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Wang T, Wang Y, Liu X, Gao X, Hu K. Combined Transcriptomics and Metabolomics Analyses in Grass Carp Under Anesthetic Stress. Front Cell Infect Microbiol 2022; 12:931696. [PMID: 35899048 PMCID: PMC9309352 DOI: 10.3389/fcimb.2022.931696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Ctenopharyngodon Idella, as a common freshwater bony fish, is more susceptible to various diseases than other carp species, so it has been proposed as a test organism for toxicological analysis In this study, C. idella were anesthetized with MS-222 and 2-PE, and the related anesthetic mechanism and toxic effects were revealed by transcriptomics and metabolomics analyses. When the concentration of MS-222 was 80 mg/L and 200 mg/L, 179 and 887 differentially expressed genes (DEGs), respectively, were identified in the brain tissue of C. idella. When the concentration of 2-PE was 0.6 mL/L and 1.2 mL/L, 498 and 514 DEGs were identified. The DEGs associated with MS-222 treatment were enriched in immune pathways, lipid metabolism, amino acid metabolism, and various signaling pathways; DEGs associated with 2-PE treatment were enriched in immunity and amino acid metabolism. In total, 304 metabolites were identified using a combination of positive and negative ion modes in mass spectrometry. The common differential metabolites identified in the MS-222 high and low concentration groups were 20-HETE and 12(R)-HETE; the common significant differential metabolite identified in the 2-PE high and low concentration groups was salidroside. In combination with the transcriptomics analysis and metabolomics analysis, the results showed that with the MS-222 and 2-PE concentrations used in this experiment, the metabolism of arachidonic acid in C. idella was inhibited by MS-222, and 2-PE affected the upstream and downstream metabolic pathways of arachidonic acid metabolism, thereby affecting the metabolism of arachidonic acid. Both anesthetics induce sedation by affecting related metabolites that affect stress response and autoimmunity. Metabolomics results showed that neither anesthetic had a significant effect on cortisol expression.
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Affiliation(s)
- Tianwei Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- National Fisheries Technical Extension Center, Ministry of Rural Agriculture, Beijing, China
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of FisherySciences, Shanghai, China
| | - Yali Wang
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- National Fisheries Technical Extension Center, Ministry of Rural Agriculture, Beijing, China
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of FisherySciences, Shanghai, China
| | - Xueting Liu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- National Fisheries Technical Extension Center, Ministry of Rural Agriculture, Beijing, China
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of FisherySciences, Shanghai, China
| | - Xiaoning Gao
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- National Fisheries Technical Extension Center, Ministry of Rural Agriculture, Beijing, China
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of FisherySciences, Shanghai, China
| | - Kun Hu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- National Fisheries Technical Extension Center, Ministry of Rural Agriculture, Beijing, China
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of FisherySciences, Shanghai, China
- *Correspondence: Kun Hu,
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Zhang Y, Huang J, Hou Q, Liu Y, Wang J, Deng S. Isolation and Functional Characterization of a Salt-Responsive Calmodulin-Like Gene MpCML40 from Semi-Mangrove Millettia pinnata. Int J Mol Sci 2021; 22:3475. [PMID: 33801703 PMCID: PMC8036263 DOI: 10.3390/ijms22073475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Salt stress is a major increasing threat to global agriculture. Pongamia (Millettia pinnata), a semi-mangrove, is a good model to study the molecular mechanism of plant adaptation to the saline environment. Calcium signaling pathways play critical roles in the model plants such as Arabidopsis in responding to salt stress, but little is known about their function in Pongamia. Here, we have isolated and characterized a salt-responsive MpCML40, a calmodulin-like (CML) gene from Pongamia. MpCML40 protein has 140 amino acids and is homologous with Arabidopsis AtCML40. MpCML40 contains four EF-hand motifs and a bipartite NLS (Nuclear Localization Signal) and localizes both at the plasma membrane and in the nucleus. MpCML40 was highly induced after salt treatment, especially in Pongamia roots. Heterologous expression of MpCML40 in yeast cells improved their salt tolerance. The 35S::MpCML40 transgenic Arabidopsis highly enhanced seed germination rate and root length under salt and osmotic stresses. The transgenic plants had a higher level of proline and a lower level of MDA (malondialdehyde) under normal and stress conditions, which suggested that heterologous expression of MpCML40 contributed to proline accumulation to improve salt tolerance and protect plants from the ROS (reactive oxygen species) destructive effects. Furthermore, we did not observe any measurable discrepancies in the development and growth between the transgenic plants and wild-type plants under normal growth conditions. Our results suggest that MpCML40 is an important positive regulator in response to salt stress and of potential application in producing salt-tolerant crops.
