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Yang Y, Jin F, Liu W, Huo G, Zhou F, Yan J, Zhou K, Li P. Comparative transcriptome, digital gene expression and proteome profiling analyses provide insights into the brachyurization from the megalopa to the first juvenile in Eriocheir sinensis. Heliyon 2023; 9:e12736. [PMID: 36685450 PMCID: PMC9853305 DOI: 10.1016/j.heliyon.2022.e12736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 12/13/2022] [Accepted: 12/26/2022] [Indexed: 01/08/2023] Open
Abstract
Eriocheir sinensis larva normally experiences 11 stages. The reduced abdomen folded beneath the thorax is the most prominent characteristic of morphological alteration from megalopa to juvenile crab. Up to date, the molecular mechanisms of brachyurization remain a mystery. Here, transcriptome library, digital gene expression (DGE) libraries and proteome libraries at two developmental stages [the megalopa stage of E. sinensis (stage M) and the first stage of juvenile crab (stage J1)] of the Chinese mitten crab larva were constructed for RNA sequencing and iTRAQ approaches followed by bioinformatics analysis, respectively. In total, 1106 genes and 871 proteins were differentially expressed between the stage M and stage J1. Moreover, several important pathways were identified, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and some disease pathways. Besides, muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway also had important functions in brachyurization process. Furthermore, the components, actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin had up-regulated expression levels in M stage compared to J1 stage.
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Affiliation(s)
- Yunxia Yang
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Fangcao Jin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Wanyi Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Guangming Huo
- School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, PR China
| | - Feng Zhou
- School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, PR China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, PR China,Corresponding author. College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, Jiangsu, PR China.
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Macerola E, Poma AM, Basolo F. NanoString in the screening of genetic abnormalities associated with thyroid cancer. Semin Cancer Biol 2020; 79:132-140. [PMID: 33091600 DOI: 10.1016/j.semcancer.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 10/12/2020] [Indexed: 11/24/2022]
Abstract
In the setting of cancer pathology, molecular characterization of tumors providing diagnostic and predictive information is acquiring more and more relevance. Moreover, the advent of innovative technologies continuously improves the knowledge of the molecular landscape of tumors and strengthens the links between clinics, tumor pathology and molecular features. In the clinical management of patients with thyroid nodules and thyroid tumors, the aid of molecular testing is encouraged but still not strongly recommended by current guidelines. Also for this reason this field of study is attracting much interest. The nCounter system is a relatively new technology based on a direct hybridization of fluorescent probes to specific nucleic acid targets, followed by digital measurement of signals; the reaction is highly multiplexable and results are robust and reproducible. This review reports and discusses the available data related to the application of this specific technique to thyroid nodules and thyroid tumors samples. The available data indicate that nCounter system represents a solid approach for the research of relevant diagnostic and prognostic biomarkers in thyroid pathology.
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Affiliation(s)
- Elisabetta Macerola
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
| | - Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi, 10, 56126, Pisa, Italy.
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Swaminathan A, Harrison PF, Preiss T, Beilharz TH. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes. Methods Mol Biol 2020; 2049:141-164. [PMID: 31602610 DOI: 10.1007/978-1-4939-9736-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing (NGS) and its application to RNA (RNA-seq) has opened up multiple aspects of RNA processing to deep transcriptome-wide analysis at nucleotide resolution. This has been useful in delineating the transcribed areas of the genome, and in quantitation of RNA isoforms. Such isoforms can diversify the regulatory repertoire of mRNAs. For example, the 3'-end of mRNA can vary in two important ways, in the position chosen for cleavage and polyadenylation, and in the length of the poly(A)-tail. Accordingly, the step-up in resolution made possible by NGS has revealed an unexpectedly high level of alternative polyadenylation (APA). Moreover, it has massively simplified the transcriptome-wide detection of poly(A)-tail length changes. Here we present our approach to the study of 3'-end dynamics using a 3'-focused RNA-seq method called PAT-seq (for poly(A)-test sequencing). The approach records gene expression, APA, and poly(A)-tail changes between transcriptomes to reveal complex interplay between transcriptional and posttranscriptional control mechanisms.
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Affiliation(s)
- Angavai Swaminathan
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - Thomas Preiss
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia.
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Long Y, Liang F, Zhang J, Xue M, Zhang T, Pei X. Identification of drought response genes by digital gene expression (DGE) analysis in Caragana korshinskii Kom. Gene 2020; 725:144170. [PMID: 31647996 DOI: 10.1016/j.gene.2019.144170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 11/22/2022]
Abstract
Caragana korshinskii Kom. is a legume shrub that is widely distributed across desert habitats with gravely, sandy, and saline soils in Asia and Africa. C. korshinskii has highly developed roots and a strong tolerance to abiotic stress. At present, there are few genetic studies of C. korshinskii because of the limited availability of genomic resources. To understand the comprehensive mechanisms that are associated with drought tolerance, we used RNA-seq to survey the differentially expressed genes (DEGs) in comparisons of drought-treated and control plants. After analysing the sequencing results, we found 440 differentially expressed genes existing in drought-treated and control plants. Among the DEGs, 39 unigenes showed up-regulated expression after drought treatment, while 401 unigenes were down-regulated. We used the KEGG database to annotate these drought-induced genes; 126 unigenes were identified by KEGG pathway annotation, and approximately 28% of the unigenes with known function fell into categories related to fatty acid metabolism, starch, sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Finally, we confirmed that one gene has a potential function in drought tolerance. Our study is the first to provide transcriptomic resources for Caragana korshinskii and to determine its digital gene expression profile under conditions of drought stress using the assembled transcriptomic data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic stress conditions.
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Lv J, Cao T, Ji C, Cong M, Zhao J, Wu H. Digital gene expression analysis in the gills of Ruditapes philippinarum after nitrite exposure. Ecotoxicol Environ Saf 2019; 184:109661. [PMID: 31520948 DOI: 10.1016/j.ecoenv.2019.109661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Due to the overload of pollutants from highly intensive anthropic activities, nitrite accumulates in offshore seawater and has been a long-lasting pollutant to the healthy aquaculture of the mollusk. In the present study, Ruditapes philippinarum was used as the target bivalve to receive nitrite exposure at environmental concentration for 1 and 7 days. Differentially expressed genes (DEGs) were detected and analyzed by a digital gene expression (DGE) approach to describe the toxicity of nitrite on the bivalve at the gene level. In the N1 group, 185 DEGs were generated and enriched in six Gene Ontology (GO) terms, including oxidoreductase activity, heme binding, tetrapyrrole binding, iron ion binding, metal binding and cation binding. The DEGs in the N1 group were also enriched in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, e.g., arachidonic acid metabolism and ovarian steroidogenesis. In the N7 group, 81 DEGs were generated without any GO enrichment but were enriched in five KEGG pathways, including protein processing in the endoplasmic reticulum, protein export, prion diseases, thyroid hormone synthesis and arachidonic acid metabolism. This suggested that nitrite exposure might cause adverse effects to the clams in several aspects, including oxidative damage, depressed immunity, and disorders in cell proliferation, hormone metabolism and tissue regeneration. Evaluation of oxidative stress indicated that nitrite exposure actually induced redox state imbalance by enhancing the contents of thiobarbituric acid reactive substances (TBARSs) and glutathione (GSH), and the activity of glutathione peroxidase (GSH-PX) but not superoxide dismutase (SOD). These results will provide valuable gene references for further study on the toxicology mechanism of bivalves under environmental nitrite stress.
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Affiliation(s)
- Jiasen Lv
- Biology School of Yantai University, Yantai, 264005, PR China
| | - Tengfei Cao
- Biology School of Yantai University, Yantai, 264005, PR China
| | - Chenglong Ji
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Provincial Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China
| | - Ming Cong
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Provincial Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China.
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Provincial Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China
| | - Huifeng Wu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Provincial Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China.
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Ke XL, Zhang DF, Li QY, Liu ZG, Gao FY, Lu MX, Yang H. Digital gene expression analysis in the liver of ScpB-vaccinated and Streptococcus agalactiae-challenged Nile tilapia. Fish Shellfish Immunol 2019; 94:249-257. [PMID: 31470139 DOI: 10.1016/j.fsi.2019.08.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
In recent years, streptococcal diseases have severely threatened the development of tilapia aquaculture, but effective prevention and control methods have not yet been established. To understand the immune responses of vaccinated Nile tilapia (Oreochromis niloticus), digital gene expression (DGE) technology was applied in this study to detect the gene expression profile of the Nile tilapia (O. niloticus) liver in response to ScpB (Streptococcal C5a peptidase from group B Streptococcus, ScpB) vaccination and a Streptococcus agalactiae-challenge. The control and the ScpB-vaccinated Nile tilapia yielded a total of 25,788,734 and 27,088,598 clean reads, respectively. A total of 1234 significant differentially expressed unigenes were detected (P < 0.05), of which 236 were significantly up-regulated, and 269 were significantly down-regulated (P < 0.05, |fold|>2, FDR<0.05). Of the differentially expressed gene, the identified genes which were enriched using databases of GO and KEGG could be categorized into a total of 67 functional groups and were mapped to 153 signaling pathways including 15 immune-related pathways. The differentially expressed genes (TLR1, TLR2, TLR3, TLR5, TLR9, MyD88, C3, IL-1β, IL-10) were detected in the expression profiles, and this was subsequently verified via quantitative real-time PCR (qPCR). The results of this study can serve as a basis for future research not only on the molecular mechanism of S. agalactiae invasion, but also on the anti-S. agalactiae mechanism in targeted tissues of Nile tilapia.
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Affiliation(s)
- Xiao-Li Ke
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - De-Feng Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Qing-Yong Li
- Fisheries Research & Extension Center of Huizhou, Huizhou, 516002, China
| | - Zhi-Gang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China
| | - Mai-Xin Lu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fisheries Science, Guangzhou, 510380, China.
| | - Hong Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi, 214081, China.
