus). FISH & SHELLFISH IMMUNOLOGY 2023; 139:108861. [PMID: 37257568 DOI: 10.1016/j.fsi.2023.108861] [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: 04/14/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Copper (Cu) contamination is commonly found in both natural water environments and fish farms, and it can cause severe damage to different fish organs, but Cu-induced intestinal damage has been rarely studied. This study subjected three groups of freshwater grouper (Acrossocheilus fasciatus) (initial weight: 1.56 ± 0.10 g) to 0 mg/L, 0.01 mg/L, and 0.04 mg/L Cu2+ for 30 days, named Con, Cu0.01, and Cu0.04 groups, respectively. The histological observation indicated that the Cu0.04 group caused a significant decrease in villus length, lamina propria width, and muscular thickness compared to the Con group (P < 0.05). Additionally, the Cu0.04 group significantly increased intestinal superoxide dismutase (SOD), glutathione peroxidase (GPx), lysozyme (LZM) activities, as well as malondialdehyde (MDA) content than the Con group (P < 0.05). Meanwhile, the Cu0.01 and Cu0.04 groups showed significantly increased immunoglobulin M (IgM), complement 3 (C3), and glutathione (GSH) contents than the Con group (P < 0.05). Transcriptomic analysis revealed a total of 101 differentially expressed genes (DEGs), including 47 up-regulated and 54 down-regulated DEGs, were identified between the Cu0.04 and Con groups. Notably, the DEGs were mainly related to intestinal structure construction, immune functions, apoptosis, and resistance to DNA damage and pathogen infection. The findings suggest that chronic Cu exposure caused intestinal histological alterations, activated the antioxidative and immune systems, and induced systematic adaptation to cope with the physical barrier injury, DNA damage, and potential pathogen growth.
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Affiliation(s)
- Lei Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China; Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, 241002, China.
| | - Bin Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Cong Hu
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Chenyang Wang
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - Chang Gao
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China
| | - He Jiang
- Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China.
| | - Yunzhi Yan
- School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China; Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, 241002, China; Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, 241002, China.
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Huang Y, Ge R, Lou G, Jiang N, Zhu X, Guo Y, Liu H, Liu X, Chen X. The influence of dietary Coenzyme Q10 on growth performance, antioxidant capacity and resistance against Aeromonas hydrophila of juvenile European eel (Anguilla anguilla). FISH & SHELLFISH IMMUNOLOGY 2023; 138:108834. [PMID: 37207885 DOI: 10.1016/j.fsi.2023.108834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
The present study was conducted to investigate the effects of dietary Coenzyme Q10 (CoQ10) on the growth performance, body composition, digestive enzyme activity, antioxidant capacity, intestinal histology, immune-antioxidant gene expression and disease resistance of juvenile European eel (Anguilla anguilla). Fish were fed a diet supplemented with CoQ10 at concentrations of 0, 40, 80 and 120 mg/kg for 56 days. The results indicated that dietary CoQ10 supplementation did not significantly affect final body weight (FBW), survival rate (SR), weight gain (WG), feed rate (FR), viscerosomatic index (VSI) or hepatosomatic index (HSI) among all experimental groups. However, the highest FBW, WG and SR were found in the 120 mg/kg CoQ10 group. Dietary 120 mg/kg CoQ10 markedly improved feed efficiency (FE) and the protein efficiency ratio (PER). The crude lipids in the body and triglycerides (TG) and total cholesterol (TC) in serum were obviously lower in the 120 mg/kg CoQ10 group than in the control group. For digestive enzymes, protease activity in the intestine was markedly boosted in the 120 mg/kg CoQ10 group. The serum activities of SOD, CAT and GST in the 120 mg/kg CoQ10 group were significantly higher than those in the control group. Dietary 120 mg/kg CoQ10 efficiently enhanced superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione S-transferase (GST) activities in the liver, while the malondialdehyde (MDA) content was significantly decreased. No significant histological changes in the liver were identified in any group. Dietary supplementation with 120 mg/kg CoQ10 improved antioxidant capacity and immunity by upregulating the expression of cyp1a, sod, gst, lysC, igma1, igmb1 and irf3 in the liver. Furthermore, the cumulative survival rate of juvenile European eel against challenge with Aeromonas hydrophila was significantly elevated in the 80 and 120 mg/kg CoQ10 supplemented groups. Conclusively, our study suggested that supplementing the diet of juvenile European eel with CoQ10 at a concentration of 120 mg/kg could promote their feed utilization, fat reduction, antioxidant capacity, digestibility, immune-antioxidant gene expression and resistance to Aeromonas hydrophila without negative effects on fish health status.