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Affiliation(s)
- Yi Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Qiongzhao Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Q.H.); (Y.L.)
| | - Yujuan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Q.H.); (Y.L.)
| | - Jun Wang
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Costal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Shulin Deng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Xiaoliang Research Station for Tropical Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510275, China
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Li X, Fei R, Chen Z, Fan C, Sun X. Plant hormonal changes and differential expression profiling reveal seed dormancy removal process in double dormant plant-herbaceous peony. PLoS One 2020; 15:e0231117. [PMID: 32240252 PMCID: PMC7117732 DOI: 10.1371/journal.pone.0231117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/16/2020] [Indexed: 01/10/2023] Open
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) is a popular ornamental and medicinal plant. Taking approximately six to seven months, the seeds germination under natural conditions experiences dual dormancies, which seriously affects horticultural cultivation. Few studies have been conducted on exploring both biological and molecular mechanism that regulates dormancy removal process in hypocotyls double dormant plants. Here, we first measured ABA and GA3 content changes at four key dormancy break stages, and then performed transcriptomic analyses to identify the differentially expressed genes (DEGs) using RNA-seq. We subsequently carried out Quantitative real-time PCR (qRT-PCR) to validate RNA-seq data. ABA content decreased during the whole dormancy removal process and GA3 content exhibited decreasing slightly and then increasing trend. RNA sequencing de novo assembly generated a total of 99,577 unigenes. 20,344 unigenes were differentially expressed in the whole dormancy release process. The qPCR results of 54 selected unigenes were consistent with the FPKM values obtained from RNA-seq. Our results summarize a valuable collection of gene expression profiles characterizing the dormancy release process. The DEGs are candidates for functional analyses of genes affecting the dormancy release, which is a precious resource for the on-going physiological and molecular investigation of seeds dormancy removal in other perennial plants.
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Affiliation(s)
- Xueting Li
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Riwen Fei
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zhijing Chen
- Forestry College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States of America
| | - Xiaomei Sun
- Horticulture College, Shenyang Agricultural University, Shenyang, Liaoning, China
- Forestry College, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
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Kitazaki K, Fukushima A, Nakabayashi R, Okazaki Y, Kobayashi M, Mori T, Nishizawa T, Reyes-Chin-Wo S, Michelmore RW, Saito K, Shoji K, Kusano M. Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs. Sci Rep 2018; 8:7914. [PMID: 29784957 PMCID: PMC5962576 DOI: 10.1038/s41598-018-25686-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m-2·s-1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Kazuhiro Shoji
- Central Research Institute of Electric Power Industry, Abiko, Chiba, 270-1194, Japan.
