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Guo Z, Zhu J, Zheng Y, Wang D, Zhang J, Jiang Z, Lu X, Jia R, Li X. Unveiling the variability in cadmium accumulation and tolerance characteristics: a comparative study of Basma and Yunyan 87 tobacco varieties. ENVIRONMENTAL TECHNOLOGY 2024:1-11. [PMID: 38623611 DOI: 10.1080/09593330.2024.2343127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024]
Abstract
Tobacco (Nicotiana tabacum L.) shows promise for remediating Cd-contaminated soil due to its significant Cd accumulation capabilities. Although various tobacco varieties exhibit distinct Cd bioaccumulation capacities, a comprehensive understanding of the underlying mechanisms is lacking. This study, conducted using hydroponics, explores differences in Cd accumulation and tolerance mechanisms between two tobacco varieties, Basma and Yunyan 87. The results showed that Cd stress reduced the dry weight, tolerance index, and root morphology for both varieties. Basma exhibited a relatively smaller decline in these indices compared to Yunyan 87. Moreover, Basma demonstrated a higher Cd bioconcentration factor (BCF), concentration, and accumulated content, signifying its superior tolerance and bioaccumulation capacity to Cd compared to Yunyan 87. The Carbonyl Cyanide3-ChloroPhenylhydrazone (CCCP) addition resulted in reduced Cd accumulation and BCFs in both tobacco species. This effect was more pronounced in Basma, suggesting that Basma relies more on an active transport process than Yunyan 87. This could potentially explain its enhanced bioaccumulation ability. Subcellular Cd distribution analysis revealed Basma's preference for distributing Cd in soluble fractions, while Yunyan 87 favoured the cell wall fractions. Transmission electron microscope showed that Basma's organelles were less damaged than Yunyan 87's under Cd stress, possibly contributing to the superior tolerance of Basma. Therefore, these results provided a theoretical foundation for development of Cd-contaminated soil tobacco remediation technology.
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Affiliation(s)
- Ziang Guo
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jinhui Zhu
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Ye Zheng
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Dan Wang
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jiahui Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Zhuoxin Jiang
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xiazi Lu
- Ecological Environment Geo-Service Center of Henan Geological Bureau, Zhengzhou, People's Republic of China
| | - Ruiqi Jia
- Zhong Yun International Engineering Co., Ltd, Zhengzhou, People's Republic of China
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou, People's Republic of China
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Wei K, Guo T. Enhancing the potential for cadmium phytoremediation by introducing Perilla frutescens genes in tobacco. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27392-5. [PMID: 37147538 DOI: 10.1007/s11356-023-27392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
To improve the potential of cadmium phytoremediation, distant hybridization between tobacco (Nicotiana tabacum L. var. 78-04), a high-biomass crop, and Perilla frutescens var. frutescens, a wild Cd-hyperaccumulator, was carried out, developing a new variety N. tabacum L. var. ZSY. Seedlings at the six-leaf stage were grown in hydroponics and treated with 0 (control), 10 µM, 180 µM, and 360 µM CdCl2 for 7 days; then, the differences in Cd tolerance and accumulation and physiological and metabolic responses were evaluated among "ZSY" and its parents. At high Cd dose, the growth of "ZSY," such as fresh weight, plant height, and root length, was evidently better than "78-04." In contrast to P. frutescens and "78-04," "ZSY" could accumulate more Cd in shoots than roots. Under the same treatment, "ZSY" accumulated greater amounts of Cd in both shoots (195-1523 mg kg-1) and roots (140-1281 mg kg-1) than "78-04" (shoots: 35-89 mg kg-1, roots: 39-252 mg kg-1), followed by P. frutescens (shoots: 156-454 mg kg-1, roots: 103-761 mg kg-1). BCF and TF values of "ZSY" reached 38-195 and 1.2-1.4, which were far higher than those of "78-04" (BCF: 2.2-35.3, TF: 0.35-0.9). Perilla frutescens was found with BCF and TF of 11-156 and 0.5-1.5. Cd stress obviously promoted the production of ROS and MDA in seedlings but reduced chlorophyll contents, especially in "78-04." As a response to Cd stress, "ZSY" had higher SOD and CAT activities when compared to P. frutescens and "78-04," while "78-04" produced more POD and proline than those of P. frutescens and "ZSY." Cd stress could affect the production and accumulation of alkaloids and phenolic compounds in root (endodermis and cortex) and mesophyll. At high Cd doses, P. frutescens and "ZSY" had more alkaloids in tissues than "78-04." Phenolic compounds in "78-04" were more obviously inhibited compared with P. frutescens and "ZSY." These secondary metabolites may play an important role in eliminating oxidative damage and enhancing Cd tolerance and accumulation in "ZSY" and P. frutescens. Results indicated that distant hybridization could be one of effective methods for introducing excellent genes from metal-hyperaccumulators into high biomass species, creating plants with superior phytoremediation potential.