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Affiliation(s)
- Ying Huang
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruxiang Ge
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gege Lou
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Nengzuo Jiang
- Fujian Institute of Testing Technology, Fuzhou, 350003, China
| | - Xiaoming Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yazhe Guo
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haokun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xuanyu Liu
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Transcriptome Analysis of Immune Responses and Metabolic Regulations of Chinese Soft-Shelled Turtle (Pelodiscus sinensis) against Edwardsiella tarda Infection. FISHES 2022. [DOI: 10.3390/fishes7020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquatic species in southern China that is threatened by many serious diseases. Edwardsiella tarda is one of the highly pathogenic bacteria that cause the white abdominal shell disease. Yet, little is known about the immune and metabolic responses of the Chinese soft-shelled turtle against E. tarda infection. In the paper, gene expression profiles in the turtle liver were obtained to study the immune responses and metabolic regulations induced by E. tarda infection using RNA sequencing. A total of 3908 differentially expressed unigenes between the experimental group and the control group were obtained by transcriptome analysis, among them, were the significantly upregulated unigenes and downregulated unigenes 2065 and 1922, respectively. Further annotation and analysis revealed that the DEGs were mainly enriched in complement and coagulation cascades, phagosome, and steroid hormone biosynthesis pathways, indicating that they were mainly associated with defense mechanisms in the turtle liver against E. tarda four days post infection. For the first time, we reported on the gene profile of anti-E. tarda response in the soft-shelled turtle, and our research might provide valuable data to support further study on anti-E. tarda defense mechanisms in turtles
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Lo CC, Liao WY, Chou MC, Wu YY, Yeh TH, Lo HR. Overexpression of Resistance-Nodulation-Division Efflux Pump Genes Contributes to Multidrug Resistance in Aeromonas hydrophila Clinical Isolates. Microb Drug Resist 2021; 28:153-160. [PMID: 34609911 DOI: 10.1089/mdr.2021.0084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aeromonas hydrophila is a Gram-negative bacterium that is a critical causative agent of infections in fish and is occasionally responsible for human infections following contact with contaminated water or food. Currently, the extensive use of antibiotics in clinical practice has led to increased number of isolates of multidrug-resistant (MDR) Aeromonas and has posed a serious public health challenge. The efflux pump system is a critical mechanism of antibiotic resistance in most Gram-negative bacteria. However, the role of resistance-nodulation-division (RND)-type efflux pumps in MDR A. hydrophila is not fully understood. We aimed to evaluate the contribution of the RND efflux pump system to MDR A. hydrophila clinical isolates. PCR results indicated a considerable variation in the presence of RND efflux pump genes in clinical isolates compared to that of the environmental reference strain ATCC7966T. Compared to non-MDR clinical isolates, the expression levels of three putative RND efflux pump genes, AHA0021, AHA1320, and AheB, were significantly elevated in MDR strains. The minimal inhibitory concentrations of piperacillin/tazobactam, imipenem, erythromycin, and polymyxin B were significantly reduced by phenylalanine-arginine β-naphthylamide (PAβN), further supporting the contribution of the RND efflux system in MDR A. hydrophila. We provided evidence supporting the contribution of the RND efflux system to multidrug resistance in A. hydrophila clinical isolates. Further studies are warranted to elucidate the detailed mechanisms that confer intrinsic resistance to antimicrobials in A. hydrophila.
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Affiliation(s)
- Chung-Cheng Lo
- Department of Internal Medicine, Kaohsiung Veterans General Hospital Pingtung Branch, Pingtung, Taiwan
| | - Wan-Yu Liao
- Department of Medical Laboratory Science and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Miao-Chen Chou
- Department of Medical Laboratory Science and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Yu-Yi Wu
- Department of Medical Laboratory Science and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Tzu-Hui Yeh
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital Pingtung Branch, Pingtung, Taiwan
| | - Horng-Ren Lo
- Department of Medical Laboratory Science and Biotechnology, Fooyin University, Kaohsiung, Taiwan
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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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Zheng R, Wu M, Wang H, Chai L, Peng J. Copper-induced sublethal effects in Bufo gargarizans tadpoles: growth, intestinal histology and microbial alternations. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:502-513. [PMID: 33587250 DOI: 10.1007/s10646-021-02356-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Copper (Cu) is one of the environmental contaminations which can pose significant risks for organisms. The current study explores the effects of Cu exposure on the growth, intestinal histology and microbial ecology in Bufo gargarizans. The results revealed that 0.5-1 μM Cu exposure induced growth retardation (including reduction of total body length and wet weight) and intestinal histological injury (including disordered enterocyte, changes in the villi and vacuoles) of tadpoles. Also, high-throughput sequencing analysis showed that Cu exposure caused changes in richness, diversity and structure of intestinal microbiota. Moreover, the composition of intestinal microbiota was altered in tadpoles exposed to different concentrations of Cu. At the phylum level, we observed the abundance of proteobacteria was increased, while the abundance of fusobacteria was decreased in the intestinal microbiota of tadpoles exposed to 1 μM Cu. At the genus level, a reduced abundance of kluyvera and aeromonas was observed in the intestinal microbiota of tadpoles under the exposure of 0-0.5 μM Cu. Finally, functional predictions revealed that tadpoles exposed to copper may be at a higher risk of developing metabolic disorders or diseases. Above all, our results will develop a comprehensive view of the Cu exposure in amphibians and will yield a new consideration for sublethal effects of Cu on aquatic organisms.