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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Takeuchi J, Mimura N, Okamoto M, Yajima S, Sue M, Akiyama T, Monda K, Iba K, Ohnishi T, Todoroki Y. Structure-Based Chemical Design of Abscisic Acid Antagonists That Block PYL-PP2C Receptor Interactions. ACS Chem Biol 2018; 13:1313-1321. [PMID: 29620349 DOI: 10.1021/acschembio.8b00105] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In Arabidopsis, signaling of the stress hormone abscisic acid (ABA) is mediated by PYR/PYL/RCAR receptors (PYLs), which bind to and inhibit group-A protein phosphatases 2C (PP2Cs), the negative regulators of ABA. X-ray structures of several PYL-ABA and PYL-ABA-PP2C complexes have revealed that a conserved tryptophan in PP2Cs is inserted into a small tunnel adjacent to the C4' of ABA in the PYL-ABA complex and plays a crucial role in the formation and stabilization of the PYL-ABA-PP2C complex. Here, 4'-modified ABA analogues were designed to prevent the insertion of the tryptophan into the tunnel adjacent to the C4' of ABA in these complexes. These analogues were predicted to block PYL-PP2C receptor interactions and thus block ABA signaling. To test this, 4'- O-phenylpropynyl ABA analogues were synthesized as novel PYL antagonists (PANs). Structural, thermodynamic, biochemical, and physiological studies demonstrated that PANs completely abolished ABA-induced PYL-PP2C interactions in vitro and suppressed stress-induced ABA responses in vivo more strongly than did 3'-hexylsulfanyl-ABA (AS6), a PYL antagonist we developed previously. The PANs and AS6 antagonized the effects of ABA to different degrees in different plants, suggesting that these PANs can function as chemical scalpels to dissect the complicated regulatory mechanism of ABA signaling in plants.
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Affiliation(s)
- Jun Takeuchi
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Naoki Mimura
- Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya 321-8505, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 243-0034, Japan
| | - Masayuki Sue
- Department of Applied Biology and Chemistry, Tokyo University of Agriculture, Tokyo 243-0034, Japan
| | - Tomonori Akiyama
- Department of Applied Biology and Chemistry, Tokyo University of Agriculture, Tokyo 243-0034, Japan
| | - Keina Monda
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Koh Iba
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Toshiyuki Ohnishi
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Yasushi Todoroki
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
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Liu X, He Z, Yin Y, Xu X, Wu W, Li L. Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb. BMC Genomics 2018; 19:343. [PMID: 29743016 PMCID: PMC5944168 DOI: 10.1186/s12864-018-4707-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 04/22/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Mandarin). The molecular events that occurred during seed development in E. ferox have not yet been characterized. In this study, we performed transcriptomic analysis of four developmental stages (T1, T2, T3, and T4) in E. ferox seeds with three biological replicates per developmental stage to understand the physiological and biochemical processes during E. ferox seeds development. RESULTS 313,844,425 clean reads were assembled into 160,107 transcripts and 85,006 unigenes with N50 lengths of 2052 bp and 1399 bp, respectively. The unigenes were annotated using five public databases (NR, COG, Swiss-Prot, KEGG, and GO). In the KEGG database, all of the unigenes were assigned to 127 pathways, of which phenylpropanoid biosynthesis was associated with the synthesis of secondary metabolites during E. ferox seed growth and development. Phenylalanine ammonia-lyase (PAL) as the first key enzyme catalyzed the conversion of phenylalanine to trans-cinnamic acid, then was related to the synthesis of flavonoids, lignins and alkaloid. The expression of PAL1 reached its peak at T3 stage, followed by a slight decrease at T4 stage. Cytochrome P450 (P450), encoded by CYP84A1 (which also called ferulate-5-hydroxylase (F5H) in Arabidopsis), was mainly involved in the biosynthesis of lignins. CONCLUSIONS Our study provides a transcriptomic analysis to better understand the morphological changes and the accumulation of medicinal components during E. ferox seed development. The increasing expression of PAL and P450 encoded genes in phenylpropanoid biosynthesis may promote the maturation of E. ferox seed including size, color, hardness and accumulation of medicinal components.