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Affiliation(s)
- Keqiang Wei
- School of Life Science, Shanxi University, 63 Nanzhonghuan East Street, Taiyuan, 030006, People's Republic of China.
| | - Tingting Guo
- School of Life Science, Shanxi University, 63 Nanzhonghuan East Street, Taiyuan, 030006, People's Republic of China
- Division of Radiology and Environmental Medicine, China Institute for Radiation Protection, Taiyuan, 030006, China
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Wang PL, Lei XJ, Wang YY, Liu BC, Wang DN, Liu ZY, Gao CQ. Transcriptomic Analysis of Cadmium Stressed Tamarix hispida Revealed Novel Transcripts and the Importance of Abscisic Acid Network. FRONTIERS IN PLANT SCIENCE 2022; 13:843725. [PMID: 35519810 PMCID: PMC9062237 DOI: 10.3389/fpls.2022.843725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on the desert and soil with 0.5 to 1% salt content, making it an ideal plant for the research on response to abiotic stresses. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida. In the study, RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 μmol L-1 CdCl2 for 24, 48, and 72 h compared with control. In total, 72,764 unigenes exhibited similar sequences in the Non-redundant nucleic acid database (NR database), while 36.3% of all these unigenes may be new transcripts. In addition, 6,778, 8,282, and 8,601 DEGs were detected at 24, 48, and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance Cd resistance ability of T. hispida by regulating the production of ROS under Cd stress and inhibit absorption of Cd. The new transcriptome resources and data that we present in this study for T. hispida may facilitate investigation of molecular mechanisms governing Cd resistance.
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Affiliation(s)
- Pei-Long Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiao-Jin Lei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuan-Yuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bai-chao Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Dan-ni Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhong-Yuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Cai-Qiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Xu X, Zhang S, Cheng Z, Li T, Jia Y, Wang G, Yang Z, Xian J, Yang Y, Zhou W. Transcriptome analysis revealed cadmium accumulation mechanisms in hyperaccumulator Siegesbeckia orientalis L. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:18853-18865. [PMID: 32207009 DOI: 10.1007/s11356-020-08387-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/10/2020] [Indexed: 05/28/2023]
Abstract
Siegesbeckia orientalis L. was identified as a novel Cd-hyperaccumulator and valuable phytoremediation material. However, the molecular mechanisms underlying Cd accumulation in S. orientalis are largely unknown. In this study, RNA-Seq analysis was performed to study the Cd-accumulating mechanisms in its roots with or without Cd treatment. The RNA-seq analysis generated 312 million pairs of clean reads and 78G sequencing data. De novo transcriptome assembly produced 355,070 transcripts with an average length of 823.59 bp and 194,207 unigenes with an average length of 605.68 bp. Comparative transcriptome analyses identified a large number of differentially expressed genes in roots under Cd stress, and functional annotation suggested that S. orientalis utilizes various biological pathways involving many gene networks working simultaneously to cope with the stress. This study revealed that four biological pathways were mainly involved in S. orientalis tolerance to Cd stress, including reactive oxygen species scavenging, phenylpropanoid biosynthesis pathway, Cd absorption and transport, and ABA signaling pathway. The genes related to photosynthesis and heavy metal transport are likely the potential candidates and could be further investigated to determine their roles in Cd tolerance in S. orientalis roots. These findings will be useful to understand the Cd accumulation mechanisms in S. orientalis and facilitate the study of phytoremediation at the molecular level in plants.