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Xue Y, Wei F, Jiang Y, Li L, Dong S, Tian X. Transcriptome signatures of the Pacific white shrimp Litopenaeus vannamei hepatopancreas in response to stress in biofloc culture systems. Fish Shellfish Immunol 2019; 91:369-375. [PMID: 30999042 DOI: 10.1016/j.fsi.2019.04.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Comparative transcriptome analysis via high throughput sequencing was applied to gain knowledge on the immune response in Litopenaeus vannamei reared in biofloc technology systems (BFT). Two types of carbon sources, namely, traditional carbon sources (molasses) and biodegradable polymers [hydroxybutyric acid-co-3-hydroxyvaleric acid (PHBV)] were used in BFT systems. Clear water systems without the addition of carbon sources were treated as the control. Water quality assays showed that the average concentrations of several stress factors, including nitrite, nitrate and TSS, were the highest in molasses-based BFT systems. After sequencing and comparing the transcriptome profiles of the L. vannamei hepatopancreas, 743 and 201 genes were significantly differentially expressed in molasses- and PHBV-based BFT systems, respectively. GO enrichment analysis, which was performed using the differentially expressed genes, revealed seven significantly over-represented GO terms in molasses-based BFT systems, including catabolic process, hydrolase activity, cellular localization, organic substance metabolic process, cellular metabolic process, establishment of localization and response to stress. The captured key genes were mainly involved in the pathways including cellular stress response, immune response and pathogen recognition. However, no GO terms were significantly over-represented in PHBV-based BFT systems compared with control. This study indicates that shrimp are subject to stress in BFT systems when molasses serves as the carbon source. Thus, PHBV may be a better alternative.
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Affiliation(s)
- Yiming Xue
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Fayi Wei
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
| | - Li Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China.
| | - Shuanglin Dong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
| | - Xiangli Tian
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, People's Republic of China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266235, China
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Guo SH, Yu L, Liu YM, Wang FF, Chen YC, Wang Y, Qiu BL, Sang W. Digital gene expression profiling in larvae of Tribolium castaneum at different periods post UV-B exposure. Ecotoxicol Environ Saf 2019; 174:514-523. [PMID: 30861439 DOI: 10.1016/j.ecoenv.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
UV-B radiation is an important environmental factor. Exposure to excess UV-B radiation can cause serious effects on the development, survival, and reproduction of different organisms. Plants and animals have developed many different strategies to cope with UV-B-induced damage, but the physiological response of insects to UV-B remains unclear. In the present study, the red flour beetle Tribolium castaneum (Herbst) was used to assess the stress response of UV-B. The underlying molecular mechanisms were explored using RNA sequencing. We investigated the transcriptomic profile of T. castaneum larvae at 4 and 24 h after treatment with UV-B radiation via digital gene expression analysis. The 310 and 996 differentially expressed genes were detected at 4 and 24 h, respectively. Then the biological functions and associated metabolic processes of these genes were determined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The reliability of the data was verified using qRT-PCR. The results indicated that several differentially expressed genes are involved in antioxidation, DNA repair, protein folding, carbon flux diversion, and the extracellular matrix to protect against UV-B-induced damage. This study will increase our understanding of the molecular mechanism underlying insect response to UV-B radiation.
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Affiliation(s)
- Shu-Hao Guo
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Lin Yu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Yan-Mei Liu
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Fei-Feng Wang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Yu-Chen Chen
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Ye Wang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Bao-Li Qiu
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China
| | - Wen Sang
- Key Laboratory of Bio-Pesticide Creation and Application, South China Agricultural University, Guangzhou 510640, China.
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Ding Z, Zhao X, Cui L, Sun Q, Zhang F, Wang J, Wang W, Liu H. Novel insights into the immune regulatory effects of ferritins from blunt snout bream, Megalobrama amblycephala. Fish Shellfish Immunol 2019; 87:679-687. [PMID: 30731213 DOI: 10.1016/j.fsi.2019.01.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Ferritins play vital roles in maintenance of iron homeostasis as iron storage proteins. Recently, the immune function of ferritins have attracted increasing attention, especially their roles in defense against pathogenic infections. However, the immune regulatory mechanism of fish ferritins are not well known. In the present study, comparative digital gene expression (DGE) profiling was performed to explore the regulatory effects of the Megalobrama amblycephala ferritins (MamFers) using MamFers overexpressed and control L8824 cells (Ctenopharyngodon idella hepatic cell line). Clean reads were aligned to the C. idella genome and differential expression analysis was conducted with representative differentially expressed genes pointed out. On that basis, further studies were performed to verify two pivotal regulated pathways in L8824 and EPC (Epithelioma Papulosum Cyprini cell line) cells, respectively. The results showed that NLRC5 (NOD-like Receptor Family CARD Domain Containing 5) mediated the regulation of MamFers on expression of MHC I (Major Histocompatibility Complex Class I) and its chaperone β2M (Beta-2-Microglobulin) in L8824 cells. Then, β2M further mediated the regulation of MamFers on hepcidin expression, indicating that MamFers regulated the expression of hepcidin via NLRC5/MHC I/β2M axis. In addition, MamFers regulated the adhesion of Aeromonas hydrophila to EPC cells by regulating the expression of two extracellular matrix proteins Intgβ1 (integrin β1) and FN (fibronectin). In a word, the present study provided novel insights into the immune regulatory functions of fish ferritins.
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Affiliation(s)
- Zhujin Ding
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Xiaoheng Zhao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; College of Marine Life and Fisheries, Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang, 222005, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Lei Cui
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Qianhui Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jixiu Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weimin Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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Zhang H, Ali A, Hou F, Wu T, Guo D, Zeng X, Wang F, Zhao H, Chen X, Xu P, Wu X. Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.). BMC Plant Biol 2018; 18:314. [PMID: 30497392 PMCID: PMC6267922 DOI: 10.1186/s12870-018-1553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. RESULTS In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). CONCLUSIONS We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
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Affiliation(s)
- Hongyu Zhang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Asif Ali
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Feixue Hou
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Tingkai Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Daiming Guo
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiufeng Zeng
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Fangfang Wang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Huixia Zhao
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiaoqiong Chen
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Peizhou Xu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xianjun Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
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Xu H, Liu X, Jia Y, Dong F, Xu J, Wu X, Yang Y, Zheng Y. Fipronil-induced toxic effects in zebrafish (Danio rerio) larvae by using digital gene expression profiling. Sci Total Environ 2018; 639:550-559. [PMID: 29800848 DOI: 10.1016/j.scitotenv.2018.05.159] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 05/07/2023]
Abstract
Fipronil residue has caused widespread concern around the world, especially after the recent "toxic eggs" event in seven European countries. To evaluate the effects of fipronil on vertebrates, zebrafish larvae were used as an animal model to examine the lethal effect, developmental phenotypes at high doses, and possible mechanisms of toxicity by employing digital gene expression (DGE) profiling at environmentally relevant doses. The results of acute toxicity test indicated that treatment with fipronil from 75 h post-fertilization (hpf) led to the death of larvae with a 96-h LC50 value of 459 μg/L, as well as abnormal development including bent spine and shortened body length. Besides, we obtained high-quality-sequencing DGE profilings at fipronil concentrations of 0.5, 5, and 50 μg/L, respectively. The results revealed that 44 differentially expressed genes, 10 GO terms, and 3 KEGG pathways were overlapped among the three concentrations. MIDN, one of the 44 differentially expressed genes, showed dose-dependent responses at the transcriptional level, indicating that it was possibly a potential biomarker to reflect fipronil toxicity in zebrafish. Furthermore, we presumed that the changing transcriptional level of AP-1 family was possibly a reason for bent spine and shortened body length in larvae exposed to fipronil. Concurrently, altered abundance of transcripts of the ELOVL family in a key step of fatty acid elongation could possibly lead to the accumulation of long-chain fatty acids. Collectively, our results suggested that exposure to fipronil caused lethal and developmental toxicity in zebrafish larvae, and demonstrated the need for a comprehensive understanding of the potential mechanisms of fipronil toxicity due to fipronil's frequent presence in the environment and its potential threat to human health.
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Affiliation(s)
- Hanqing Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yang Jia
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Mao R, Chen J, Chen Y, Guo Z. Identification of early jasmonate-responsive genes in Taxus × media cells by analyzing time series digital gene expression data. Physiol Mol Biol Plants 2018; 24:715-727. [PMID: 30150849 PMCID: PMC6103953 DOI: 10.1007/s12298-018-0527-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Jasmonate, an effective elicitor, can induce the biosynthesis of paclitaxel, a well-known anticancer drug, in Taxus cell culture. The jasmonate signaling pathway has been well studied in Arabidopsis, and many early jasmonate-responsive genes have been found to be involved in signaling pathway. In Taxus, only a few late jasmonate-responsive genes related to paclitaxel biosynthesis were identified. So, identification of early responsive genes and knowledge of the jasmonate signaling pathway are essential for understanding the effects of jasmonate on paclitaxel biosynthesis and for improving paclitaxel production in Taxus cells. In this study, total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 h of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the paired-end method. A total of 45,583 transcript clusters were obtained by de novo assembly of the sequenced reads. Based on the transcriptome data, the digital gene expressions of each RNA sample were investigated. We found that after 0.5, 3, and 24 h of methyl jasmonate treatment; 134, 1008, and 987 unigenes were differentially expressed. For the secondary metabolism pathways, phenylalanine pathway unigenes were responsive to jasmonate after 3 h of treatment, while genes related to paclitaxel biosynthesis were induced after 0.5 h of treatment. The digital gene expression levels of candidate genes related to paclitaxel biosynthesis were confirmed by qRT-PCR. Transcriptome sequencing and digital gene expression profiling identified early jasmonate-responsive genes in cultured Taxus × media cells. The comprehensive time series jasmonate-responsive gene expression data have provided transcriptome-wide information about the mechanism of paclitaxel biosynthesis regulation by jasmonate signaling.
