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Hembrom PS, Deepthi M, Biswas G, Mappurath B, Babu A, Reeja N, Mano N, Grace T. Reference genes for qPCR expression in black tiger shrimp, Penaeus monodon. Mol Biol Rep 2024; 51:422. [PMID: 38485790 DOI: 10.1007/s11033-024-09409-5] [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: 12/02/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Gene expression profiling via qPCR is an essential tool for unraveling the intricate molecular mechanisms underlying growth and development. Identifying and validating the most appropriate reference genes is essential for qPCR experiments. Nevertheless, there exists a deficiency in a thorough assessment of reference genes concerning the expression of the genes in the research in the context of the growth and development of the Black Tiger Shrimp, P. monodon. This popular marine crustacean is extensively raised for human consumption. In this study, we assessed the expression stability of seven reference genes (ACTB, 18S, EF-1α, AK, PK, cox1, and CLTC) in adult tissues (hepatopancreas, gills, and stomach) of small and large polymorphs of P. monodon. METHODS AND RESULTS The stability of gene expressions was assessed utilizing NormFinder, BestKeeper, and geNorm, and a comprehensive ranking of these genes was conducted through the online tool RefFinder. In the overall ranking, 18S and CLTC emerged as the most stable genes in the hepatopancreas and stomach, while CLTC and AK exhibited significant statistical reliability in the gills of adult P. monodon. The validation of these identified stable genes was carried out using a growth-associated gene, insr-1. CONCLUSION The results indicated that 18S and CLTC stand out as the most versatile reference genes for conducting qPCR analysis focused on the growth of P. monodon. This study represents the first comprehensive exploration that identifies and assesses reference genes for qPCR analysis in P. monodon, providing valuable tools for research involving similar crustaceans.
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Affiliation(s)
- Preety Sweta Hembrom
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Mottakunja Deepthi
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Gourav Biswas
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Bhagya Mappurath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Adon Babu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Narchikundil Reeja
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Neeraja Mano
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Tony Grace
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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Yan F, Li H, Chen X, Yu J, Su S, Li J, Ye W, Tang Y. Screening of Suitable Reference Genes for Immune Gene Expression Analysis Stimulated by Vibrio anguillarum and Copper Ions in Chinese Mitten Crab ( Eriocheir sinensis). Genes (Basel) 2023; 14:genes14051099. [PMID: 37239459 DOI: 10.3390/genes14051099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The reference gene expression is not always stable under different experimental conditions, and screening of suitable reference genes is a prerequisite in quantitative real-time polymerase chain reaction (qRT-PCR). In this study, we investigated gene selection, and the most stable reference gene for the Chinese mitten crab (Eriocheir sinensis) was screened under the stimulation of Vibrio anguillarum and copper ions, respectively. Ten candidate reference genes were selected, including arginine kinase (AK), ubiquitin-conjugating enzyme E2b (UBE), glutathione S-transferase (GST), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF-1α), α-tubulin (α-TUB), heat shock protein 90 (HSP90), β-actin (β-ACTIN), elongation factor 2 (EF-2) and phosphoglucomutase 2 (PGM2). Expression levels of these reference genes were detected under the stimulation of V. anguillarum at different times (0 h, 6 h, 12 h, 24 h, 48 h and 72 h) and copper ions in different concentrations (11.08 mg/L, 2.77 mg/L, 0.69 mg/L and 0.17 mg/L). Four types of analytical software, namely geNorm, BestKeeper, NormFinder and Ref-Finder, were applied to evaluate the reference gene stability. The results showed that the stability of the 10 candidate reference genes was in the following order: AK > EF-1α > α-TUB > GAPDH > UBE > β-ACTIN > EF-2 > PGM2 > GST > HSP90 under V. anguillarum stimulation. It was GAPDH > β-ACTIN > α-TUB > PGM2 > EF-1α > EF-2 > AK > GST > UBE > HSP90 under copper ion stimulation. The expression of E. sinensis Peroxiredoxin4 (EsPrx4) was detected when the most stable and least stable internal reference genes were selected, respectively. The results showed that reference genes with different stability had great influence on the accurate results of the target gene expression. In the Chinese mitten crab (E. sinensis), AK and EF-1α were the most suitable reference genes under the stimulation of V. anguillarum. Under the stimulation of copper ions, GAPDH and β-ACTIN were the most suitable reference genes. This study provided important information for further research on immune genes in V. anguillarum or copper ion stimulation.
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Affiliation(s)
- Fengyuan Yan
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hui Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xue Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junjie Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Shengyan Su
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wei Ye
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yongkai Tang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Wang Z, Yang L, Zhou F, Li J, Wu X, Zhong X, Lv H, Yi S, Gao Q, Yang Z, Zhao P, Wu Y, Wu C, Zhang L, Wang H, Zhang L. Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of crayfish (Procambarus clarkii) to copper stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130820. [PMID: 36860031 DOI: 10.1016/j.jhazmat.2023.130820] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
One of the significant limitations of aquaculture worldwide is the prevalence of divalent copper (Cu). Crayfish (Procambarus clarkii) are economically important freshwater species adapted to a variety of environmental stimuli, including heavy metal stresses; however, large-scale transcriptomic data of the hepatopancreas of crayfish in response to Cu stress are still scarce. Here, integrated comparative transcriptome and weighted gene co-expression network analyses were initially applied to investigate gene expression profiles of the hepatopancreas of crayfish subjected to Cu stress for different periods. As a result, 4662 significant differentially expressed genes (DEGs) were identified following Cu stress. Bioinformatics analyses revealed that the "focal adhesion" pathway was one of the most significantly upregulated response pathways following Cu stress, and seven DEGs mapped to this pathway were identified as hub genes. Furthermore, the seven hub genes were examined by quantitative PCR, and each was found to have a substantial increase in transcript abundance, suggesting a critical role of the "focal adhesion" pathway in the response of crayfish to Cu stress. Our transcriptomic data can be a good resource for the functional transcriptomics of crayfish, and these results may provide valuable insights into the molecular response mechanisms underlying crayfish to Cu stress.