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Affiliation(s)
- Xiaoxun Xu
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Soil Environment Protection of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shirong Zhang
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory of Soil Environment Protection of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Zhang Cheng
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting Li
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongxia Jia
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guiyin Wang
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory of Soil Environment Protection of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhanbiao Yang
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junren Xian
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanxiang Yang
- School of Environment Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
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5
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Bovet L, Cheval C, Hilfiker A, Battey J, Langlet D, Broye H, Schwaar J, Ozelley P, Lang G, Bakaher N, Laparra H, Goepfert S. Asparagine Synthesis During Tobacco Leaf Curing. PLANTS 2019; 8:plants8110492. [PMID: 31718005 PMCID: PMC6918383 DOI: 10.3390/plants8110492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022]
Abstract
Senescence is a genetically controlled mechanism that modifies leaf chemistry. This involves significant changes in the accumulation of carbon- and nitrogen-containing compounds, including asparagine through the activity of asparagine synthetases. These enzymes are required for nitrogen re-assimilation and remobilization in plants; however, their mechanisms are not fully understood. Here, we report how leaf curing—a senescence-induced process that allows tobacco leaves to dry out—modifies the asparagine metabolism. We show that leaf curing strongly alters the concentration of the four main amino acids, asparagine, glutamine, aspartate, and glutamate. We demonstrate that detached tobacco leaf or stalk curing has a different impact on the expression of asparagine synthetase genes and accumulation of asparagine. Additionally, we characterize the main asparagine synthetases involved in the production of asparagine during curing. The expression of ASN1 and ASN5 genes is upregulated during curing. The ASN1-RNAi and ASN5-RNAi tobacco plant lines display significant alterations in the accumulation of asparagine, glutamine, and aspartate relative to wild-type plants. These results support the idea that ASN1 and ASN5 are key regulators of asparagine metabolism during leaf curing.
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6
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Chen M, Yan G, Wang X, Huang Z, Shao X, Wu D, Zhang X, Liu B. Investigating the proteomic expression profile of tobacco (Nicotiana tabacum) leaves during four growth stages using the iTRAQ method. Anal Bioanal Chem 2019; 411:403-411. [PMID: 30478513 DOI: 10.1007/s00216-018-1453-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/28/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Despite the importance of tobacco (Nicotiana tabacum) in agriculture and model organism investigations, the proteomic changes that occur in the tobacco leaf as it matures remain to be explored. In this study, an isobaric tags for relative and absolute quantification (iTRAQ) strategy was applied to investigate the proteomic profiles of K326 and Honghua Dajinyuan (HD) tobacco leaves at four growth stages. The proteomic profile varied with growth stage in both K326 and HD. Gene ontology (GO) classification was used to identify the biological processes that showed the greatest changes in protein expression between growth stages of HD and K326. Moreover, the number of differentially expressed proteins was greater in HD than in K326, especially during the rosette growth stage and the fast-growing stage. The galactose metabolism and glycosphingolipid biosynthesis-globo series pathways appeared only during the rosette growth stage of HD. It therefore appears that these pathways may be correlated with tobacco mosaic disease. The identification of these pathways should prove useful in investigations of the pathogenesis of tobacco mosaic virus. Graphical abstract ᅟ.
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Affiliation(s)
- Min Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xuantang Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zhi Huang
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Xi Shao
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Da Wu
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China
| | - Xiangmin Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Baizhan Liu
- Technology R&D Center, Shanghai Tobacco Group Co., Ltd., Shanghai, 200082, China.