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Affiliation(s)
- Rongjia Mao
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China
| | - Jing Chen
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China
| | - Yuejun Chen
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China
| | - Zhigang Guo
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China
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Na W, Wu YY, Gong PF, Wu CY, Cheng BH, Wang YX, Wang N, Du ZQ, Li H. Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content. BMC Genomics 2018; 19:384. [PMID: 29792171 PMCID: PMC5966864 DOI: 10.1186/s12864-018-4776-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background In avian species, liver is the main site of de novo lipogenesis, and hepatic lipid metabolism relates closely to adipose fat deposition. Using our fat and lean chicken lines of striking differences in abdominal fat content, post-hatch lipid metabolism in both liver and adipose tissues has been studied extensively. However, whether molecular discrepancy for hepatic lipid metabolism exists in chicken embryos remains obscure. Results We performed transcriptome and proteome profiling on chicken livers at five embryonic stages (E7, E12, E14, E17 and E21) between the fat and lean chicken lines. At each stage, 521, 141, 882, 979 and 169 differentially expressed genes were found by the digital gene expression, respectively, which were significantly enriched in the metabolic, PPAR signaling and fatty acid metabolism pathways. Quantitative proteomics analysis found 20 differentially expressed proteins related to lipid metabolism, PPAR signaling, fat digestion and absorption, and oxidative phosphorylation pathways. Combined analysis showed that genes and proteins related to lipid transport (intestinal fatty acid-binding protein, nucleoside diphosphate kinase, and apolipoprotein A-I), lipid clearance (heat shock protein beta-1) and energy metabolism (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 and succinate dehydrogenase flavoprotein subunit) were significantly differentially expressed between the two lines. Conclusions For hepatic lipid metabolism at embryonic stages, molecular differences related to lipid transport, lipid clearance and energy metabolism exist between the fat and lean chicken lines, which might contribute to the striking differences of abdominal fat deposition at post-hatch stages. Electronic supplementary material The online version of this article (10.1186/s12864-018-4776-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yuan-Yuan Wu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Peng-Fei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun-Yan Wu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Bo-Han Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Yu-Xiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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Liu X, Jin G, Qian J, Yang H, Tang H, Meng X, Li Y. Digital gene expression profiling analysis and its application in the identification of genes associated with improved response to neoadjuvant chemotherapy in breast cancer. World J Surg Oncol 2018; 16:82. [PMID: 29685151 PMCID: PMC5914024 DOI: 10.1186/s12957-018-1380-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/03/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND This study aimed to screen sensitive biomarkers for the efficacy evaluation of neoadjuvant chemotherapy in breast cancer. METHODS In this study, Illumina digital gene expression sequencing technology was applied and differentially expressed genes (DEGs) between patients presenting pathological complete response (pCR) and non-pathological complete response (NpCR) were identified. Further, gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed. The genes in significant enriched pathways were finally quantified by quantitative real-time PCR (qRT-PCR) to confirm that they were differentially expressed. Additionally, GSE23988 from Gene Expression Omnibus database was used as the validation dataset to confirm the DEGs. RESULTS After removing the low-quality reads, 715 DEGs were finally detected. After mapping to KEGG pathways, 10 DEGs belonging to the ubiquitin proteasome pathway (HECTD3, PSMB10, UBD, UBE2C, and UBE2S) and cytokine-cytokine receptor interactions (CCL2, CCR1, CXCL10, CXCL11, and IL2RG) were selected for further analysis. These 10 genes were finally quantified by qRT-PCR to confirm that they were differentially expressed (the log2 fold changes of selected genes were - 5.34, 7.81, 6.88, 5.74, 3.11, 19.58, 8.73, 8.88, 7.42, and 34.61 for HECTD3, PSMB10, UBD, UBE2C, UBE2S, CCL2, CCR1, CXCL10, CXCL11, and IL2RG, respectively). Moreover, 53 common genes were confirmed by the validation dataset, including downregulated UBE2C and UBE2S. CONCLUSION Our results suggested that these 10 genes belonging to these two pathways might be useful as sensitive biomarkers for the efficacy evaluation of neoadjuvant chemotherapy in breast cancer.
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Affiliation(s)
- Xiaozhen Liu
- Pathology Department, Zhejiang Cancer Hospital, Hangzhou, 3110022, Zhejiang Province, China
| | - Gan Jin
- The 2nd Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Jiacheng Qian
- The 2nd Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Hongjian Yang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Building NO. 1, East of Banshan Road, Gongshu District, Hangzhou, 3110022, Zhejiang Province, China
| | - Hongchao Tang
- The 2nd Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Xuli Meng
- Department of Breast Surgery, Zhejiang Cancer Hospital, Building NO. 1, East of Banshan Road, Gongshu District, Hangzhou, 3110022, Zhejiang Province, China.
- Department of General Surgery, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China.
| | - Yongfeng Li
- Department of Breast Surgery, Zhejiang Cancer Hospital, Building NO. 1, East of Banshan Road, Gongshu District, Hangzhou, 3110022, Zhejiang Province, China.
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Yang T, Huang XS. Deep sequencing-based characterization of transcriptome of Pyrus ussuriensis in response to cold stress. Gene 2018; 661:109-18. [PMID: 29580898 DOI: 10.1016/j.gene.2018.03.067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 01/14/2023]
Abstract
Pyrus ussuriensis is extremely cold hardy when fully acclimated, but knowledge relevant to the molecular mechanisms underlying this economically valuable trait is still limited so far. In this study, global transcriptome profiles of Pyrus ussuriensis under cold conditions (4 °C) over a time course were generated by high-throughput sequencing. In total, >57,121,199 high quality clean reads were obtained with approximately 11.0 M raw data for each library. Among them, the values of 66.84%-72.03% of clean reads in the digital transcript abundance measurement could be well mapped to the pear genome database, resulting in the identification of 8544 differentially expressed genes (DEGs) having 43 Gene Ontology (GO) terms and 17 clusters of orthologous groups (COG) involved in 385 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. These comprised 3124 (1033 up-regulated, 2091 down-regulated), 1243 (729 up-regulated, 514 down-regulated), and 750 (458 up-regulated, 292 down-regulated) genes from the cold-treated samples at 5, 12 and 24 h, respectively. The accuracy of the RNA-Seq derived transcript expression data was validated by analyzing the expression patterns of 16 DGEs by quantitative real-time PCR. Plant-pathogen interaction, plant hormone signal transduction, Photosynthesis, signal transduction, innate immune response and response to biotic stimulus were the most significantly enriched GO categories among in the DEGs. A total of 335 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones were significantly affected by the cold stress. The RNA-Seq and digital expression profiling provides valuable insights into the understanding the molecular events related to cold responses in Pyrus ussuriensis and dataset may help guide future identification and functional analysis of potential genes that are important for enhancing cold hardiness.
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Cong M, Wu H, Cao T, Lv J, Wang Q, Ji C, Li C, Zhao J. Digital gene expression analysis in the gills of Ruditapes philippinarum exposed to short- and long-term exposures of ammonia nitrogen. Aquat Toxicol 2018; 194:121-131. [PMID: 29179147 DOI: 10.1016/j.aquatox.2017.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Previous study revealed severe toxic effects of ammonia nitrogen on Ruditapes philippinarum including lysosomal instability, disturbed metabolic profiles, gill tissues with damaged structure, and variation of neurotransmitter concentrations. However, the underlying molecular mechanism was not fully understood yet. In the present study, digital gene expression technology (DGE) was applied to globally screen the key genes and pathways involved in the responses to short- and long-term exposures of ammonia nitrogen. Results of DGE analysis indicated that short-term duration of ammonia exposure affected pathways in Dorso-ventral axis formation, Notch signaling, thyroid hormone signaling and protein processing in endoplasmic reticulum. The long-term exposure led to DEGs significantly enriched in gap junction, immunity, signal and hormone transduction, as well as key substance metabolism pathways. Functional research of significantly changed DEGs suggested that the immunity of R. philippinarum was weakened heavily by toxic effects of ammonia nitrogen, as well as neuro-transduction and metabolism of important substances. Taken together, the present study provides a molecular support for the previous results of the detrimental toxicity of ammonia exposure in R. philippinarum, further work will be performed to investigate the specific genes and their certain functions involved in ammonia toxicity to molluscs.
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Affiliation(s)
- Ming Cong
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Huifeng Wu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.
| | - Tengfei Cao
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Jiasen Lv
- Biology School of Yantai University, Yantai 264005, PR China
| | - Qing Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Chenglong Ji
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
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Zhang QL, Qiu HY, Liang MZ, Luo B, Wang XQ, Chen JY. Exploring gene expression changes in the amphioxus gill after poly(I:C) challenge using digital expression profiling. Fish Shellfish Immunol 2017; 70:57-65. [PMID: 28866273 DOI: 10.1016/j.fsi.2017.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC). Six libraries were created for the control and treatment groups including three biological replicates per group. A total of 1999 differently expressed genes (DEGs) were obtained, with 571 and 1428 DEGs showing up- or down-regulation, respectively, in the treatment group. Enrichment analysis of gene ontology (GO) terms and pathways revealed that the DEGs were primarily related to immune and defense response, apoptosis, human disease, cancer, protein metabolism, enzyme activity, and regulatory processes. In addition, eight DEGs were randomly selected to validate the RNA-seq data using real-time quantitative PCR (qRT-PCR), and the results confirmed the accuracy of the RNA-seq approach. Next, we screened eight key responding genes to examine the dynamic changes in expression levels at different time points in more detail. The results indicated that expressions of TRADD, MARCH, RNF31, NF-κb, CYP450, TNFRSF6B, IFI and LECT1 were induced to participate in the antiviral response against pIC. This study provides a valuable resource for understanding the role of the amphioxus gill in antiviral immunity and the evolution of gill immunity in vertebrates.
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Affiliation(s)
- Qi-Lin Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China.
| | - Han-Yue Qiu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China
| | - Ming-Zhong Liang
- Department of Marine Science, Qinzhou University, Qinzhou, 535000 China
| | - Bang Luo
- Guangxi Academy of Fishery Sciences, Nanning, 530000 China
| | - Xiu-Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China; LPS, Nanjing Institute of Geology and Paleontology, CAS, Nanjing, 210008 China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China; LPS, Nanjing Institute of Geology and Paleontology, CAS, Nanjing, 210008 China.