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Affiliation(s)
- Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Fan Zhou
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - He Lv
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Quanxin Gao
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Pengfei Zhao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yi Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Choufei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hua Wang
- Huzhou Key Laboratory of Medical and Environmental Application Technologies, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
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Liu Z, Xiao J, Xia Y, Wu Q, Zhao C, Li D. Selection and validation of reference genes for RT-qPCR-based analyses of Anastatus japonicus Ashmead (Hymenoptera: Helicopteridae). Front Physiol 2022; 13:1046204. [PMID: 36338494 PMCID: PMC9626802 DOI: 10.3389/fphys.2022.1046204] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
RT-qPCR remains a vital approach for molecular biology studies aimed at quantifying gene expression in a range of physiological or pathological settings. However, the use of appropriate reference genes is essential to attain meaningful RT-qPCR results. Anastatus japonicus Ashmead (Hymenoptera: Helicopteridae) is an important egg parasitoid wasp and natural enemy of fruit bugs and forest caterpillars. While recent transcriptomic studies have analyzed gene expression profiles in A. japonicus specimens, offering a robust foundation for functional research focused on this parasitoid, no validated A. japonicus reference genes have yet been established, hampering further research efforts. Accordingly, this study sought to address this issue by screening for the most stable internal reference genes in A. japonicus samples to permit reliable RT-qPCR analyses. The utility of eight candidate reference genes (ACTIN, TATA, GAPDH, TUB, RPL13, RPS6, EF1α, RPS3a) was assessed under four different conditions by comparing developmental stages (larvae, pupae, adults), tissues (abdomen, chest, head), sex (male or female adults), or diapause states (diapause induction for 25, 35, 45, or 55 days, or diapause termination). RefFinder was used to calculate gene stability based on the integration of four algorithms (BestKeeper, Normfinder, geNorm, and ΔCt method) to determine the optimal RT-qPCR reference gene. Based on this approach, RPS6 and RPL13 were found to be the most reliable reference genes when assessing different stages of development, while ACTIN and EF1α were optimal when comparing adults of different sexes, RPL13 and EF1α were optimal when analyzing different tissues, and TATA and ACTIN were optimal for different diapause states. These results provide a valuable foundation for future RT-qPCR analyses of A. japonicus gene expression and function under a range of experimental conditions.
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Affiliation(s)
- Zixin Liu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Junjiang Xiao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yue Xia
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qifeng Wu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Can Zhao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Can Zhao, Dunsong Li,
| | - Dunsong Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Can Zhao, Dunsong Li,
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Liu QN, Huang L, Wang SY, Li YT, Tang YY, Zhang DZ, Tang BP, Yang H, He JX, Ding F. Transcriptome analysis of differentially expressed genes in the red swamp crayfish Procambarus clarkii challenged with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2021; 119:280-288. [PMID: 34571158 DOI: 10.1016/j.fsi.2021.09.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/10/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
As an important economic species in China, aquaculture of the crayfish Procambarus clarkii has suffered huge losses due to infection by pathogenic bacteria, mainly by Aeromonas hydrophila, which leads to high mortality and huge economic loss. To better understand the immune response of crayfish against bacterial infection, we compared and analyzed transcriptome data of hepatopancreatic tissue from P. clarkii that were either challenged with A. hydrophila or treated with PBS. After assembly and annotation of the data, 32,041 unigenes with an average length of 1512 base pairs were identified. Compared to control group, Differential gene expression (DEG) analysis revealed 608 DEGs were obtained, of which 274 unigenes were upregulated and 334 were downregulated in the A. hydrophila group. Furthermore, the expression levels of eight selected immune-related DEGs were validated by qRT-PCR, substantiating the reliability of RNA-seq results. This study not only provides effective data support for immune defense strategies of P. clarkii in response to bacterial infections, but also provides new information about the P. clarkii immune system and defense mechanisms, and a valuable basis for further studies to elucidate the molecular immune mechanisms of this species.
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Affiliation(s)
- Qiu-Ning Liu
- Anhui Province Key Laboratory of Aquaculture ampersand Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China; Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Long Huang
- Anhui Province Key Laboratory of Aquaculture ampersand Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Shu-Yu Wang
- Anhui Province Key Laboratory of Aquaculture ampersand Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Yue-Tian Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, China; College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ying-Yu Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China; College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China.
| | - Hui Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.
| | - Ji-Xiang He
- Anhui Province Key Laboratory of Aquaculture ampersand Stock Enhancement, Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei, China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China.
| | - Feng Ding
- Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
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Comparative transcriptome analysis of the gills of Procambarus clarkii provide novel insights into the response mechanism of ammonia stress tolerance. Mol Biol Rep 2021; 48:2611-2618. [PMID: 33811573 DOI: 10.1007/s11033-021-06315-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Procambarus clarkii is an important model crustacean organism in many researches. Ammonia nitrogen is one of common contaminants in aquatic environment, influencing the health of aquatic organisms. The primary objective of this study was to investigate molecular mechanisms on ammonia stress in gills of P. clarkii to provide new insights into the strategies of aquatic animals in responding to high concentration of ammonia in the environment. Procambarus clarkii were randomly assigned into two groups (ammonia stress group, AG; control group, CG), and gill samples were dependently excised from AG and CG. Then response mechanisms on ammonia stress were investigated based on transcriptome data of P. clarkii. 9237 differentially expressed genes were identified in ammonia stress group. The genes of ion transport enzymes (NKA and SLC6A5S) were significantly up-regulated. Whereas the immune-related genes (e.g. MAP3K7, HSP70, HSP90A, CTSF, CTSL1, CHI and CTL4) and pathways were significantly up-regulated, which played an important role in reacting to ammonia stress. Procambarus clarkii may enhance immune defense to counteract ammonia toxicity by the up-regulation of immune-related genes and signaling pathways. The activities of ion transport enzymes are changed to mobilise signal transduction and ion channel regulation for adapting to ammonia environment. These previous key genes play an important role in resistance to ammonia stress to better prepare for survival in high concentration of ammonia.