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Affiliation(s)
- Rui Zheng
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Minyao Wu
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Hongyuan Wang
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, People's Republic of China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an, 710062, People's Republic of China
| | - Jufang Peng
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
- Basic Experimental Teaching Center, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
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Hu Q, Liu Y, Liao X, Tian H, Ji X, Zhu J, Xiao H. A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 2021; 22:230. [PMID: 33794798 PMCID: PMC8017863 DOI: 10.1186/s12864-021-07550-0] [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: 05/01/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. RESULTS In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. CONCLUSION We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China.
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaolin Liao
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, 430079, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
| | - Xiangshan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Nanning, 530021, Guangxi Province, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, Hubei, China
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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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Pan J, Lian H, Shang M, Jin W, Hao R, Ning Y, Zhang X, Tang Y. Physicochemical properties of Chinese giant salamander (Andrias davidianus) skin gelatin as affected by extraction temperature and in comparison with fish and bovine gelatin. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00512-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Shi Y, Vistro WA, Bai X, Wu R, Chen C, Huang Y, Fazlani SA, Tarique I, Yang P, Chen Q. Effect of seasonal variance on intestinal epithelial barriers and the associated innate immune response of the small intestine of the Chinese soft-shelled turtles. FISH & SHELLFISH IMMUNOLOGY 2020; 97:173-181. [PMID: 31857223 DOI: 10.1016/j.fsi.2019.12.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
It is conceivable that pathological conditions can cause intestinal barrier disruption and innate immune dysfunction. However, very limited information has been reported on the effect of seasonal variance on intestinal barriers and innate immunity. The present study was designed to investigate the seasonal variance in intestinal epithelial barriers and the associated innate immune response of turtle intestines during hibernation and nonhibernation periods. Goblet cells (GCs) demonstrated dynamic actions of the mucosal barrier with strong Muc2 protein expression during hibernation. However, weak Muc2 expression during nonhibernation was confirmed by immunohistochemistry, immunofluorescence and immunoblotting. Furthermore, light and transmission electron microscopy revealed that the hypertrophy of GCs resulted in the hypersecretion of mucus granules (MGs) and created a well-developed mucosal layer during hibernation. The absorptive cells (ACs), forming a physical barrier of tight junctions, and desmosomes were firmly anchored during hibernation. Conversely, during nonhibernation, the integrity of tight junctions, adherence junctions and desmosomes was noticeable expanded, causing increased paracellular permeability. As further confirmation, there was strong zonula occluden-1 (ZO-1) and connexins 43 (Cx43) protein expression during hibernation and weak ZO-1 and Cx43 expression during nonhibernation. Moreover, the expression level of the innate immune response proteins Toll-like receptors 2 and 4 (TLR2 and 4) were enhanced during hibernation and were reduced during nonhibernation. These results provide rich information about the seasonal fluctuations that interrupt intestinal epithelial barriers and innate immune response, which might be essential for protection and intestinal homeostasis.
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Affiliation(s)
- Yonghong Shi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China; Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Waseem Ali Vistro
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Xuebing Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ruizhi Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Chang Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yufei Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Surfaraz Ali Fazlani
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Imran Tarique
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ping Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China.
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13
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Geng X, Zhang L, Zang X, Guo J, Xu C. RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus. Dev Genes Evol 2019; 229:197-206. [PMID: 31734771 DOI: 10.1007/s00427-019-00641-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
The Chinese giant salamander Andrias davidianus is regarded as an ideal model for studying local adaptations, such as longevity, tolerance to starvation, and cutaneous respiration. Transcriptome analysis is useful for studying the large and complex genomes of amphibians. Based on the coding gene set of adult A. davidianus, dozens of A. davidianus-specific genes were identified and three signaling pathway (JAK-STAT, HIF-1, and FoxO) genes were expanded as compared with other amphibians. The results of the pathway analysis of A. davidianus-specific genes indicated that the molecular adaptation of A. davidianus may have required a more rapid evolution of the immune system. Additionally, for the first time, the gene expressions in different parts of the skin tissue were compared. The results of the comparison analysis demonstrated that lateral skin could be more focused on mucus secretion, dorsal skin on immunity and melanogenesis, and abdominal skin on water and salt metabolism. This study provides the first insight into studying longevity and starvation tolerance in A. davidianus, and offers a basis for further investigation of the molecular mechanisms of adaptations in amphibians.