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Liang C, Wang W, Wang J, Ma J, Li C, Zhou F, Zhang S, Yu Y, Zhang L, Li W, Huang X. Identification of differentially expressed genes in sunflower (Helianthus annuus) leaves and roots under drought stress by RNA sequencing. Bot Stud 2017; 58:42. [PMID: 29071432 PMCID: PMC5656504 DOI: 10.1186/s40529-017-0197-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/02/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sunflower is recognized as one of the most important oil plants with strong tolerance to drought in the world. In order to study the response mechanisms of sunflower plants to drought stress, gene expression profiling using high throughput sequencing was performed for seedling leaves and roots (sunflower inbred line R5) after 24 h of drought stress (15% PEG 6000). The transcriptome assembled using sequences of 12 samples was used as a reference. RESULTS 805 and 198 genes were identified that were differentially expressed in leaves and roots, respectively. Another 71 genes were differentially expressed in both organs, in which more genes were up-regulated than down-regulated. In agreement with results obtained for other crops or from previous sunflower studies, we also observed that nine genes may be associated with the response of sunflower to drought. CONCLUSIONS The results of this study may provide new information regarding the sunflower drought response, as well as add to the number of known genes associated with drought tolerance.
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Affiliation(s)
- Chunbo Liang
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Xuefu Road 368, Harbin, 150086 People’s Republic of China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Wenjun Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Jing Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Jun Ma
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Cen Li
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Fei Zhou
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Shuquan Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Ying Yu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Liguo Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Weizhong Li
- Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150036 People’s Republic of China
| | - Xutang Huang
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Xuefu Road 368, Harbin, 150086 People’s Republic of China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
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Liu K, Li H, Li W, Zhong J, Chen Y, Shen C, Yuan C. Comparative transcriptomic analyses of normal and malformed flowers in sugar apple (Annona squamosa L.) to identify the differential expressed genes between normal and malformed flowers. BMC Plant Biol 2017; 17:170. [PMID: 29061115 PMCID: PMC5653983 DOI: 10.1186/s12870-017-1135-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/18/2017] [Indexed: 06/03/2023]
Abstract
BACKGROUND Sugar apple (Annona squamosa L.), a popular fruit with high medicinal and nutritional properties, is widely cultivated in tropical South Asia and America. The malformed flower is a major cause for a reduction in production of sugar apple. However, little information is available on the differences between normal and malformed flowers of sugar apple. RESULTS To gain a comprehensive perspective on the differences between normal and malformed flowers of sugar apple, cDNA libraries from normal and malformation flowers were prepared independently for Illumina sequencing. The data generated a total of 70,189,896 reads that were integrated and assembled into 55,097 unigenes with a mean length of 783 bp. A large number of differentially expressed genes (DEGs) were identified. Among these DEGs, 701 flower development-associated transcript factor encoding genes were included. Furthermore, a large number of flowering- and hormone-related DEGs were also identified, and most of these genes were down-regulated expressed in the malformation flowers. The expression levels of 15 selected genes were validated using quantitative-PCR. The contents of several endogenous hormones were measured. The malformed flowers displayed lower endogenous hormone levels compared to the normal flowers. CONCLUSIONS The expression data as well as hormone levels in our study will serve as a comprehensive resource for investigating the regulation mechanism involved in floral organ development in sugar apple.
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Affiliation(s)
- Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
| | - Haili Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
| | - Weijin Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
| | - Jundi Zhong
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
| | - Yan Chen
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
| | - Changchun Yuan
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong 524048 People’s Republic of China
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Xu YG, Chai LH, Shi W, Wang DD, Zhang JY, Xiao XH. Transcriptome profiling and digital gene expression analysis of the skin of Dybowski's frog (Rana dybowskii) exposed to Aeromonas hydrophila. Appl Microbiol Biotechnol 2017. [PMID: 28647779 DOI: 10.1007/s00253-017-8385-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recently, populations of Rana dybowskii, an important amphibian species in Northeast China, have decreased, mainly owing to the disease caused by Aeromonas hydrophila. However, effective control methods have not yet been developed. In order to explore the immune responses of R. dybowskii upon exposure to A. hydrophila infection, Illumina high-throughput transcriptome sequencing and digital gene expression (DGE) technology were employed to investigate transcriptomic changes in the skin of R. dybowskii exposed to A. hydrophila. In this work, a total of 26,244,446 transcriptome sequencing reads were obtained and assembled into 109,089 unique unigenes using de novo assembly, and a total of 37,105 unigenes (34.0%) were functionally annotated against the non-redundant (Nr), Swiss-Prot, Cluster of Orthologous Groups of Proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Gene expression changes in the skin tissue of R. dybowskii exposed to A. hydrophila were investigated by a tag-based DGE system, and a total of 1435 significantly differentially expressed genes were identified, including 460 that were up-regulated and 975 that were down-regulated, indicating a large change in the host transcriptome profile exposed to A. hydrophila. Among these, 478 genes were associated with immune-relevant pathways, metabolic pathways, cellular components, growth, migration, and muscle and hormone signaling pathways. We confirmed the differential expression of 106 immune-relevant genes associated with innate and adaptive immune responses. Our data provide a fairly comprehensive molecular biology background for the deeper understanding of the amphibian immune system following A. hydrophila infection.
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Affiliation(s)
- Yi-Gang Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China. .,College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
| | - Long-Hui Chai
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wen Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Dan-Dan Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Jing-Yu Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiang-Hong Xiao
- College of Wildlife Resources, Northeast Forestry University, Harbin, China.
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Zhu B, Tang L, Yu Y, Yu H, Wang L, Qian C, Wei G, Liu C. Identification of ecdysteroid receptor-mediated signaling pathways in the hepatopancreas of the red swamp crayfish, Procambarus clarkii. Gen Comp Endocrinol 2017; 246:372-381. [PMID: 28069422 DOI: 10.1016/j.ygcen.2017.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 12/30/2022]
Abstract
The hepatopancreas of crustaceans plays an important role in lipid and carbohydrate metabolism, digestion of food, and biogenesis. In this study, the hepatopancreas transcriptome from the red crayfish Procambarus clarkii was characterized for the first time using high-throughput sequencing, producing approximately 41.4 million reads were obtained. After de novo assembly, 57,363 unigenes with an average length of 725bp were identified, Gene Ontology analysis categorized 22,580 as being involved in biological processes, among which metabolic process and cellular process groups were the most highly enriched. A total of 8034 unigenes were assigned to 223 metabolic pathways following mapping against the Kyoto encyclopedia of genes and genomes (KEGG) database. Ecdysteroid receptor (EcR)-mediated signaling pathways were investigated using digital gene expression (DGE) analysis following RNA interference targeting the EcR. A total of 529 differentially expressed genes (DEGs) were identified, including 322 downregulated and 207 upregulated unigenes. Of these, 445 (84.12%) were annotated successfully by alignment with known sequences, many of which were related to catalytic activity and binding functional categories. Using KEGG enrichment analysis, 183 DEGs were clustered into 78 pathways, and six significantly enriched pathways were predicted. The expression patterns of candidate genes identified by real-time PCR were consistent with the DGE results.
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Affiliation(s)
- Baojian Zhu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China.
| | - Lin Tang
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Yingying Yu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Huimin Yu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Lei Wang
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Cen Qian
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Guoqing Wei
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
| | - Chaoliang Liu
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, PR China
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22
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Guo Y, Qiu C, Long S, Chen P, Hao D, Preisner M, Wang H, Wang Y. Digital gene expression profiling of flax (Linum usitatissimum L.) stem peel identifies genes enriched in fiber-bearing phloem tissue. Gene 2017; 626:32-40. [PMID: 28479385 DOI: 10.1016/j.gene.2017.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/11/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
To better understand the molecular mechanisms and gene expression characteristics associated with development of bast fiber cell within flax stem phloem, the gene expression profiling of flax stem peels and leaves were screened, using Illumina's Digital Gene Expression (DGE) analysis. Four DGE libraries (2 for stem peel and 2 for leaf), ranging from 6.7 to 9.2 million clean reads were obtained, which produced 7.0 million and 6.8 million mapped reads for flax stem peel and leave, respectively. By differential gene expression analysis, a total of 975 genes, of which 708 (73%) genes have protein-coding annotation, were identified as phloem enriched genes putatively involved in the processes of polysaccharide and cell wall metabolism. Differential expression genes (DEGs) was validated using quantitative RT-PCR, the expression pattern of all nine genes determined by qRT-PCR fitted in well with that obtained by sequencing analysis. Cluster and Gene Ontology (GO) analysis revealed that a large number of genes related to metabolic process, catalytic activity and binding category were expressed predominantly in the stem peels. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the phloem enriched genes suggested approximately 111 biological pathways. The large number of genes and pathways produced from DGE sequencing will expand our understanding of the complex molecular and cellular events in flax bast fiber development and provide a foundation for future studies on fiber development in other bast fiber crops.
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Affiliation(s)
- Yuan Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Caisheng Qiu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Songhua Long
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Ping Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Dongmei Hao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Marta Preisner
- Faculty of Biotechnology, University of Wrocław, Wrocław 51-148, Poland
| | - Hui Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Yufu Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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Meng C, Quan TY, Li ZY, Cui KL, Yan L, Liang Y, Dai JL, Xia GM, Liu SW. Transcriptome profiling reveals the genetic basis of alkalinity tolerance in wheat. BMC Genomics 2017; 18:24. [PMID: 28056779 PMCID: PMC5217398 DOI: 10.1186/s12864-016-3421-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 12/14/2016] [Indexed: 12/14/2022] Open
Abstract
Background Soil alkalinity shows significant constraints to crop productivity; however, much less attention has been paid to analyze the effect of soil alkalinity on plant growth and development. Shanrong No. 4 (SR4) is an alkalinity tolerant bread wheat cultivar selected from an asymmetric somatic hybridization between the bread wheat cultivar Jinan 177 (JN177) and tall wheatgrass (Thinopyrum ponticum), which is a suitable material for studying alkalinity tolerant associate genes. Results The growth of SR4 plant seedlings was less inhibited than that of JN177 when exposed to alkalinity stress conditions. The root cytosolic Na+/K+ ratio in alkalinity stressed SR4 was lower than in JN177, while alkalinity stressed SR4 contained higher level of nutrient elements than in JN177. SR4 plant seedlings accumulated less malondialdehyde (MDA) and reactive oxygen species (ROS), it also showed higher activity of ROS scavenging enzymes than JN177 under alkalinity stress. The root intracellular pH decreased in both alkalinity stressed JN177 and SR4, however, it was much lower in SR4 than in JN177 under alkalinity stress. The transcriptomes of SR4 and JN177 seedlings exposed to alkalinity stress were analyzed by digital gene expression tag profiling method. Alkalinity stress conditions up- and down-regulated a large number of genes in the seedling roots that play the functions in the categories of transcription regulation, signal transduction and protein modification. Conclusions SR4 expresses a superior tolerance to alkaline stress conditions which is due to its strong absorbing ability for nutrient ions, a strong regulating ability for intracellular and rhizosphere pH and a more active ROS scavenging ability. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3421-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chen Meng
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Tai-Yong Quan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Zhong-Yi Li
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Kang-Li Cui
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Li Yan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Yu Liang
- Forest and Wetland Institute, Shandong Academy of Forestry, Jinan, 250014, People's Republic of China
| | - Jiu-Lan Dai
- Environment Research Institute, Shandong University, Jinan, 250100, People's Republic of China
| | - Guang-Min Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Shu-Wei Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China.