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Affiliation(s)
- Xian Liu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Yulai Yin
- Suzhou Vegetable Research Institute, 188 Xitang Road, Suzhou, Jiangsu Province 215008 People’s Republic of China
| | - Xu Xu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Weiwen Wu
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - Liangjun Li
- School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu Province 225009 People’s Republic of China
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Xu HH, Liu SJ, Song SH, Wang WQ, Møller IM, Song SQ. Proteome changes associated with dormancy release of Dongxiang wild rice seeds. JOURNAL OF PLANT PHYSIOLOGY 2016; 206:68-86. [PMID: 27697673 DOI: 10.1016/j.jplph.2016.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/20/2016] [Accepted: 08/28/2016] [Indexed: 06/06/2023]
Abstract
Seed dormancy provides optimum timing for seed germination and subsequent seedling growth, but the mechanism of seed dormancy is still poorly understood. Here, we used Dongxiang wild rice (DXWR) seeds to investigate the dormancy behavior and the differentially changed proteome in embryo and endosperm during dormancy release. DXWR seed dormancy was caused by interaction of embryo and its surrounding structure, and was an intermediate physiological dormancy. During seed dormancy release, a total of 109 and 97 protein spots showed significant change in abundance and were successfully identified in embryo and endosperm, respectively. As a result of dormancy release, the abundance of nine proteins involved in storage protein, cell defense and rescue and energy changed in the same way in both embryo and endosperm, while 67 and 49 protein spots changed differentially in embryo and endosperm, respectively. Dormancy release of DXWR seeds was closely associated with degradation of storage proteins in both embryo and endosperm. At the same time, the abundance of proteins involved in metabolism, glycolysis and TCA cycle, cell growth and division, protein synthesis and destination and signal transduction increased in embryos while staying constant or decreasing in endosperms.
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Affiliation(s)
- Heng-Heng Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shun-Hua Song
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Song-Quan Song
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Liu GH, Xu MJ, Chang QC, Gao JF, Wang CR, Zhu XQ. De novo transcriptomic analysis of the female and male adults of the blood fluke Schistosoma turkestanicum. Parasit Vectors 2016; 9:143. [PMID: 26968659 PMCID: PMC4788885 DOI: 10.1186/s13071-016-1436-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/05/2016] [Indexed: 12/19/2022] Open
Abstract
Background Schistosoma turkestanicum is a parasite of considerable veterinary importance as an agent of animal schistosomiasis in many countries, including China. The S. turkestanicum cercariae can also infect humans, causing cercarial dermatitis in many countries and regions of the world. In spite of its significance as a pathogen of animals and humans, there is little transcriptomic and genomic data in the public databases. Methods Herein, we performed the transcriptome Illumina RNA sequencing (RNA-seq) of adult males and females of S. turkestanicum and de novo transcriptome assembly. Results Approximately 81.1 (female) and 80.5 (male) million high-quality clean reads were obtained and then 29,526 (female) and 41,346 (male) unigenes were assembled. A total of 34,624 unigenes were produced from S. turkestanicum females and males, with an average length of 878 nucleotides (nt) and N50 of 1480 nt. Of these unigenes, 25,158 (72.7 %) were annotated by blast searches against the NCBI non-redundant protein database. Among these, 21,995 (63.5 %), 22,189 (64.1 %) and 13,754 (39.7 %) of the unigenes had significant similarity in the NCBI non-redundant protein (NR), non-redundant nucleotide (NT) and Swiss-Prot databases, respectively. In addition, 3150 unigenes were identified to be expressed specifically in females and 1014 unigenes were identified to be expressed specifically in males. Interestingly, several pathways associated with gonadal development and sex maintenance were found, including the Wnt signaling pathway (103; 2 %) and progesterone-mediated oocyte maturation (77; 1.5 %). Conclusions The present study characterized and compared the transcriptomes of adult female and male blood fluke, S. turkestanicum. These results will not only serve as valuable resources for future functional genomics studies to understand the molecular aspects of S. turkestanicum, but also will provide essential information for ongoing whole genome sequencing efforts on this pathogenic blood fluke.
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Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
| | - Min-Jun Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China.,College of Animal Science, South China Agricultural University, Guangzhou, Guangdong Province, 510642, PR China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, PR China
| | - Jun-Feng Gao
- Department of Parasitology, Heilongjiang Institute of Veterinary Science, Qiqihar, Heilongjiang Province, 161006, PR China
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, PR China.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China. .,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu Province, 225009, PR China.
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De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora). Int J Mol Sci 2015; 16:29047-59. [PMID: 26690126 PMCID: PMC4691086 DOI: 10.3390/ijms161226139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/13/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora.
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