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Shen C, Tang D, Zhang Y, Wu L, Luo Y, Tang B, Wang Z. Identification of putative ingestion-related olfactory receptor genes in the Chinese mitten crab (Eriocheir japonica sinensis). Genes Genomics 2021; 43:479-490. [PMID: 33689153 DOI: 10.1007/s13258-021-01065-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Olfaction plays a central role in mating, spawning, obtaining food and escaping predators, which is essential for survival and reproduction of animals. The nature of the olfactory perception in crabs, which is a major group of crustaceans, has remained elusive. OBJECTIVE This project aims to explore the molecular mechanism of olfaction in crabs and further improve our understanding of olfactory perception in crustaceans. METHODS The olfactory receptors and ingestion-related gene expression in Eriocheir japonica sinensis were studied by transcriptomic techniques. The de novo assembly, annotation and functional evaluation were performed with bioinformatics tools. RESULTS A series of chemosensory receptors associated with olfaction were identified including 33 EsIRs, 24 EsIGluRs, 58 EsVIGluRs, 1 EsOR and 1 EsGC-D. We found IRs were key odorant receptors demonstrating a specific species evolutionary trend in crustaceans. Furthermore, we identified ORs in E. j. sinensis and Litopenaeus vannamei. The incomplete EsOR and LvOR1 structures implied that ORs exist in crustaceans, and may have been degenerated or even lost in the olfactory evolutionary process. In addition, comparative transcriptome analysises demonstrated two possible olfactory transduction pathways of E. j. sinensis: the cGMP-mediated olfactory pathway related to vegetable odor molecules and the cAMP-mediated olfactory pathway related to meat odor molecules. The above results were consistent with its omnivorous ingestion of E. j. sinensis. CONCLUSIONS Our study revealed the unique olfactory molecular mechanism of omnivorous crabs and provided valuable information for further functional research on the chemoreception mechanisms in crustaceans.
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Affiliation(s)
- Chenchen Shen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Dan Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
| | - Yiping Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Lv Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Yaqi Luo
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China.
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Azemi NFH, Misnan R, Keong PB, Yadzir ZHM. Reference gene and tropomyosin expression in mud crab Scylla olivacea, Scylla paramamosain and Scylla tranquebarica. Mol Biol Rep 2020; 47:9765-9777. [PMID: 33170423 DOI: 10.1007/s11033-020-05966-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Tropomyosin, a muscle tissue protein is a major allergen in most of shellfish including mud crab. Quantitative real time-PCR (qRT-PCR) using a stable reference gene is the most sensitive approach to produce accurate relative gene expression that has yet to be demonstrated for allergenic tropomyosin in mud crab species. This study was conducted to identify the suitable reference gene and tropomyosin expression in different body parts of local mud crabs, Scylla olivacea, Scylla paramamosain and Scylla tranquebarica. Myosin, 18S rRNA, GADPH and EF1α were selected as candidate reference genes and their expression was measured in the abdomen, walking leg and cheliped tissues of local Scylla spp. The expression stability was analyzed using the comparative delta-Ct method, BestKeeper, NormFinder and geNorm then comprehensively ranked by RefFinder algorithm. Findings showed that EF1α was the most suitable reference gene across three mud crab species. Meanwhile, the abdomen, walking leg and cheliped selected their own suitable reference gene either Myosin, 18S rRNA, EF1α or GADPH. Overall, tropomyosin was the highest in S. tranquebarica, whereas the least was in S. paramamosain. Interestingly, tropomyosin was the highest in the abdomen of all mud crab species. This is the first analysis on reference genes selection for qRT-PCR data normalization of tropomyosin expression in mud crab. These results will provide more accurate findings for further gene expression and allergen analysis in Scylla spp.
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Affiliation(s)
- Nur Farah Hani Azemi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
| | - Rosmilah Misnan
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia.
| | - Poh Bun Keong
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
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Xie M, Zhong Y, Lin L, Zhang G, Su W, Ni W, Qu M, Chen H. Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita. PLoS One 2020; 15:e0240972. [PMID: 33085726 PMCID: PMC7577503 DOI: 10.1371/journal.pone.0240972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qPT-PCR) is commonly used to analyze gene expression, however, the accuracy of the normalized results is affected by the expression stability of reference genes. Holotrichia oblita (Coleoptera: Scarabaeidae) causes serious damage to crops. Reliable reference genes in H. oblita are needed for qRT-PCR analysis. Therefore, we evaluated 13 reference genes under biotic and abiotic conditions. RefFinder provided a comprehensive stability ranking, and geNorm suggested the optimal number of reference genes for normalization. RPL13a and RPL18 were the most suitable reference genes for developmental stages, tissues, and temperature treatments; RPL13a and RPS3 were the most suitable for pesticide and photoperiod treatments; RPS18 and RPL18 were the most suitable for the two sexes. We validated the normalized results using odorant-binding protein genes as target genes in different tissues. Compared with the selected suitable reference genes, the expression of OBP1 in antennae, abdomen, and wings, and OBP2 in antennae and wings were overestimated due to the instability of ACTb. These results identified several reliable reference genes in H. oblita for normalization, and are valuable for future molecular studies.