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Gill RA, Ali B, Cui P, Shen E, Farooq MA, Islam F, Ali S, Mao B, Zhou W. Comparative transcriptome profiling of two Brassica napus cultivars under chromium toxicity and its alleviation by reduced glutathione. BMC Genomics 2016; 17:885. [PMID: 27821044 PMCID: PMC5100228 DOI: 10.1186/s12864-016-3200-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chromium (Cr) being multifarious industrial used element, is considered a potential environmental threat. Cr found to be a prospective water and soil pollutant, and thus it is a current area of concern. Oilseed rape (Brassica napus L.) is well known as a major source of edible oil around the globe. Due to its higher growth, larger biomass and capability to uptake toxic materials B. napus is considered a potential candidate plant against unfavorable conditions. To date, no study has been done that described the Cr and GSH mechanism at RNA-Seq level. RESULTS Both digital gene expression (DGE) and transcriptome profile analysis (TPA) approaches had opened new insights to uncover the several number of genes related to Cr stress and GSH alleviating mechanism in two leading cultivars (ZS 758 and Zheda 622) of B. napus plants. Data showed that Cr inhibited KEGG pathways i.e. stilbenoid, diarlyheptanoid and gingerol biosynthesis; limonene and pentose degradation and glutathione metabolism in ZS 758; and ribosome and glucosinolate biosynthesis in Zheda-622. On the other hand, vitamin B6, tryptophan, sulfur, nitrogen and fructose and manose metabolisms were induced in ZS 758, and zeatin biosynthesis, linoleic acid metabolism, arginine and proline metabolism, and alanine, asparate and glutamate metabolism pathways in Zheda 622. Cr increased the TFs that were related to hydralase activity, antioxidant activity, catalytic activity phosphatase and pyrophosphatase activity in ZS 758, and vitamin binding and oxidoreductase activity in Zheda 622. Cr also up-regulated the promising proteins related to intracellular membrane bounded organelles, nitrile hyrdatase activity, cytoskeleton protein binding and stress response. It also uncovered, a novel Cr-responsive protein (CL2535.Contig1_All) that was statistically increased as compared to control and GSH treated plants. Exogenously applied GSH successfully not only recovered the changes in metabolic pathways but also induced cysteine and methionine metabolism in ZS 758 and ubiquinone and other terpenoid-quinone biosynthesis pathways in Zheda 622. Furthermore, GSH increased the level of TFs i.e. the gene expression of antioxidant and catalytic activities, iron ion binding and hydrolase activity as compared with Cr. Moreover, results pointed out a novel GSH responsive protein (CL827.Contig3_All) whose expression was found to be significantly increased when compared than Cr stress. Results further delineated that GSH induced TFs such as glutathione disulphide oxidoreducatse and aminoacyl-tRNA ligase activity, and beta glucosidase activity in ZS 758. Similarly in Zheda 622, GSH induced the TFs for instance DNA binding and protein dimerization activity. GSH also highlighted the proteins that were involved in transportation, photosynthesis process, RNA polymerase activity, and against the metal toxicity. These results indicated that cultivar ZS 758 had better metabolism and showed higher tolerance against Cr toxicity. CONCLUSION The responses of ZS 758 and Zheda 622 differed considerably at both physiological and transcriptional level. Moreover, RNA-Seq method explored the hazardous behavior of Cr as well as GSH up-regulating mechanism by activating plant metabolism, stress responsive genes, TFs and protein encyclopedia.
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Affiliation(s)
- Rafaqat A Gill
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Peng Cui
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad A Farooq
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Shafaqat Ali
- Department of Environmental Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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Guo H, Xian JA, Wang AL. Analysis of digital gene expression profiling in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress. Fish Shellfish Immunol 2016; 56:1-11. [PMID: 27377029 DOI: 10.1016/j.fsi.2016.06.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of nitrite in water is highly toxic to aquatic animals. To understand immune responses in shrimp under such environmental stress, a digital gene expression (DGE) technology was applied to detect the gene expression profile of the Litopenaeus vannamei hemocytes in response to nitrite for 48 h. A total of 1922 differently expressed unigenes were generated. Of these transcripts, 1269 and 653 genes were up- or down-regulated respectively. Functional categorization and pathways of the differentially expressed genes revealed that immune defense, xenobiotics biodegradation and metabolism, amino acid and nucleobase metabolic process, apoptosis were the differentially regulated processes occurring during nitrite stress. We selected 19 differential expression transcripts (DETs) to validate the sequencing results by real time quantitative PCR (qPCR). The Pearson's correlation coefficient (R) of the 19 DETs was 0.843, which confirmed the consistency and accuracy between these two approaches. Subsequently, we screened 10 genes to examine the changes in the time course of gene expression in more detail. The results indicated that expressions of ATP-binding cassette transporter (ABC transporter), caspase10, QM protein, C type lectin 4 (CTL4), protein disulfide isomerase (PDI), serine protease inhibitor 8 (SPI8), transglutaminase (TGase), chitinase1, inhibitors of apoptosis proteins (IAP) and cytochrome P450 enzyme (CYP450) were induced to participate in the anti-stress defense against nitrite. These results will provide a reference for follow-up study of molecular toxicology and valuable gene information for better understanding of immune response in L. vannamei under environmental stress.
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Affiliation(s)
- Hui Guo
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, People's Republic of China.
| | - Jian-An Xian
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, People's Republic of China
| | - An-Li Wang
- Key Laboratory of Ecology and Environmental Science of Guangdong Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou, 510631, People's Republic of China
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Wang ZJ, Liu XH, Jin L, Pu DY, Huang J, Zhang YG. Transcriptome profiling analysis of rare minnow (Gobiocypris rarus) gills after waterborne cadmium exposure. Comp Biochem Physiol Part D Genomics Proteomics 2016; 19:120-128. [PMID: 27292131 DOI: 10.1016/j.cbd.2016.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 05/22/2016] [Indexed: 12/13/2022]
Abstract
Rare minnow (Gobiocypris rarus) is a widely used experimental fish in risk assessments of aquatic pollutants in China. Cadmium (Cd) is one of the most toxic heavy metals in the world; however, few studies have used fish gills, a multi-functional organ. In this study, we characterized the differential expression of adult female rare minnow gills after sub-chronic waterborne Cd (75μg/L CdCl2) exposure for 35d. A total of 452 genes (209 up-regulated and 243 down-regulated) were identified by gene expression profiling using RNA-Seq before and after treatment. Of these differentially expressed genes, 75, 21, and 54 differentially expressed genes are related to ion transport, oxidation-reduction processes, and the immune response, respectively. The results of GO and KEGG enrichment analyses, together with the altered transcript levels of major histocompatibility complex (MHC) class I and class II molecules and the significant increases in the levels of serum tumor necrosis factor α (TNF-α), interleukin 1β (IL1β) and nuclear factor-κB (NF-κB), indicated a disruption of the immune system, particularly the induction of inflammation and autoimmunity. The significant down-regulation of coagulation factor XIII A1 polypeptide (F13A1), tripartite motif-containing protein 21 (TRIM21), and Golgi-associated plant pathogenesis-related protein (GAPr) during both acute (≤96h) and sub-chronic (35d) waterborne Cd exposure, as well as their dosage dependence, suggested that these three genes could be used as sensitive biomarkers for aquatic Cd risk assessment.
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Affiliation(s)
- Zhi-Jian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China
| | - Xiao-Hong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China
| | - De-Yong Pu
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China
| | - Jing Huang
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China
| | - Yao-Guang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, 400715 Chongqing, China.
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Park YJ, Li X, Noh SJ, Kim JK, Lim SS, Park NI, Kim S, Kim YB, Kim YO, Lee SW, Arasu MV, Al-Dhabi NA, Park SU. Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei. BMC Genomics 2016; 17:303. [PMID: 27107812 PMCID: PMC4842265 DOI: 10.1186/s12864-016-2616-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 04/13/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Valeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei. RESULTS A total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei. CONCLUSIONS We have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid.
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Affiliation(s)
- Yun Ji Park
- />Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 Korea
| | - Xiaohua Li
- />Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 Korea
| | - Seung Jae Noh
- />Code Division, Insilicogen Inc., Suwon, Gyeonggi-do 441-813 Korea
| | - Jae Kwang Kim
- />Division of Life Sciences and Bio-Resource and Environmental Center, Incheon National University, Yeonsu-gu, Incheon, 406-772 Korea
| | - Soon Sung Lim
- />Department of Food and Nutrition and Institute of Natural Medicine, Hallym University, Chuncheon, 200-702 Korea
| | - Nam Il Park
- />Deptartment of Plant Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do 210-702 Korea
| | - Soonok Kim
- />Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170 Korea
| | - Yeon Bok Kim
- />Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk 369-873 Republic of Korea
| | - Young Ock Kim
- />Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk 369-873 Republic of Korea
| | - Sang Won Lee
- />Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk 369-873 Republic of Korea
| | - Mariadhas Valan Arasu
- />Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- />Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Sang Un Park
- />Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 Korea
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Li F, Hu J, Tian J, Xu K, Ni M, Wang B, Shen W, Li B. Effects of phoxim on nutrient metabolism and insulin signaling pathway in silkworm midgut. Chemosphere 2016; 146:478-485. [PMID: 26741554 DOI: 10.1016/j.chemosphere.2015.12.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Silkworm (Bombyx mori) is an important economic insect. Each year, poisoning caused by phoxim pesticide leads to huge economic losses in sericulture in China. Silkworm midgut is the major organ for food digestion and nutrient absorption. In this study, we found that the activity and expression of nutrition metabolism-related enzymes were dysregulated in midgut by phoxim exposure. DGE analysis revealed that 40 nutrition metabolism-related genes were differentially expressed. qRT-PCR results indicated that the expression levels of insulin/insulin growth factor signaling (IIS) pathway genes Akt, PI3K, PI3K60, PI3K110, IRS and PDK were reduced, whereas PTEN's expression was significantly increased in the midgut at 24 h after phoxim treatment. However, the transcription levels of Akt, PI3K60, PI3K110, IRS, InR and PDK were elevated and reached the peaks at 48 h, which were 1.48-, 1.35-, 1.21-, 2.24-, 2.89-, and 1.44-fold of those of the control, respectively. At 72 h, the transcription of these genes was reduced. Akt phosphorylation level was increasing along with the growth of silkworms in the control group. However, phoxim treatment led to increased Akt phosphorylation that surged at 24 h but gradually decreased at 48 h and 72 h. The results indicated that phoxim dysregulated the expression of IIS pathway genes and induced abnormal nutrient metabolism in silkworm midgut, which may be the reason of the slow growth of silkworms.