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Affiliation(s)
- Xiaofang Geng
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Lu Zhang
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, 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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14
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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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15
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Pei J, Chen D, Jin W, Geng J, Wang W, Zhang S, Yue T, Zhang H. Structure and mode of action of a novel antibacterial peptide from the blood of Andrias davidianus. Lett Appl Microbiol 2019; 69:312-317. [PMID: 31529504 DOI: 10.1111/lam.13219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022]
Abstract
Andrias davidianus is widely recognized in traditional medicine as a cure-all to treat a plethora of ailments. In a previous study, a novel antibacterial peptide named andricin B was isolated from A. davidianus blood. In this study, we investigated andricin B structure and its mode of action. Circular dichroism spectra suggested that andricin B adopts a random coil state in aqueous solution and a more rigid conformation in the presence of bacteria. Moreover propidium iodide/fluorescein diacetate double staining indicated that bacteria treated with andricin B were not immediately eliminated. Rather, there is a gradual bacterial death, followed by a sublethal stage. Scanning electronic microscope imaging indicates that andricin B might form pores on cell membranes, leading to the release of cytoplasmic contents. These results were consistent with flow cytometry analysis. Furthermore, Fourier transform infrared spectroscopy suggests that andricin B induces changes in the chemical properties in the areas surrounding these "pores" on the cell membranes. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study suggested the new perspectives about the mode of action of antimicrobial peptide (AMP) active against sensitive bacteria. The AMP was able to be in a random coiled state in aqueous solution but to change to a more rigid one in the presence of sensitive bacteria. Exposure to AMP might not lead to immediate death of treated bacteria, rather bacteria concentration decreased gradually flattening at a sublethal stage. These findings will help people to understand better how the AMPs activate against sensitive bacteria.
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Affiliation(s)
- J Pei
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - D Chen
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - W Jin
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - J Geng
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - W Wang
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - S Zhang
- Shaanxi Key Laboratory of Biology and Bioresources, College of Bioscience and Bioengineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - T Yue
- College of Food Science, Northwest University, Xi'an, Shaanxi, China
| | - H Zhang
- College of Food Science, Qilu University of Technology, Shandong, China
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16
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Hu Q, Xiao H, Wang Q, Tian H, Meng Y. Identification and expression of forkhead box genes in the Chinese giant salamander Andrias davidianus. Reprod Fertil Dev 2019; 30:634-642. [PMID: 28945985 DOI: 10.1071/rd17049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/07/2017] [Indexed: 11/23/2022] Open
Abstract
In the present study, 21 forkhead box (Fox) genes were identified in Andrias davidianus, including 13 full-length genes and eight partial sequences. Phylogenetic analysis showed that most were conserved in other investigated amphibians, whereas the Foxk1 gene was found exclusively in A. davidianus. Molecular evolution analysis indicated that most Fox genes underwent purifying selection, whereas two sites of the adFoxp4 gene showed positive selection and were located on the adFoxp4 protein surface. Expression profiles of all Fox genes identified were analysed in the hypothalamic-pituitary-gonad axis by reverse transcription-quantitative polymerase chain reaction. Eighteen genes exhibited sexually dimorphic expression (15 ovary-biased and three testis-biased genes), whereas two genes showed no difference between ovary and testis. Further investigation of 12 selected sexually dimorphic Fox genes showed changes in the expression profile of 11 genes in the ovary of larvae reared at high temperatures (28°C). The results of the present study provide information on Fox genes in an amphibian and suggest that they play key roles in sexual development and reproduction in A. davidianus.
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Affiliation(s)
- Qiaomu Hu
- 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
| | - Qilong Wang
- Tengzhou Fisheries Center, Tengzhou, Shandong, 277500, China
| | - Haifeng Tian
- 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
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17
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Liu T, Han Y, Chen S, Zhao H. Genome-wide identification of Toll-like receptors in the Chinese soft-shelled turtle Pelodiscus sinensis and expression analysis responding to Aeromonas hydrophila infection. FISH & SHELLFISH IMMUNOLOGY 2019; 87:478-489. [PMID: 30716519 DOI: 10.1016/j.fsi.2019.01.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Toll-like receptors (TLRs) recognizing specific pathogen-associated molecular patterns play crucial roles in immune defence against pathogen invasion. Although recent advances in many species have reported the characterization and functional roles of TLRs in innate immunity, systematic knowledge of TLRs is still lacking in the Chinese soft-shelled turtle Pelodiscus sinensis. In this study, a genome-wide search was performed and identified 15 candidate PsTLR family genes in P. sinensis. Protein structure analysis revealed the conserved domain arrangements for these PsTLR proteins. Phylogenetic analysis indicated the evolutionary conservation of TLRs among various species. Additionally, a putative interaction network among PsTLR proteins was proposed and several functional partner proteins involved in TLR signalling pathway were predicted in P. sinensis. Expression profiling showed that these PsTLRs exhibited constitutive expression patterns in different tissues of P. sinensis. Moreover, several genes were highly expressed in the major immune organ spleen. Remarkably, the mRNA levels of PsTLR2-1, PsTLR4 and several TLR signalling molecules were significantly up-regulated in the spleen after Aeromonas hydrophila infection, indicating that PsTLRs and these genes responded to bacterial stress. These results provide rich information for the functional exploration of PsTLRs and will facilitate uncovering the molecular mechanisms underlying immune regulation in P. sinensis.