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Affiliation(s)
- Minghui Xie
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Yongzhi Zhong
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Lulu Lin
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Guangling Zhang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Weihua Su
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Wanli Ni
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Mingjing Qu
- Shandong Peanut Research Institute, Qingdao, Shandong, China
| | - Haoliang Chen
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
- * E-mail:
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10
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Validation of Real-time PCR Reference Genes of Muscle Metabolism in Harvested Spiny-Cheek Crayfish ( Faxonius limosus) Exposed to Seasonal Variation. Animals (Basel) 2020; 10:ani10071140. [PMID: 32640616 PMCID: PMC7401605 DOI: 10.3390/ani10071140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 01/23/2023] Open
Abstract
Real-time quantitative reverse transcription PCR (RT-qPCR) is a sensitive and broadly used technique of assessing gene activity. To obtain a reliable result, stably expressed reference genes are essential for normalization of transcripts in various samples. To our knowledge, this is the first systematic analysis of reference genes for normalization of RT-qPCR data in spiny-cheek crayfish (Faxonius limosus). In this study, expression of five candidate reference genes (actb, β-actin; gapdh, glyceraldehyde-3-phosphate dehydrogenase; eif, eukaryotic translation initiation factor 5a; ef-1α, elongation factor-1α; and tub, α-tubulin) in muscle samples from male and female F. limosus in spring and autumn was analyzed. Additionally, the most stable reference genes were used for accurate normalization of five target genes, i.e., tnnc, troponin c; ak, arginine kinase; fr, ferritin; ccbp-23, crustacean calcium-binding protein 23; and actinsk8, skeletal muscle actin 8. Results obtained using the geNorm and NormFinder algorithms showed high consistency, and differences in the activity of the selected actb with eif genes were successfully identified. The spring and autumn activities of the target genes (except ak) in the muscle tissue of males and females differed significantly, showing that both sexes are immensely involved in an array of breeding behaviors in spring, and females intensively recover in the autumn season. Characterization of first reference genes in spiny-cheek crayfish will facilitate more accurate and reliable expression studies in this key species.
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11
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Foysal MJ, Fotedar R, Tay CY, Gupta SK. Biological filters regulate water quality, modulate health status, immune indices and gut microbiota of freshwater crayfish, marron (Cherax cainii, Austin, 2002). CHEMOSPHERE 2020; 247:125821. [PMID: 31972484 DOI: 10.1016/j.chemosphere.2020.125821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Water quality has significant impacts on the health and immune responses of aquaculture species. This study aimed to analyse and compare the effects of two biological filters namely, gravel and, Bio-Ball with a recently developed filter called Water-cleanser on regulation of water quality parameters, health and immune response of marron reared in plastic tanks for 60 days. Results showed that addition of Bio-Ball significantly (P < 0.05) reduced the concentration of ammonia, nitrate and phosphate while Water-cleanser showed the ability to reduce ammonia and nitrate from water in aquaculture tanks. Although the biological filters had no significant effect on marron growth but inclusion of Bio-Ball and Water-cleanser positively influenced the biochemical composition of tail muscle and some haemolymph parameters of marron. The next generation sequence data demonstrated higher bacterial diversity in the hindgut of marron with Water-cleanser, followed by Bio-Ball and gravel, respectively. In addition, the predicted metabolic pathways revealed a significantly higher bacterial activity and gene function correlated to metabolism and biosynthesis of protein, energy and secondary metabolites in Bio-Ball and Water-cleanser. Bio-Ball and Water-cleanser were also associated with up-regulation of innate immune responsive genes of marron gut. Overall, Bio-Ball and Water-cleanser proved to have higher water remediation and immune response modulation capabilities, and therefore could be used as preferred filters for growth of beneficial bacteria in crayfish culture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Sanjay K Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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12
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Foysal MJ, Fotedar R, Siddik MAB, Tay A. Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii). Sci Rep 2020; 10:5916. [PMID: 32246011 PMCID: PMC7125160 DOI: 10.1038/s41598-020-62655-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/13/2020] [Indexed: 12/25/2022] Open
Abstract
This study aimed to investigate the combined effects of two most potent probiotic bacteria Lactobacillus acidophilus and Lactobacillus plantarum on overall health and immune status of freshwater crayfish, marron under laboratory conditions. A total of 36 marron were distributed into six different tanks and two different feeding groups, control and probiotic-fed group. After acclimation, control group was fed with basal diet while probiotic group was fed 109 CFU/mL per kg of bacterial supplemented feed for 60 days. The results showed no significant differences in weight gain, however, probiotic feed significantly enhanced some hemolymph parameters and biochemical composition of tail muscle. Histology data revealed better hepatopancreas health and higher microvilli counts in the marron gut fed probiotic diet. The probiotic bacteria triggered significant shift of microbial communities at different taxa level, mostly those reported as beneficial for crayfish. The probiotic diet also enriched the metabolic functions and genes associated with innate immune response of crayfish. Further correlation analysis revealed significant association of some taxa with increased activity for hemolymph and immune genes. Therefore, dietary Lactobacillus supplementation can modulate the overall health and immunity as well as gut microbial composition and interaction network between gut microbiota and immune system in crayfish.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Muhammad A B Siddik
- Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Alfred Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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13
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Foysal MJ, Chua EG, Gupta SK, Lamichhane B, Tay CY, Fotedar R. Bacillus mycoides supplemented diet modulates the health status, gut microbiota and innate immune response of freshwater crayfish marron (Cherax cainii). Anim Feed Sci Technol 2020. [DOI: 10.1016/j.anifeedsci.2020.114408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Wang Z, Meng Q, Zhu X, Sun S, Liu A, Gao S, Gou Y. Identification and Evaluation of Reference Genes for Normalization of Gene Expression in Developmental Stages, Sexes, and Tissues of Diaphania caesalis (Lepidoptera, Pyralidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5700579. [PMID: 31925425 PMCID: PMC6954454 DOI: 10.1093/jisesa/iez130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 05/04/2023]
Abstract
Diaphania caesalis (Walker) is an important boring insect mainly distributed in subtropical and tropical areas and attacked tropical woody grain crops, such as starchy plants of Artocarpus. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful approach for investigating target genes expression profiles at the transcriptional level. However, the identification and selection of internal reference genes, which is often overlooked, is the most vital step before the analysis of target gene expression by qRT-PCR. So far, the reliable internal reference genes under a certain condition of D. caesalis have not been investigated. Therefore, this study evaluated the expression stability of eight candidate reference genes including ACT, β-TUB, GAPDH, G6PDH, RPS3a, RPL13a, EF1α, and EIF4A in different developmental stages, tissues and sexes using geNorm, NormFinder and BestKeeper algorithms. To verify the stability of the recommended internal reference genes, the expression levels of DcaeOBP5 were analyzed under different treatment conditions. The results indicated that ACT, RPL13a, β-TUB, RPS3a, and EF1α were identified as the most stable reference genes for further studies on target gene expression involving different developmental stages of D. caesalis. And ACT and EIF4A were recommended as stable reference genes for different tissues. Furthermore, ACT, EF1α, and RPS3a were ranked as the best reference genes in different sexes based on three algorithms. Our research represents the critical first step to normalize qRT-PCR data and ensure the accuracy of expression of target genes involved in phylogenetic and physiological mechanism at the transcriptional level in D. caesalia.