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Affiliation(s)
- Fanchi Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Jingsheng Hu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Jianghai Tian
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Kaizun Xu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Min Ni
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Binbin Wang
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Weide Shen
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Bing Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China; National Engineering Laboratory for Modern Silk, Soochow University, Suzhou, Jiangsu 215123, PR China.
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Tao L, Zhao Y, Wu Y, Wang Q, Yuan H, Zhao L, Guo W, You X. Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim. Gene 2015; 578:17-24. [PMID: 26657036 DOI: 10.1016/j.gene.2015.11.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 11/21/2015] [Accepted: 11/30/2015] [Indexed: 11/19/2022]
Abstract
Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.
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Affiliation(s)
- Lei Tao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yue Zhao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Ying Wu
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Qiuyu Wang
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Hongmei Yuan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Lijuan Zhao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Wendong Guo
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
| | - Xiangling You
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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ZHANG S, LU Z, LIANG H, FU X, ZHANG Y, LIU X, BAO G, JING T, WANG X, WANG M, WU J, CHEN G. The Analysis of Gene Expression on Fertility Decline in Caenorhabditis elegans after the Treatment with 5-Fluorouracil. Iran J Public Health 2015; 44:1061-71. [PMID: 26587470 PMCID: PMC4645726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
BACKGROUND 5-Fluorouracil could lead to a decline in fertility in Caenorhabditis elegans. The aim of this study was to describe the mechanisms underlying such an altered fertility phenotype and to illustrate the specific genes and pathways that are involved in the related phenotypic changes in C. elegans. METHODS We isolated total RNA from the samples and used a new method called Digital Gene Expression (DGE), which can rapidly identify genes with altered transcript levels. The random genes were confirmed by real-time RT-PCR. RESULTS We analyzed the results of two methods to draw conclusions based on a comparison between C. elegans and other harmful parasites. Compared with controls, 1147 genes were up-regulated, and 1067 were down-regulated. Overall, 101 up-regulated genes had a log2 ratio higher than 8, whereas the log2 ratio of 141 down-regulated genes was higher than 8. After mapping to the reference database, 4 pathways were confirmed to be involved in this phenomenon, with statistically significant participation from 19 genes. CONCLUSION For the first time, the transcript sequence of 5-Fu-treated worms and controls was detected. We found that 4 possible pathways, i.e., ECM-receptor interaction pathway, TGF-beta signaling pathway, Focal adhesion and Hypertrophic cardiomyopathy, may be involved in the number decline in the embryos of C. elegans. Specifically, the ECM-receptor interaction pathway and Focal adhesion may be very important pathways that alter the reproduction of C. elegans.
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Affiliation(s)
- Si ZHANG
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China, Maternal and Child Health Hospital of Fengtai District of Beijing City, Beijing, China
| | - Zhaolian LU
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Hongmei LIANG
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Ximei FU
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Yan ZHANG
- Dept. of Anesthesiology, First Hospital, Lanzhou University, Gansu, China
| | - Xin LIU
- Institute of Integrated Chinese and Western Medicine, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Genshu BAO
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Tao JING
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China
| | - Xuan WANG
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China, Suqian Hospital of Traditional Chinese Medicine, Jiangsu, China
| | - Meng WANG
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China, Tianjin First Center Hospital, Tianjin, China
| | - Julong WU
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China, Shandong Center for Disease Control and Prevention, Shandong, China
| | - Gen CHEN
- Pathogens Biology Institute, School of Basic Medical Sciences, Lanzhou University, Gansu, China, Key Lab of Preclinical Study for New Drugs of Gansu Province, Gansu, China,Corresponding Author:
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Lv Xj, Zhang Yj, Lu Wz, Wang Q, Li Sy, Guo L, Qian Gs, Zhou Sw, Li Yy. Digital gene expression analysis of transcriptomes in lipopolysaccharide-induced acute respiratory distress syndrome. Clin Chim Acta 2016; 453:182-9. [PMID: 26216187 DOI: 10.1016/j.cca.2015.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The mortality from acute respiratory distress syndrome (ARDS) is high, and its exact pathogenesis remains unclear, which forms a major obstacle for prevention and treatment of this disease. In the present study, we used digital gene expression (DGE) to detect the differentially expressed genes of the lung at 4h after lipopolysaccharide (LPS) exposure in a mouse model. METHODS Mice were treated with LPS or control saline by intratracheal instillation for 4h, and their lung tissues were collected for DGE analysis. We used a false discovery rate ≤0.001 and an absolute value of the log2 ratio≥1 as the thresholds for judging the significance of any difference in gene expression between the two members of each pair of mice. RESULTS We obtained 3,387,842 clean tags (i.e., after filtering to remove potentially erroneous tags) and about 84,513 corresponding distinct clean tags (i.e., types of tag). Approximately 91.20% of the clean tags could be mapped, and 82.71% could be uniquely mapped, to the reference tags, and 3.82% were unknown tags. At least 2200 differentially expressed genes were identified and analyzed for enrichment of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway. Twenty genes with the greatest difference in expression levels between the two members of every pair of mice were chosen. The majority of these genes are involved in signaling transduction, molecular adhesion, and metabolic pathways. CONCLUSIONS Using the powerful technology of DGE, we present, to our knowledge, the first in-depth transcriptomic analysis of mouse lungs after LPS exposure. We found some differentially expressed genes that might play important roles in the pathogenesis of ARDS.
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Li M, Liu M, Peng F, Fang L. Influence factors and gene expression patterns during MeJa-induced gummosis in peach. J Plant Physiol 2015; 182:49-61. [PMID: 26056992 DOI: 10.1016/j.jplph.2015.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 03/02/2015] [Accepted: 03/16/2015] [Indexed: 05/21/2023]
Abstract
Jasmonates (JAs) play important roles in gummosis in peach. Mechanical damage, methyl jasmonate (MeJa), and ethylene can induce gummosis on peach shoots in the field. In this study, we used MeJa (2%, w/w) to induce gummosis on current-year shoots in peach on high temperature (35°C). Based on the experimental model, we studied the influence of factors on the development of peach gummosis. Our experimental results showed that high temperature could promote gummosis development induced by MeJa. Exogenous CaCl2 treatment reduced the degree of gummosis by increasing the calcium content in shoots, which is conducive to the synthesis and maintenance of the cell wall. Using digital gene expression (DGE), 3831 differentially expressed genes were identified in the MeJa treatment versus the control. By analyzing changes in gene expression associated with cell wall degradation, genes encoding pectin methylesterase (PME) and endo-polygalacturonase (PG) were found to be significantly induced, suggesting that they are key enzymes in cell wall degradation that occurs during MeJa-induced gummosis. Genes for glycosyltransferase (GT) and cellulose synthase (CS) were also significantly upregulated by MeJa. This result suggests that MeJa treatment not only promotes the degradation of polysaccharides to destroy the cell wall, but also promotes the synthesis of new polysaccharides. We also analyzed changes in gene expression associated with sugar metabolism, senescence, and defense. MeJa treatment affected the expression of genes related to sugar metabolism and promoted plant senescence. Among the defense genes, the expression pattern of phenylalanine ammonium lyase (PAL) suggested that PAL may play an important role in protecting against the effects of MeJa treatment. Our experimental results showed that MeJa treatment can promote the biosynthesis and signal transduction of ethylene in peach shoots; they can induce gummosis on peach shoots respectively, and there are overlaps between the molecular mechanisms of gummosis induced by them, the intersection point between them remains unclear.
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Affiliation(s)
- Minji Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Meiyan Liu
- Xintai Forestry Bureau of Shandong Province, Shandong, PR China.
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Long Fang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
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Zhang D, Lu K, Jiang G, Liu W, Dong Z, Tian H, Li X. A global transcriptional analysis of Megalobrama amblycephala revealing the molecular determinants of diet-induced hepatic steatosis. Gene 2015; 570:255-63. [PMID: 26074088 DOI: 10.1016/j.gene.2015.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/19/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023]
Abstract
Blunt snout bream (Megalobrama amblycephala), a prevalent species in China's intensive polyculture systems, is highly susceptible to hepatic steatosis, resulting in considerable losses to the fish farming industry. Due to a lack of genomic resources, the molecular mechanisms of lipid metabolism in M. amblycephala are poorly understood. Here, a hepatic cDNA library was generated from equal amounts of mRNAs isolated from M. amblycephala fed normal-fat and high-fat diets. Sequencing of this library using the Illumina/Solexa platform produced approximately 51.87 million clean reads, which were assembled into 48,439 unigenes with an average length of 596 bp and an N50 value of 800 bp. These unigenes were searched against the nucleotide (NT), non-redundant (NR), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases using the BLASTn or BLASTx algorithms (E-value ≤ 10(-5)). A total of 8602 unigenes and 22,155 unigenes were functionally classified into 25 COG categories and 259 KEGG pathways, respectively. Furthermore, 22,072 unigenes were grouped into 62 sub-categories belonging to three main Gene Ontology (GO) terms. Using a digital gene expression analysis and the M. amblycephala transcriptome as a reference, 477 genes (134 up-regulated and 343 down-regulated) were identified as differentially expressed in fish fed a high-fat diet versus a normal-fat diet. KEGG and GO functional enrichment analyses of the differentially expressed unigenes were performed and 12 candidate genes related to lipid metabolism were identified. This study provides a global survey of hepatic transcriptome profiles and identifies candidate genes that may be related to lipid metabolism in M. amblycephala. These findings will facilitate further investigations of the mechanisms underlying hepatic steatosis in M. amblycephala.