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Affiliation(s)
- Tengfei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Yawen Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Shulin Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Huiying Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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18
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Tran HB, Lee YH, Guo JJ, Cheng TC. De novo transcriptome analysis of immune response on cobia (Rachycentron canadum) infected with Photobacterium damselae subsp. piscicida revealed inhibition of complement components and involvement of MyD88-independent pathway. FISH & SHELLFISH IMMUNOLOGY 2018; 77:120-130. [PMID: 29578048 DOI: 10.1016/j.fsi.2018.03.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/02/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Cobia, Rachycentron canadum, one of the most important aquatic species in Taiwan, has suffered heavy losses from Photobacterium damselae subsp. piscicida, which is the causal agent of photobacteriosis. In this study, the transcriptomic profiles of livers and spleens from Pdp-infected and non-infected cobia were obtained for the first time by Illumina-based paired-end sequencing method with a focus on immune-related genes. In total, 164,882 high quality unigenes were obtained in four libraries. Following Pdp infection, 7302 differentially expressed unigenes from liver and 8600 differentially expressed unigenes from spleen were identified. Twenty-seven of the differently expressed genes were further validated by RT-qPCR (average correlation coefficient 0.839, p-value <0.01). Results indicated a negative regulation of complement components and increased expression of genes involved in MyD88-independent pathway. Moreover, a remarkable finding was the increased expression of IL-10, implying an inadequacy of immune responses. This study not only characterized several putative immune pathways, but also provided a better understanding of the molecular responses to photobacteriosis in cobia.
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Affiliation(s)
- Hung Bao Tran
- Laboratory of Molecular Fish Immunology and Genetics, Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Yen-Hung Lee
- Tungkang Biotechnology Research Center, Fisheries Research Institute, Pingtung 92845, Taiwan
| | - Jiin-Ju Guo
- Tungkang Biotechnology Research Center, Fisheries Research Institute, Pingtung 92845, Taiwan
| | - Ta-Chih Cheng
- Laboratory of Molecular Fish Immunology and Genetics, Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan; Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
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19
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Structural characterization and in vitro antioxidant activities of chondroitin sulfate purified from Andrias davidianus cartilage. Carbohydr Polym 2018; 196:398-404. [PMID: 29891311 DOI: 10.1016/j.carbpol.2018.05.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/12/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Origin and manufacturing process are key factors affecting the biological activities of chondroitin sulfate (CS), which can be utilized as a nutraceutical in dietary supplements. Herein, we extracted and purified CS from the cartilage of artificially breeding Andrias davidianus (ADCS), i.e., Chinese giant salamander (CGS), one of the prospective functional food source materials in China. Low molecular weight CS (LMWADCS) was then prepared by free radical depolymerization of ADCS. High-performance gel permeation chromatography (HPGPC) analysis showed that the average molecular weight (Mw) of ADCS was 49.2 kDa, while the Mw of LMWADCS was 6.4 kDa. After the eliminative degradation of ADCS by chondroitinase ABC, strong anion-exchange high-performance liquid chromatography (SAX-HPLC) analysis showed that the disaccharide composition of ADCS was 14.6% ΔDi0S, 60.9% ΔDi6S and 24.5% ΔDi4S. Then, in vitro antioxidant assays were performed with ADCS, LMWADCS and CS from a commercial source. Our results showed that LMWADCS exerted the highest total antioxidant activity out of the total antioxidant capacity, including the capacity of scavenging DPPH radicals, hydroxyl radicals and superoxide anion radicals. From the results of this study, we can conclude that the Mw and composition of ADCS are different from those reported for bovine and shark CS, and LMWADCS can be utilized as a valuable and potential nutraceutical for the functional food industry.