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Affiliation(s)
- Zheng Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Qianqian Meng
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Corresponding author, e-mail:
| | - Xi Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shiwei Sun
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Aiqin Liu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shengfeng Gao
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Yafeng Gou
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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15
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Zhao BR, Zheng Y, Gao J, Wang XW. Maturation of an Antimicrobial Peptide Inhibits Aeromonas hydrophila Infection in Crayfish. THE JOURNAL OF IMMUNOLOGY 2019; 204:487-497. [PMID: 31852752 DOI: 10.4049/jimmunol.1900688] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023]
Abstract
Rapid synthesis and release of active antimicrobial peptides (AMPs) is an important strategy in innate immune. Processing of the precursor into the active form is a common posttranslational modification of AMPs in mammals. However, in invertebrates, the mechanism of AMP maturation is largely unknown. In the current study, to our knowledge, a novel potential AMP, designated as PcnAMP, was identified because of its significant induction by bacterial infection in the red swamp crayfish (Procambarus clarkii). PcnAMP was cleaved into a short fragment postinfection. Using the purified native peptide, this cleavage was found to be mediated by trypsin after synthesis. Proteolysis produced an N-terminal peptide that exerted the antibacterial function. Although the N-terminal peptide did not show significant similarity to any other sequences, it was predicted to have an overall helical structure and high amphipathicity, both of which are typical features of many AMPs. The N-terminal active peptide exhibited a wide spectrum of antimicrobial activity. Atomic force microscope imaging and flow cytometry analysis showed that treatment with the active form of PcnAMP led to the collapse of the bacterial cell wall and permeabilization of the bacterial cell membrane. Thus, this study provided a new candidate for therapeutic agent development, and revealed new insights into the maturation of AMPs in invertebrates.
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Affiliation(s)
- Bao-Rui Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; and
| | - Yi Zheng
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; and
| | - Jie Gao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; and
| | - Xian-Wei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; and .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266071, China
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16
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Jiao T, Yang TT, Wang D, Gao ZQ, Wang JL, Tang BP, Liu QN, Zhang DZ, Dai LS. Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 95:140-150. [PMID: 31629063 DOI: 10.1016/j.fsi.2019.09.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.
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Affiliation(s)
- Ting Jiao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, PR China
| | - Dong Wang
- Instrumental Analysis Center, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhen-Qiu Gao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmacy, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China.
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
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17
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Mo A, Wang J, Yuan M, Zhao D, Gu Z, Liu Y, Huang H, Yuan YC. Effect of sub-chronic dietary L-selenomethionine exposure on reproductive performance of Red Swamp Crayfish, (Procambarus clarkii). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:749-758. [PMID: 31344537 DOI: 10.1016/j.envpol.2019.07.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/18/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The effect of selenium (Se) on the reproductive system has been investigated in both humans and vertebrates, but few studies of female fertility and reproduction in invertebrate have been reported. This study is aimed to investigate the effect of SeMet on growth performance and reproductive system after crayfish were fed with graded levels of dietary SeMet (0, 1.49, 3.29, 10.02, 30.27 or 59.8 μg Se/g dry weight) for 60 days. Crayfish treated with the high levels of SeMet (10.02, 30.27 and 59.76 μg Se/g) exhibited decreasing FW and CL in both male and female. Interestingly, Se accumulation was higher in ovary than in other tissues, suggesting that ovary may serve as a target organ for Se accumulation. We found that dietary Se concentration of 10.02 μg Se/g significantly improved the spawning rate, promoted the synchronized spawning, and up-regulated the expressions of mRNA of cdc2 and vitellogenin, with significantly increased E2 and VTG concentrations in hemolymph of female crayfish. However, a marked decrease of the E2 contents and spawning rate was observed in the groups treated with 30.27 and 59.76 μg Se/g diets. In conclusion, the results of this study indicated that the Se had maximum accumulation in ovary, affecting the reproductive capacity by intervening the expression of cdc2 and vitellogenin in the reproductive system. The LOAEL to induce FW was observed in crayfish fed with 10.02 μg Se/g diet, and its value can cause toxicity within the range of natural concentration, so the addition of Se in the feed should be within 10.02 μg Se/g.
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Affiliation(s)
- Aijie Mo
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianghua Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingrui Yuan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Dengxiao Zhao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zemao Gu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ya Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongying Huang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yong Chao Yuan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shuangshui Shuanglu Institute, Huazhong Agricultural University, Wuhan 430070, China; National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan 430070, China.