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Affiliation(s)
- Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Kangle Lu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Hongyan Tian
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Gu X, Chen Y, Gao Z, Qiao Y, Wang X. Transcription factors and anthocyanin genes related to low-temperature tolerance in rd29A:RdreB1BI transgenic strawberry. Plant Physiol Biochem 2015; 89:31-43. [PMID: 25686702 DOI: 10.1016/j.plaphy.2015.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 02/09/2015] [Indexed: 05/08/2023]
Abstract
Dehydration-responsive element-binding (DREB) transcription factors play critical roles in plant stress responses and signal transduction. To further understand how DREB regulates genes expression to promote cold-hardiness, Illumina/Solexa sequencing technology was used to compare the transcriptomes of non-transgenic and rd29A:RdreB1BI transgenic strawberry plants exposed to low temperatures. Approximately 3.5 million sequence tags were obtained from non-transgenic (NT) and transgenic (T) strawberry untreated (C) or low-temperature treated (LT) leaf samples. Over 1000 genes were differentially expressed between the NT-C and T-C plants, and also the NT-C and NT-LT, as well as the T-C and T-LT plants. Analysis of the genes up-regulated following low-temperature treatment revealed that the majority are linked to metabolism, biosynthesis, transcription and signal transduction. Uniquely up-regulated transcription factors as well as anthocyanin biosynthetic pathway genes are discussed. Accumulation of anthocyanin in the stolon and the base of the petiole differed between non-treated NT and T plants, and this correlated with gene expression patterns. The differentially expressed genes that encode transcription factors and anthocyanin enzymes may contribute to the cold hardiness of RdreB1BI transgenic strawberry. The transcriptome data provide a valuable resource for further studies of strawberry growth and development and DREB-mediated gene regulation under low-temperature stress.
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Affiliation(s)
- Xianbin Gu
- College of Horticulture, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China; College of Life Sciences, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China
| | - Yushan Qiao
- College of Horticulture, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China
| | - Xiuyun Wang
- College of Agro-grassland Science, Nanjing Agricultural University, No 1 Weigang, Nanjing 210095, People's Republic of China
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Zhao Q, Pan L, Ren Q, Hu D. Digital gene expression analysis in hemocytes of the white shrimp Litopenaeus vannamei in response to low salinity stress. Fish Shellfish Immunol 2015; 42:400-407. [PMID: 25463292 DOI: 10.1016/j.fsi.2014.11.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/02/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
The white shrimp Litopenaeus vannamei has been greatly impacted by low salinity stress. To gain knowledge on the immune response in L. vannamei under such stress, we investigated digital gene expression (DEG) in L. vannamei hemocytes using the deep-sequencing platform Illumina HiSeq 2000. In total, 38,155 high quality unigenes with average length 770 bp were generated; 145 and 79 genes were identified up- or down-regulated, respectively. Functional categorization and pathways of the differentially expressed genes revealed that immune signaling pathways, cellular immunity, humoral immunity, apoptosis, cellular protein synthesis, lipid transport and energy metabolism were the differentially regulated processes occurring during low salinity stress. These results will provide a resource for subsequent gene expression studies regarding environmental stress and a valuable gene information for a better understanding of immune mechanisms of L. vannamei under low salinity stress.
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Affiliation(s)
- Qun Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, PR China.
| | - Qin Ren
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, PR China
| | - Dongxu Hu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao 266003, PR China
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Yang C, Jiang M, Wen H, Tian J, Liu W, Wu F, Gou G. Analysis of differential gene expression under low-temperature stress in Nile tilapia (Oreochromis niloticus) using digital gene expression. Gene 2015; 564:134-40. [PMID: 25617524 DOI: 10.1016/j.gene.2015.01.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/08/2014] [Accepted: 01/17/2015] [Indexed: 01/05/2023]
Abstract
Tilapia (Oreochromis niloticus) do not survive well at low temperatures. Therefore, improvement of the low-temperature resistance has become an important issue for aquaculture development of tilapia. The objective of this study was to construct a digital gene expression tag profile to identify genes potentially related to low temperature in tilapia. In this study, tilapia was treated at 30°C to lethal temperature 10°C in decrement of 1°CD(-1). Digital gene expression analysis was performed using the Illumina technique to investigate differentially expressed genes in tilapia cultured at different temperatures (30°C, 26°C, 20°C, 16°C, and 10°C). A total of 206,861, 188,082, 185,827, 188,067, and 214,171 distinct tags were obtained by sequencing these five libraries, respectively. Compared with the 30°C library, there were 304, 407, 709, and 772 upregulated genes and 342, 793, 771, and 1466 downregulated genes in 26°C, 20°C, 16°C, and 10°C libraries, respectively. Trend analysis of these differentially expressed genes identified six statistically significant trends. Functional annotation analysis of the differentially expressed genes identified various functions associated with the response to low-temperature stress. When tilapia are subjected to low-temperature stress, expression changes were observed in genes associated with nucleic acid synthesis and metabolism, amino acid metabolism and protein synthesis, lipid and carbohydrate content and types, material transport, apoptosis, and immunity. The differentially expressed genes obtained in this study may provide useful insights to help further understand the effects of low temperature on tilapia.
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Affiliation(s)
- Changgeng Yang
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Ming Jiang
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Hua Wen
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Juan Tian
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Wei Liu
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Fan Wu
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Gengwu Gou
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
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Jin Q, Pan L, Liu T, Hu F. RNA-seq based on transcriptome reveals differ genetic expressing in Chlamys farreri exposed to carcinogen PAHs. Environ Toxicol Pharmacol 2015; 39:313-320. [PMID: 25543213 DOI: 10.1016/j.etap.2014.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
The effects of a mixture of carcinogen polycyclic aromatic hydrocarbons (BaP, BaA, BbF and CHR) on transcriptional responses in the digestive gland of scallop, Chlamys farreri, were investigated by high-throughput RNA-sequencing (RNA-seq) technologies. In total, 209 and 260 genes were identified as significantly up- or down-regulated, respectively. Functional analysis based on gene ontology (GO) classification system and the Kyoto encyclopedia of genes and genomes (KEGG) database revealed that PAHs significantly altered the expression of genes involved in stress response, detoxication, antioxidation which were extensively discussed. In particular, CYP450 2P1 and QO mRNA expression were found to be up-regulated by exposure to PAHs mixture, suggesting that CYP450 2P1 and QO mRNA expression can be a potential marker for prediction of the biological effects of a mixture of PAHs on scallops.
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Affiliation(s)
- Qian Jin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Luqing Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China.
| | - Tong Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Fengxiao Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
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Hu F, Pan L, Cai Y, Liu T, Jin Q. Deep sequencing of the scallop Chlamys farreri transcriptome response to tetrabromobisphenol A (TBBPA) stress. Mar Genomics 2014; 19:31-8. [PMID: 25260812 DOI: 10.1016/j.margen.2014.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 11/30/2022]
Abstract
Tetrabromobisphenol-A (TBBPA) is currently the most widely used brominated flame retardant (BFR) and has been proven to have a very high toxicity to aquatic organisms including bivalves. However, molecular responses to TBBPA in bivalve remain largely unknown. Novel high-throughput deep sequencing technology has been a powerful tool for looking at molecular responses to toxicological stressors in organisms. Using Illumina's digital gene expression (DGE) system, we investigated TBBPA-induced transcriptome response in the digestive gland tissue of scallop Chlamys farreri. In total, 173 and 266 genes were identified as significantly up- or down-regulated, respectively. Functional analysis based on gene ontology (GO) classification system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that TBBPA significantly altered the expression of genes involved in stress response, detoxification, antioxidation, and innate immunity which were extensively discussed. In particular, evidence for the endocrine disrupting effect of TBBPA on bivalve was first obtained in this study. Quantitative real-time PCR was performed to ascertain the mRNA expression of several genes identified by the DGE analysis. The results of this study may serve as a basis for future research on molecular mechanism of toxic effects of TBBPA on marine bivalves.
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Affiliation(s)
- Fengxiao Hu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China.
| | - Yuefeng Cai
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Tong Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Qian Jin
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
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39
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Yu Y, Huang W, Chen H, Wu G, Yuan H, Song X, Kang Q, Zhao D, Jiang W, Liu Y, Wu J, Cheng L, Yao Y, Guan F. Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline-alkaline stress by digital gene expression. Gene 2014; 549:113-22. [PMID: 25058012 DOI: 10.1016/j.gene.2014.07.053] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/17/2014] [Accepted: 07/19/2014] [Indexed: 01/04/2023]
Abstract
The salinization and alkalization of soil are widespread environmental problems, and alkaline salt stress is more destructive than neutral salt stress. Therefore, understanding the mechanism of plant tolerance to saline-alkaline stress has become a major challenge. However, little attention has been paid to the mechanism of plant alkaline salt tolerance. In this study, gene expression profiling of flax was analyzed under alkaline-salt stress (AS2), neutral salt stress (NSS) and alkaline stress (AS) by digital gene expression. Three-week-old flax seedlings were placed in 25 mM Na2CO3 (pH11.6) (AS2), 50mM NaCl (NSS) and NaOH (pH11.6) (AS) for 18 h. There were 7736, 1566 and 454 differentially expressed genes in AS2, NSS and AS compared to CK, respectively. The GO category gene enrichment analysis revealed that photosynthesis was particularly affected in AS2, carbohydrate metabolism was particularly affected in NSS, and the response to biotic stimulus was particularly affected in AS. We also analyzed the expression pattern of five categories of genes including transcription factors, signaling transduction proteins, phytohormones, reactive oxygen species proteins and transporters under these three stresses. Some key regulatory gene families involved in abiotic stress, such as WRKY, MAPKKK, ABA, PrxR and ion channels, were differentially expressed. Compared with NSS and AS, AS2 triggered more differentially expressed genes and special pathways, indicating that the mechanism of AS2 was more complex than NSS and AS. To the best of our knowledge, this was the first transcriptome analysis of flax in response to saline-alkaline stress. These data indicate that common and diverse features of saline-alkaline stress provide novel insights into the molecular mechanisms of plant saline-alkaline tolerance and offer a number of candidate genes as potential markers of tolerance to saline-alkaline stress.