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20
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Wang Z, Hang P, Zhang Q, Xu Q, Qi Z. Molecular characterization and expression analysis of cathepsin C in Chinese giant salamander ( Andrias davidianus ) after Aeromonas hydrophila infection. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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21
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Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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22
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Fan W, Jiang Y, Zhang M, Yang D, Chen Z, Sun H, Lan X, Yan F, Xu J, Yuan W. Comparative transcriptome analyses reveal the genetic basis underlying the immune function of three amphibians' skin. PLoS One 2017; 12:e0190023. [PMID: 29267366 PMCID: PMC5739465 DOI: 10.1371/journal.pone.0190023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 12/06/2017] [Indexed: 02/06/2023] Open
Abstract
Skin as the first barrier against external invasions plays an essential role for the survival of amphibians on land. Understanding the genetic basis of skin function is significant in revealing the mechanisms underlying immunity of amphibians. In this study, we de novo sequenced and comparatively analyzed skin transcriptomes from three different amphibian species, Andrias davidianus, Bufo gargarizans, and Rana nigromaculata Hallowell. Functional classification of unigenes in each amphibian showed high accordance, with the most represented GO terms and KEGG pathways related to basic biological processes, such as binding and metabolism and immune system. As for the unigenes, GO and KEGG distributions of conserved orthologs in each species were similar, with the predominantly enriched pathways including RNA polymerase, nucleotide metabolism, and defense. The positively selected orthologs in each amphibian were also similar, which were primarily involved in stimulus response, cell metabolic, membrane, and catalytic activity. Furthermore, a total of 50 antimicrobial peptides from 26 different categories were identified in the three amphibians, and one of these showed high efficiency in inhibiting the growth of different bacteria. Our understanding of innate immune function of amphibian skin has increased basis on the immune-related unigenes, pathways, and antimicrobial peptides in amphibians.
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Affiliation(s)
- Wenqiao Fan
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Yongchuan, Chongqing, China
- Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Yongchuan, Chongqing, China
| | - Yusong Jiang
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Meixia Zhang
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Donglin Yang
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Yongchuan, Chongqing, China
- Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Yongchuan, Chongqing, China
| | - Zhongzhu Chen
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Yongchuan, Chongqing, China
- Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Yongchuan, Chongqing, China
| | - Hanchang Sun
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- * E-mail:
| | - Xuelian Lan
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
- Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Yongchuan, Chongqing, China
- Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Yongchuan, Chongqing, China
| | - Fan Yan
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Jingming Xu
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Wanan Yuan
- Chongqing Research Center of Conservation and Development on Rare and Endangered Aquatic Resources, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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23
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Pei J, Feng Z, Ren T, Sun H, Han H, Jin W, Dang J, Tao Y. Purification, characterization and application of a novel antimicrobial peptide from Andrias davidianus
blood. Lett Appl Microbiol 2017; 66:38-43. [DOI: 10.1111/lam.12823] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 11/26/2022]
Affiliation(s)
- J. Pei
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
- Qinghai Key Laboratory of Tibetan Medicine Research; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining China
| | - Z. Feng
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
| | - T. Ren
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
| | - H. Sun
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
| | - H. Han
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
| | - W. Jin
- Shaanxi Key Laboratory of Biology and Bioresources; Shaanxi University of Technology; Shaanxi China
| | - J. Dang
- Qinghai Key Laboratory of Tibetan Medicine Research; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining China
| | - Y. Tao
- Qinghai Key Laboratory of Tibetan Medicine Research; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining China
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24
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Zhang Q, Han P, Huang B, Wang Z, Qiao G, Wang P, Qi Z. Molecular Cloning, Characterization, and Expression Analysis of Cathepsin A in the Chinese Giant Salamander Andrias davidianus. JOURNAL OF AQUATIC ANIMAL HEALTH 2017; 29:199-207. [PMID: 28992444 DOI: 10.1080/08997659.2017.1349007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cathepsin A (CTSA) is serine carboxypeptidase, an important protease in the lysosome. In this study, the full complementary DNA (cDNA) sequence of CTSA in Chinese giant salamanders Andrias davidianus was cloned, and its sequence features were analyzed. Tissue expression patterns of CTSA in healthy and Aeromonas hydrophila-infected salamanders were also investigated. The full cDNA sequence of salamander CTSA was 1,620 base pairs in length, encoding 472 amino acids. Salamander CTSA shared high sequence identities with other vertebrates' CTSAs, ranging from 62.7% to 68.9%. In healthy salamanders, CTSA was highly expressed in spleen, followed by brain, intestine, and stomach. After A. hydrophila infection, salamander CTSA was significantly upregulated in lung, heart, muscle, and kidney; was downregulated in liver, spleen, and intestine; and exhibited no significant changes in stomach and skin, indicating that salamander CTSA might play defense roles in multiple tissues during bacterial infection. These results provide a solid basis for further study of the immune function of amphibian CTSA. Received September 18, 2016; accepted June 18, 2017.