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18
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Foysal MJ, Nguyen TTT, Chaklader MR, Siddik MAB, Tay CY, Fotedar R, Gupta SK. Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron ( Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum. PeerJ 2019; 7:e7553. [PMID: 31523510 PMCID: PMC6716501 DOI: 10.7717/peerj.7553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022] Open
Abstract
This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Muhammad A B Siddik
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.,Department of Fisheries Biology and Genetics, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Sanjay Kumar Gupta
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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19
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Foysal MJ, Fotedar R, Tay CY, Gupta SK. Dietary supplementation of black soldier fly ( Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron ( Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets. PeerJ 2019; 7:e6891. [PMID: 31149398 PMCID: PMC6534111 DOI: 10.7717/peerj.6891] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/01/2019] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Sanjay Kumar Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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Singh S, Gupta M, Pandher S, Kaur G, Goel N, Rathore P, Palli SR. RNA sequencing, selection of reference genes and demonstration of feeding RNAi in Thrips tabaci (Lind.) (Thysanoptera: Thripidae). BMC Mol Biol 2019; 20:6. [PMID: 30777032 PMCID: PMC6380046 DOI: 10.1186/s12867-019-0123-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/12/2019] [Indexed: 11/21/2022] Open
Abstract
Background Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time. Results From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified. About 85.4% of CDS identified showed positive Blast hits. The homologs of most of the core RNAi machinery genes were identified in this transcriptome. To select reference genes for reverse-transcriptase real-time quantitative PCR (RT-qPCR) experiments, 14 housekeeping genes were identified in the transcriptome and their expression was analyzed by (RT-qPCR). UbiCE in adult, 28s in nymphs and SOD under starvation stress were identified as the most stable reference genes for RT-qPCR. Feeding dsSNF7 and dsAQP caused 16.4- and 14.47-fold reduction in SNF7 and AQP mRNA levels respectively, when compared to their levels in dsGFP fed control insects. Feeding dsSNF7 or dsAQP also caused 62 and 72% mortality in T. tabaci. Interestingly, simultaneous feeding of dsRNAs targeting SNF7 or AQP and one of the RNAi pathway genes (Dicer-2/Aubergine/Staufen) resulted in a significant reduction in RNAi of target genes. These data suggest the existence of robust RNAi machinery in T. tabaci. Conclusion The current research is the first report of the assembled, analyzed and annotated RNAseq resource for T. tabaci, which may be used for future molecular studies in this insect. Reference genes validated across stages and starvation stress provides first-hand information on stable genes in T. tabaci. The information on RNAi machinery genes and significant knockdown of the target gene through dsRNA feeding in synthetic diet confirms the presence of efficient RNAi in this insect. These data provide a solid foundation for further research on developing RNAi as a method to manage this pest. Electronic supplementary material The online version of this article (10.1186/s12867-019-0123-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Satnam Singh
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India.
| | - Mridula Gupta
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Suneet Pandher
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Gurmeet Kaur
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Neha Goel
- Forest Research Institute, Dehradun, Uttaranchal, India
| | - Pankaj Rathore
- Punjab Agricultural University, Regional Station, Faridkot, Punjab, 151203, India
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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Singh S, Pandher S, Gupta M, Kaur G, Rathore P. Reference Gene Selection in Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) and Their Normalization Impact on Gene Expression in RNAi Studies. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:371-381. [PMID: 30329069 DOI: 10.1093/jee/toy328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Phenacoccus solenopsis, the cotton mealybug (Hemiptera: Pseudococcidae), is one of the major cotton pests in India. Scanty information is available on molecular studies in this insect due to limited genomic or transcriptomic sequence data. With advancement in sequencing technology, enormous genomic and sequencing data are being generated, and RNAi studies are being undertaken in insects, which require reverse transcription quantitative polymerase chain reaction evaluation. These gene expression studies require normalization of mRNA levels with reference genes to account for sample variability. To supplement the molecular studies in this insect, candidate reference genes were identified and evaluated for their expression stability across various developmental stages and starvation stress. Fourteen candidate reference genes including several commonly used ones were investigated across five different stages and under starvation stress using four different statistical algorithms (NormFinder, genNorm, BestKeeper, and RefFinder). Based on this analysis, GST (third, fourth, and adult stage), Actin (Crawler, second instar), TFIID (starvation stress), SDHA, and 28s were identified as best reference genes for expression studies in mealybug.
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Affiliation(s)
- Satnam Singh
- Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Suneet Pandher
- Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Mridula Gupta
- Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Gurmeet Kaur
- Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
| | - Pankaj Rathore
- Punjab Agricultural University, Regional Research Station, Faridkot, Punjab, India
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Validation and Evaluation of Reference Genes for Quantitative Real-Time PCR in Macrobrachium Nipponense. Int J Mol Sci 2018; 19:ijms19082258. [PMID: 30071669 PMCID: PMC6121487 DOI: 10.3390/ijms19082258] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/02/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is widely used in molecular biology, although the accuracy of the quantitative results is determined by the stability of the reference genes used. Recent studies have investigated suitable reference genes for some crustaceans under various conditions, but studies in Macrobrachium nipponense are currently lacking. In this study, we selected the following seven genes from among 35 commonly used housekeeping genes as candidate qPCR reference genes for temporal and spatial expression: EIF (eukaryotic translation initiation factor 5A), 18S (18S ribosomal RNA), EF-1α (elongation factor-1α), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), TUB (α-tubulin), β-act (β-actin), and RPL18 (Ribosomal protein L18). The stability of each reference gene was evaluated by GeNorm, NormFinder, BestKeeper, and comparative ∆C t methods, and was comprehensively ranked using RefFinder. RPL18 was shown to be the most suitable reference gene for adult M. nipponense tissues, while EIF was the most stable in different ovarian and embryo stages and in white spot syndrome virus infection, and β-act was the most stable reference gene under hypoxia stress. The reliability of the rankings was confirmed by RNA interference experiments. To the best of our knowledge, this represents the first systematic analysis of reference genes for qPCR experiments in M. nipponense, and the results will provide invaluable information for future research in closely related crustaceans.