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Affiliation(s)
- Ying Yu
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Wengong Huang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Hongyu Chen
- College of Life Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Guangwen Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Xixia Song
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Qinghua Kang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Dongsheng Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Weidong Jiang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Yan Liu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Jianzhong Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Lili Cheng
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Yubo Yao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Fengzhi Guan
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, PR China; Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China.
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40
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Li QR, Xiao Y, Wu FQ, Ye MQ, Luo GQ, Xing DX, Li L, Yang Q. Analysis of midgut gene expression profiles from different silkworm varieties after exposure to high temperature. Gene 2014; 549:85-96. [PMID: 25046138 DOI: 10.1016/j.gene.2014.07.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 07/02/2014] [Accepted: 07/17/2014] [Indexed: 11/18/2022]
Abstract
The silkworm is a poikilothermic animal, whose growth and development is significantly influenced by environmental temperature. To identify genes and metabolic pathways involved in the heat-stress response, digital gene expression analysis was performed on the midgut of the thermotolerant silkworm variety '932' and thermosensitive variety 'HY' after exposure to high temperature (932T and HYT). Deep sequencing yielded 6,211,484, 5,898,028, 5,870,395 and 6,088,303 reads for the 932, 932T, HY and HYT samples, respectively. The annotated genes associated with these tags numbered 4357, 4378, 4296 and 4658 for the 932, 932T, HY and HYT samples, respectively. In the HY-vs-932, 932-vs-932T, and HY-vs-HYT comparisons, 561, 316 and 281 differentially expressed genes were identified, which could be assigned to 179, 140 and 123 biological pathways, respectively. It was found that some of the biological pathways, which included oxidative phosphorylation, related to glucose and lipid metabolism, are greatly affected by high temperature and may lead to a decrease in the ingestion of fresh mulberry. When subjected to an early period of continuous heat stress, HSP genes, such as HSP19.9, HSP23.7, HSP40-3, HSP70, HSP90 and HSP70 binding protein, are up-regulated but then reduced after 24h and the thermotolerant '932' strain has higher levels of mRNA of some HSPs, except HSP70, than the thermosensitive variety during continuous high temperature treatment. It is suggested that HSPs and the levels of their expression may play important roles in the resistance to high temperature stress among silkworm varieties. This study has generated important reference tools that can be used to further analyze the mechanisms that underlie thermotolerance differences among silkworm varieties.
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Affiliation(s)
- Qing Rong Li
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Yang Xiao
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Fu Quan Wu
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Ming Qiang Ye
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Guo Qing Luo
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Dong Xu Xing
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Li Li
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China
| | - Qiong Yang
- The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, GuangZhou, China.
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41
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Zhao W, Xia W, Li J, Sheng S, Lei L, Zhao S. Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4'-tetrahydroxy stilbene-2-O-β-D-glucoside. Gene 2014; 547:126-35. [PMID: 24967942 DOI: 10.1016/j.gene.2014.06.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/28/2023]
Abstract
The compound 2,3,5,4'-tetrahydroxy stilbene-2-O-ß-d-glucoside (THSG) synthesized by Fallopia multiflora (F. multiflora) exhibits pharmacological potency. However, the mechanistic details of its biosynthesis pathway are still vague. To clear this ambiguity, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of F. multiflora using the Illumina RNA-seq system. RNA-seq generated approximately 70 million high-quality reads that were assembled into 65,653 unigenes (mean length=750 bp), including 26,670 clusters and 38,983 singletons. A total of 48,173 (73.4%) unigenes were annotated using public protein databases with a cut-off e-value above 10(-5). Furthermore, we investigated the transcriptome difference of four different F. multiflora tissues using DGE profiling. Variations in gene expression were identified based on comparisons of transcriptomes from various parts of a high-level THSG- and a low-level THSG-producing F. multiflora plant. Clusters with similar differential expression patterns and enriched metabolic pathways with regard to the differentially expressed genes putatively involved in THSG biosynthesis were revealed for the first time. Our data provides the most comprehensive sequence resource regarding F. multiflora so far. Taken together, the results of this study considerably extend the knowledge on THSG production.
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Affiliation(s)
- Wei Zhao
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510640, People's Republic of China; Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China.
| | - Wanxia Xia
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510640, People's Republic of China; Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China
| | - Jiewen Li
- Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China
| | - Shujing Sheng
- Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China
| | - Lei Lei
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510640, People's Republic of China; Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China
| | - Shujing Zhao
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510640, People's Republic of China; Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, People's Republic of China.
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Gu Z, Zhou Y, Xie Y, Li F, Ma L, Sun S, Wu Y, Wang B, Wang J, Hong F, Shen W, Li B. The adverse effects of phoxim exposure in the midgut of silkworm, Bombyx mori. Chemosphere 2014; 96:33-38. [PMID: 23899924 DOI: 10.1016/j.chemosphere.2013.06.089] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/29/2013] [Indexed: 06/02/2023]
Abstract
The silkworm is an important economic insect. Poisoning of silkworms by organophosphate pesticides causes tremendous loss to the sericulture. In this study, Solexa sequencing technology was performed to profile the gene expression changes in the midgut of silkworms in response to 24h of phoxim exposure and the impact on detoxification, apoptosis and immune defense were addressed. The results showed that 254 genes displayed at least 2.0-fold changes in expression levels, with 148 genes up-regulated and 106 genes down-regulated. Cytochrome P450 played an important role in detoxification. Histopathology examination and transmission electron microscope revealed swollen mitochondria and disappearance of the cristae of mitochondria, which are the important features in insect apoptotic cells. Cytochrome C release from mitochondria into the cytoplasm was confirmed. In addition, the Toll and immune deficiency (IMD) signal pathways were all inhibited using qRT-PCR. Our results could help better understand the impact of phoxim exposure on silkworm.
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Affiliation(s)
- ZhiYa Gu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
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Gao P, Chen AL, Zhao QL, Shen XJ, Qiu ZY, Xia DG, Tang SM, Zhang GZ. Differentially expressed genes in the ovary of the sixth day of pupal "Ming" lethal egg mutant of silkworm, Bombyx mori. Gene 2013; 527:161-6. [PMID: 23769927 DOI: 10.1016/j.gene.2013.05.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 05/10/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
Abstract
The "Ming" lethal egg mutant (l-em) is a vitelline membrane mutant in silkworm, Bombyx mori. The eggs laid by the l-em mutant lose water, ultimately causing death within an hour. Previous studies have shown that the deletion of BmEP80 is responsible for the l-em mutation in silkworm, B. mori. In the current study, digital gene expression (DGE) was performed to investigate the difference of gene expression in ovaries between wild type and l-em mutant on the sixth day of the pupal stage to obtain a global view of gene expression profiles using the ovaries of three l-em mutants and three wild types. The results showed a total of 3,463,495 and 3,607,936 clean tags in the wild type and the l-em mutant libraries, respectively. Compared with those of wild type, 239 differentially expressed genes were detected in the l-em mutant, wherein 181 genes are up-regulated and 58 genes are down-regulated in the mutant strain. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis results showed that no pathway was significantly enriched and three pathways are tightly related to protein synthesis among the five leading pathways. Moreover, the expression profiles of eight important differentially expressed genes related to oogenesis changed. These results provide a comprehensive gene expression analysis of oogenesis and vitellogenesis in B. mori which facilitates understanding of both the specific molecular mechanism of the 1-em mutant and Lepidopteran oogenesis in general.
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Affiliation(s)
- Peng Gao
- Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
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Gu J, Huang LX, Gong YJ, Zheng SC, Liu L, Huang LH, Feng QL. De novo characterization of transcriptome and gene expression dynamics in epidermis during the larval-pupal metamorphosis of common cutworm. Insect Biochem Mol Biol 2013; 43:794-808. [PMID: 23796435 DOI: 10.1016/j.ibmb.2013.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 05/11/2013] [Accepted: 06/05/2013] [Indexed: 06/02/2023]
Abstract
Larval cuticle is degraded and replaced by the pupal counterpart during larval-pupal metamorphosis in the holometabolous insects. In addition to the extrinsic transformation, the epidermis goes through significant changes at molecular levels. To elucidate the intrinsic mechanism of epidermal metamorphosis, the dynamics of chitin content in the cuticle was examined in an important agricultural lepidopteran, the common cutworm, and the transcriptome was analyzed using Illumina sequencing technology. Gene expression profiles during the metamorphosis were further studied by both the digital gene expression (DGE) system and real-time quantitative PCR. The results showed that the chitin content decreased in prepupae and then increased in pupae. A total of 58 million sequencing reads were obtained and assembled into 70,346 unigenes. Over 9000 unigenes were identified to express differentially during the transformation process. As compared with the 6th instar feeding larvae, the most significant changes took place in the proteasome and metabolic pathways in prepupae and pupae, respectively. The cytochrome P450s, VHDLs, chitinase, serine protease and genes involved in sex pheromone biosynthesis changed their mRNA levels remarkably. Three chitinolytic enzymes (chitinase, β-N-acetylglucosaminidase and chitin deacetylase) showed distinct mRNA expression patterns, the former two enzymes revealed the highest expression in prepupae, however the latter one showed its climax mRNA level in pupae. The gene expression patterns suggest that chitinase and β-N-acetylglucosaminidase may be responsible for the degradation of larval cuticles, whereas chitin deacetylase may help to degrade the pupal counterparts. Gene expression dynamics also implied that the chitin of pupal cuticle might be formed by recycling of the degraded chitin of larval cuticle rather than through de novo synthesis. The 20E-induced nuclear receptors seem to be important factors regulating chitin metabolic enzymes during the cuticle remodeling. Our data provide a comprehensive resource for exploring the molecular mechanism of epidermal metamorphosis in insects.
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Affiliation(s)
- Jun Gu
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 55 W. Zhongshan Ave., Guangzhou 510631, China
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