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Affiliation(s)
- Qihuan Zhang
- a Key Laboratory of Biochemistry and Biotechnology of Marine Wetland of Jiangsu Province , Yancheng Institute of Technology , Yancheng , Jiangsu 224051 , China
- b School of Animal Science , Yangtze University , Jingzhou 434020 , China
| | - Panpan Han
- b School of Animal Science , Yangtze University , Jingzhou 434020 , China
| | - Bei Huang
- c College of Fisheries , Jimei University , Xiamen , Fujian 361021 , China
| | - Zisheng Wang
- d Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province , Yancheng Institute of Technology , Yancheng , Jiangsu 224051 , China
| | - Guo Qiao
- d Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province , Yancheng Institute of Technology , Yancheng , Jiangsu 224051 , China
| | - Puze Wang
- a Key Laboratory of Biochemistry and Biotechnology of Marine Wetland of Jiangsu Province , Yancheng Institute of Technology , Yancheng , Jiangsu 224051 , China
| | - Zhitao Qi
- a Key Laboratory of Biochemistry and Biotechnology of Marine Wetland of Jiangsu Province , Yancheng Institute of Technology , Yancheng , Jiangsu 224051 , China
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Qin C, Gong Q, Wen Z, Yuan D, Shao T, Wang J, Li H. Transcriptome analysis of the spleen of the darkbarbel catfish Pelteobagrus vachellii in response to Aeromonas hydrophila infection. FISH & SHELLFISH IMMUNOLOGY 2017; 70:498-506. [PMID: 28927687 DOI: 10.1016/j.fsi.2017.09.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/17/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
Intensive aquaculture has increased the susceptibility of fish to Aeromonas hydrophila, and this has led to severe economic damage. There has been little study of the host defense mechanism against A. hydrophila infection in scaleless fish. Therefore, in the present study, the transcriptome profiles of the spleen of Pelteobagrus vachellii were examined after infection with A. hydrophila. In total, 37,730 unigenes from 322 KEGG pathways were identified. Following A. hydrophila infection, 27,803 differentially expressed genes were identified, including 13,934 upregulated and 13,869 downregulated genes. Significant enrichment analysis of these differentially expressed unigenes showed that the major immune pathways were involved, including toll-like receptor pathways, B-cell receptor signaling pathways, Fcγ receptor-mediated phagocytosis, complement and coagulation cascades, and natural killer cell-mediated cytotoxicity pathways. From these pathways, 59 key immune-related differentially expressed genes were selected: 53 genes that were upregulated, including those coding for complement components, interferons, and interleukins, and six DEGs that were downregulated, including inhibitor of nuclear factor kappa-B kinase. Finally, nine DEGs, which were randomly selected, were confirmed by qRT-PCR to be differentially expressed. The results indicated that complement components, interferons and Fcγ receptor-mediated phagocytosis played key role in the response to A. hydrophila infection in the spleen of P. vachellii, which may prove useful in the future for the development of therapeutic regimens.
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Affiliation(s)
- Chuanjie Qin
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR China.
| | - Quan Gong
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 611731, PR China
| | - Zhengyong Wen
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR China
| | - Dengyue Yuan
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR China
| | - Ting Shao
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR China
| | - Jun Wang
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR China
| | - Huatao Li
- College of Life Science, Neijiang Normal University, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang 641000, PR 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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Functional characterization of a short peptidoglycan recognition protein from Chinese giant salamander ( Andrias davidianus). Oncotarget 2017; 8:99323-99335. [PMID: 29245904 PMCID: PMC5725095 DOI: 10.18632/oncotarget.21470] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 09/08/2017] [Indexed: 11/25/2022] Open
Abstract
Peptidoglycan (PGN) recognition proteins (PGRPs) are important pattern recognition receptors (PRRs) involved in immune defense against bacterial infections. In this study, a short PGRP (termed AdPGRP-S1) was cloned and functionally characterized from Chinese giant salamander (Andrias davidianus), the largest extant urodela amphibian species. AdPGRP-S1 was 184 aa in length and shared 38.7%-54.9% sequence identities with other vertebrates’ short PGRPs. It contained one typical PGRP domain at the C-terminal region and several conserved amino acid (aa) residues involved in amidase and PGN binding. AdPGRP-S1 was constitutively expressed in all tissues examined, with the highest expression level seen in spleen and intestine. It has been shown that AdPGRP-S1 could bind and degrade Lys-PGN and Dap-PGN. Further, AdPGRP-S1 had antibacterial activity against the Gram-negative bacteria, Edwardsiella tarda, and was able to trigger the activation of NF-κB signaling. These results demonstrated that AdPGRP-S1 possesses multiple functions in pathogen recognition, mediating ceullular signaling, and initiating antibacterial response. This is the first functional study of a salamander PGRP, providing insight to further understand the functional evolution of verterbates’ PGRPs.