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Silveyra GR, Silveyra P, Vatnick I, Medesani DA, Rodríguez EM. Effects of atrazine on vitellogenesis, steroid levels and lipid peroxidation, in female red swamp crayfish Procambarus clarkii. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 197:136-142. [PMID: 29482076 DOI: 10.1016/j.aquatox.2018.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/16/2018] [Accepted: 02/18/2018] [Indexed: 06/08/2023]
Abstract
Atrazine, a widely use herbicide, has been classified as a potential endocrine disruptor, especially for freshwater species. In this study, we tested the hypothesis that atrazine can affect reproduction in crayfish through dysregulation of vitellogenin expression and hormone synthesis. Adult female crayfish (Procambarus clarkii) were exposed during one month to atrazine at concentrations of either 1 or 5 mg/L. At the end of the exposure, ovaries, hepatopancreas, and hemolymph samples were harvested for analysis of vitellogenin expression and steroid hormone levels. Ovarian tissue was also sampled for both biochemical and histological analyses. Our results show that atrazine-exposed crayfish had a lower expression of vitellogenin in the ovary and hepatopancreas, as well as smaller oocytes, and reduced vitellogenin content in the ovary. Despite these effects, circulating levels of estradiol increased in females exposed to 5 mg/L of atrazine, showing that the inhibiting effect of atrazine on vitellogenin production was not related to a lower secretion of sexual steroids. Instead, some early stimulating effects of estradiol on vitellogenesis could have occurred, particularly in the hepatopancreas. On the other hand, atrazine caused a higher metabolic effort, in terms of lactate production, presumably triggered to provide the energy needed to face the unspecific stress produced by the herbicide. Lipid peroxidation was not affected by atrazine, but glutathione levels were significantly increased.
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Affiliation(s)
- Gabriela Romina Silveyra
- Dept. of Biodiversity and Experimental Biology, FCEN, University of Buenos Aires, Institute of Biodiversity, Experimental and Applied Biology (IBBEA), CONICET-UBA, Ciudad Universitaria, Pab. II, C1428EGA, Buenos Aires, Argentina.
| | - Patricia Silveyra
- Pulmonary Immunology and Physiology Laboratory, Dept. of Pediatrics, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Itzick Vatnick
- Dept. of Biology, Widener University, Chester, PA 19809, USA.
| | - Daniel Alberto Medesani
- Dept. of Biodiversity and Experimental Biology, FCEN, University of Buenos Aires, Institute of Biodiversity, Experimental and Applied Biology (IBBEA), CONICET-UBA, Ciudad Universitaria, Pab. II, C1428EGA, Buenos Aires, Argentina.
| | - Enrique Marcelo Rodríguez
- Dept. of Biodiversity and Experimental Biology, FCEN, University of Buenos Aires, Institute of Biodiversity, Experimental and Applied Biology (IBBEA), CONICET-UBA, Ciudad Universitaria, Pab. II, C1428EGA, Buenos Aires, Argentina.
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Selection and validation of reference genes for quantitative real-time PCR in Artemisia sphaerocephala based on transcriptome sequence data. Gene 2018; 657:39-49. [PMID: 29505835 DOI: 10.1016/j.gene.2018.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 11/24/2022]
Abstract
Artemisia sphaerocephala, a dicotyledonous perennial semi-shrub belonging to the Artemisia genus of the Compositae family, is widely distributed in northwestern China. This shrub is one of the most important pioneer plants which is capable of protecting rangelands from wind erosion. It therefore plays a vital role in maintaining desert ecosystem stability. In addition, to its use as a forage grass, it has excellent prospective applications as a source of plant oil and as a plant-based fuel. The use of internal genes is the basis for accurately assessing Real time quantitative PCR. In this study, based on transcriptome data of A. sphaerocephala, we analyzed 21 candidate internal genes to determine the optimal internal genes in this shrub. The stabilities of candidate genes were evaluated in 16 samples of A. sphaerocephala. Finally, UBC9 and TIP41-like were determined as the optimal reference genes in A. sphaerocephala by Delta Ct and three various programs. There were GeNorm, NormFinder and BestKeeper.
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Mahanty A, Purohit GK, Mohanty S, Nayak NR, Mohanty BP. Suitable reference gene for quantitative real-time PCR analysis of gene expression in gonadal tissues of minnow Puntius sophore under high-temperature stress. BMC Genomics 2017; 18:617. [PMID: 28810828 PMCID: PMC5557063 DOI: 10.1186/s12864-017-3974-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 07/31/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poorly understood. Gonadal gene expression influence the gonadal development, physiology and the quality of egg/sperm produced in teleosts and the mechanistic understanding of spatio-temporal changes in the gonadal gene expression could be instrumental in controlling the fate of egg/sperm and the quality of seed produced. Real time-quantititative polymerase chain reaction (RT-qCR), is a high throughput, sensitive and reproducible methodology used for understanding gene expression patterns by measuring the relative abundance of mRNA transcripts. However, its accuracy relies upon a suitable reference gene whose expression levels remain stable across various experimental conditions. In the present study, we evaluated the suitability of ten potential reference genes to be used as internal controls in RT-qPCR analysis in gonadal tissues (ovary and testis) of minnow Puntius sophore exposed to high temperature stress for different time periods (7 days, 60 days). Expression analysis of ten different constitutively expressed genes viz. 18S ribosomal RNA (18S rRNA), beta actin (βactin), β-2 microglobulin (b2mg), eukaryotic elongation factor-1 (eef1), glyceraldehyde-3phosphate dehydrogenase (gapdh), glucose-6-phosphate dehydrogenase (g6pd), ribosomal binding protein L13 (rpl13), tubulin (tub), tata box binding protein (tbp), ubiquitin (ubi) was carried out by using RT-qPCR and the stability in their expressions were evaluated by using four different algorithms; namely, delta Ct, BestKeeper, geNorm and NormFinder. RESULTS In ovary, eef1 was found to be the most suitable reference gene in all the algorithms used. In testis, b2mg was found to be the most suitable reference gene in delta Ct, BestKeeper, NormFinder analysis while tbp and eef1 were found to be the most suitable reference genes in geNorm analysis. CONCLUSIONS In conclusion, eef1 and b2mg were found to be the most suitable reference genes in ovary and testis, respectively, of Puntius sophore exposed to high temperature stress, and could be used as internal controls for gene expression analysis in gonadal tissues of Puntius sophore.
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Affiliation(s)
- Arabinda Mahanty
- Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | | | - Sasmita Mohanty
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
| | - Nihar Ranjan Nayak
- Wayne State University Perinatal Initiative, Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
| | - Bimal Prasanna Mohanty
- Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
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Jaramillo ML, Ammar D, Quispe RL, Guzman F, Margis R, Nazari EM, Müller YMR. Identification and evaluation of reference genes for expression studies by RT-qPCR during embryonic development of the emerging model organism, Macrobrachium olfersii. Gene 2016; 598:97-106. [PMID: 27825774 DOI: 10.1016/j.gene.2016.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/25/2016] [Accepted: 11/02/2016] [Indexed: 11/28/2022]
Abstract
RT-qPCR is a sensitive and highly efficient technique that is widely used in gene expression analysis and to provide insight into the molecular mechanisms underlying embryonic development. The freshwater prawn, Macrobrachium olfersii is an emerging model organism, but, the stable reference genes of this species need to be identified and validated for RT-qPCR analysis. Thus, the aim of this study was to evaluate the expression stability of six genes (β-act, GAPDH, EF-1α, RpL8, RpS6, AK) in embryos and in adult tissues (cerebral ganglia, muscle and hepatopancreas) of M. olfersii. The expression stabilities of these genes were evaluated using geNorm, NormFinder, BestKeeper, ΔCt method and integrated tool RefFinder. In the general ranking, RpL8 and RpS6 were the most stable genes in embryos, while RpS6 and RpL8 were the most stable in a combined adult tissue analysis. Analysis of the adult tissues revealed that β-act and AK were the most stable genes in cerebral ganglia, RpL8 and AK in muscle, and RpS6 and β-act in hepatopancreas. EF-1α and GAPDH were the least stable genes and as normalizer genes in RT-qPCR affected expression of the Distal-less gene during M. olfersii development. This study provides suitable reference genes for RT-qPCR analysis and allows future studies of the gene expression in M. olfersii for understanding the molecular mechanisms of their development. To our knowledge, this is the first published study that identifies and evaluates reference genes for RT-qPCR analysis in M. olfersii and could be useful as basis for evaluations of reference genes in other prawns.
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Affiliation(s)
- Michael L Jaramillo
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Dib Ammar
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil; Centro Universitário - Católica de Santa Catarina, 89203-005 Joinville, SC, Brazil
| | - Ruth L Quispe
- Universidade Federal de Santa Catarina, Programa de Pós-Graduação em Neurociências, Campus Universitário, 88040-900 Florianópolis, SC, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, PPGBCM, Centro de Biotecnologia, 91501-970 Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, 91501-970 Porto Alegre, RS, Brazil
| | - Evelise M Nazari
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Yara M R Müller
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
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Shi C, Yang F, Zhu X, Du E, Yang Y, Wang S, Wu Q, Zhang Y. Evaluation of Housekeeping Genes for Quantitative Real-Time PCR Analysis of Bradysia odoriphaga (Diptera: Sciaridae). Int J Mol Sci 2016; 17:ijms17071034. [PMID: 27399679 PMCID: PMC4964410 DOI: 10.3390/ijms17071034] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/15/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
The soil insect Bradysia odoriphaga (Diptera: Sciaridae) causes substantial damage to Chinese chive. Suitable reference genes in B. odoriphaga (Bradysia odoriphaga) have yet to be identified for normalizing target gene expression among samples by quantitative real-time PCR (qRT-PCR). This study was focused on identifying the expression stability of 12 candidate housekeeping genes in B. odoriphaga under various experiment conditions. The final stability ranking of 12 housekeeping genes was obtained with RefFinder, and the most suitable number of reference genes was analyzed by GeNorm. The results revealed that the most appropriate sets of internal controls were RPS15, RPL18, and RPS18 across developmental phases; RPS15, RPL28, and GAPDH across temperatures; RPS15 and RPL18 across pesticide treatments; RSP5, RPS18, and SDHA across photoperiods; ACTb, RPS18, and RPS15 across diets; RPS13 and RPL28 across populations; and RPS15, ACTb, and RPS18 across all samples. The use of the most suitable reference genes versus an arbitrarily selected reference gene resulted in significant differences in the analysis of a target gene expression. HSP23 in B. odoriphaga was found to be up-regulated under low temperatures. These results will contribute to the standardization of qRT-PCR and will also be valuable for further research on gene function in B. odoriphaga.
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Affiliation(s)
- Caihua Shi
- College of Agriculture, Yangtze University, Jingzhou 434025, China.
| | - Fengshan Yang
- College of Life Science, Heilongjiang University, Harbin 150080, China.
| | - Xun Zhu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Erxia Du
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Yuting Yang
- College of Agriculture, Yangtze University, Jingzhou 434025, China.
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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