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Pei J, Jiang L. Antimicrobial peptide from mucus of Andrias davidianus : screening and purification by magnetic cell membrane separation technique. Int J Antimicrob Agents 2017; 50:41-46. [DOI: 10.1016/j.ijantimicag.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 01/25/2017] [Accepted: 02/10/2017] [Indexed: 10/19/2022]
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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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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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31
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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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32
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Qi Z, Meng F, Zhang Q, Wang Z, Qiao G, Xu W, Shao R, Chen C. Structural insights into ligand binding of PGRP1 splice variants in Chinese giant salamander (Andrias davidianus) from molecular dynamics and free energy calculations. J Mol Model 2017; 23:135. [PMID: 28341996 DOI: 10.1007/s00894-017-3315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/13/2017] [Indexed: 11/24/2022]
Abstract
Peptidoglycan (PGN) recognition proteins (PGRPs) are important pattern recognition receptors of the innate immune system. A number of PGRP splicing variants produced by alternative splicing of PGRP genes have been reported. However, several important aspects of interactions between PGRP splice variants and their ligands are still unclear. In the present study, three dimensional models of salamander PGRP1 (adPGRP1) and its splice variant (adPGRP1a) were constructed, and their key amino acids involved in interacting with PGNs were analyzed. The results revealed that adPGRP1a has a typical PGRPs structure containing five β-sheets and four α-helices, while adPGRP1 contained five β-sheets and only one α-helix due to the lack of 51 amino acids at its C-terminus. Molecular docking revealed that van der Waals and Coulombic interactions contributed to interactions in the protein-ligand complex. Further binding energy of adPGRP-PGNs computed by the MM-PBSA method revealed that adPGRP1a and adPGRP1 might selectively bind to different PGNs; the former might selectively bind Dap-type PGNs and the latter both types of PGNs. In addition, the binding energy of each residue of adPGRP1a and adPGRP1 was also calculated, revealing that residues involved in the interaction of protein-ligand complexes were different in adPGRP1a and adPGRP1. These results provided a first insight into the potential basis for interaction between PGRPs generated by alternative splicing and PGN derivatives.
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Affiliation(s)
- Zhitao Qi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China. .,Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China.
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, China
| | - Qihuan Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Zisheng Wang
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Guo Qiao
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Wei Xu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Rong Shao
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China.
| | - Chenglung Chen
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan, Republic of China
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Du J, Wang L, Wang Y, Shen J, Pan C, Meng Y, Yang C, Ji H, Dong W. Autophagy and apoptosis induced by Chinese giant salamander (Andrias davidianus) iridovirus (CGSIV). Vet Microbiol 2016; 195:87-95. [PMID: 27771075 DOI: 10.1016/j.vetmic.2016.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/04/2016] [Accepted: 09/20/2016] [Indexed: 02/07/2023]
Abstract
The outbreak of Chinese Giant Salamander (Andrias davidianus, CGS) Iridovirus (CGSIV) caused massive death of CGSs. However, some CGSs with low level of CGSIV usually could survive. In our study, major capsid protein (MCP) DNA replicates of CGSIV in shedding skin were employed to assess the relative content of CGSIV in the living CGSs by qPCR. Furthermore, the examinations of autophagy and apoptosis in CGSs in vivo and in the primary renal cells in vitro were performed, respectively. The results showed that the relative contents of CGSIV in the shedding skin could reflect those in liver, spleen, and kidney of the CGSs. In these tissues of the CGSs with low-level replicates of CGSIV, there were not obviously macroscopic lesions. But the irregularly-shaped vesicles perhaps involving in autophagosome were observed by transmission electron microscopy (TEM). The LC3B protein displayed uneven distribution by Immunohistochemistry and the level mRNA of Atg5 was higher in these tissues than that in the tissues of healthy CGSs using qRT-PCR. Meanwhile, the apoptosis also appeared in these tissues by TUNEL staining and higher level mRNA of type I IFN were detected in these tissues using qRT-PCR. Further, both the expression level of LC3B II protein and Atg5 mRNA increased significantly at 2h after the virus infected the primary renal cells from the health CGSs in vitro. In addition, apoptosis and type I IFN mRNA began to increase significantly at 4h after the virus infected the renal cells. It was suggested that autophagy may be a pivotal role for survival of CGSIV in the CGSs during early infection and the rapid proliferation of CGSIV could be inhibited by innate immune response and apoptosis.
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Affiliation(s)
- Jian Du
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Liqing Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Yuanxian Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Jian Shen
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Chuanyin Pan
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Changming Yang
- Animal Husbandry and Veterinary Station of Chenggu County, Hanzhong 723200, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A & F University, Yangling 712100, China.
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Dang Y, Xu X, Shen Y, Hu M, Zhang M, Li L, Lv L, Li J. Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila. PLoS One 2016; 11:e0157413. [PMID: 27383749 PMCID: PMC4934786 DOI: 10.1371/journal.pone.0157413] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/27/2016] [Indexed: 02/02/2023] Open
Abstract
The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.
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Affiliation(s)
- Yunfei Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Xiaoyan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Moyan Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Meng Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Lisen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Liqun Lv
- National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, PR China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
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