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7
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da Silva CP, de Almeida TE, Zittel R, de Oliveira Stremel TR, Domingues CE, Kordiak J, de Campos SX. Translocation of metal ions from soil to tobacco roots and their concentration in the plant parts. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:663. [PMID: 27837364 DOI: 10.1007/s10661-016-5679-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/31/2016] [Indexed: 05/11/2023]
Abstract
This paper presents a study on the translocation factors (TFs) and bioconcentration factors (BCFs) of copper (Cu), manganese (Mn), zinc (Zn), cobalt (Co), chromium (Cr), cadmium (Cd), lead (Pb), iron (Fe), nickel (Ni), and arsenic (As) ions in roots, stems, and leaves of tobacco. The results revealed that during the tobacco growth, the roots are able to increase the sensitiveness of the physiological control, reducing the translocation of the metals Ni (0.38) and Pb (0.48) to the leaves. Cd and Zn presented factors TF and BCF >1 in the three tissues under analysis, which indicates the high potential for transportation and accumulation of these metals in all plant tissues. The TF values for Cr (0.65) and As (0.63) revealed low translocation of these ions to the aerial parts, indicating low mobility of ions from the roots. Therefore, tobacco can be considered an efficient accumulator of Ni, Cr, As and Pb in roots and Cd and Zn in all plant parts.
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Affiliation(s)
- Cleber Pinto da Silva
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil.
| | - Thiago E de Almeida
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Rosimara Zittel
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Tatiana R de Oliveira Stremel
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Cinthia E Domingues
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Januário Kordiak
- Research Group in Chemistry Simulation, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
| | - Sandro Xavier de Campos
- Research Group on Environmental and Sanitary Analytical Chemistry, Ponta Grossa State University (UEPG), Av. General Carlos Cavalcanti, 4748, Ponta Grossa, PR, 84030-900, Brazil
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8
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Gu L, Xue L, Song Q, Wang F, He H, Zhang Z. Classification of the fragrant styles and evaluation of the aromatic quality of flue-cured tobacco leaves by machine-learning methods. J Bioinform Comput Biol 2016; 14:1650033. [PMID: 27696927 DOI: 10.1142/s0219720016500335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
During commercial transactions, the quality of flue-cured tobacco leaves must be characterized efficiently, and the evaluation system should be easily transferable across different traders. However, there are over 3000 chemical compounds in flue-cured tobacco leaves; thus, it is impossible to evaluate the quality of flue-cured tobacco leaves using all the chemical compounds. In this paper, we used Support Vector Machine (SVM) algorithm together with 22 chemical compounds selected by ReliefF-Particle Swarm Optimization (R-PSO) to classify the fragrant style of flue-cured tobacco leaves, where the Accuracy (ACC) and Matthews Correlation Coefficient (MCC) were 90.95% and 0.80, respectively. SVM algorithm combined with 19 chemical compounds selected by R-PSO achieved the best assessment performance of the aromatic quality of tobacco leaves, where the PCC and MSE were 0.594 and 0.263, respectively. Finally, we constructed two online tools to classify the fragrant style and evaluate the aromatic quality of flue-cured tobacco leaf samples. These tools can be accessed at http://bioinformatics.fafu.edu.cn/tobacco .
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Affiliation(s)
- Li Gu
- * Institute of Tobacco Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- † Research Institute of Plateau Ecological, Agriculture and Animal Husbandry College, Tibet University, Linzhi 860000, China
| | - Lichun Xue
- ‡ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qi Song
- ‡ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fengji Wang
- * Institute of Tobacco Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaqin He
- ‡ College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongyi Zhang
- * Institute of Tobacco Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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9
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Zhou Q, Guo JJ, He CT, Shen C, Huang YY, Chen JX, Guo JH, Yuan JG, Yang ZY. Comparative Transcriptome Analysis between Low- and High-Cadmium-Accumulating Genotypes of Pakchoi (Brassica chinensis L.) in Response to Cadmium Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6485-94. [PMID: 27228483 DOI: 10.1021/acs.est.5b06326] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
To reduce cadmium (Cd) pollution of food chains, screening and breeding of low-Cd-accumulating cultivars are the focus of much study. Two previously identified genotypes, a low-Cd-accumulating genotype (LAJK) and a high-Cd-accumulating genotype (HAJS) of pakchoi (Brassica chinesis L.), were stressed by Cd (12.5 μM) for 0 h (T0), 3 h (T3) and 24 h (T24). By comparative transcriptome analysis for root tissue, 3005 and 4343 differentially expressed genes (DEGs) were identified in LAJK at T3 (vs T0) and T24 (vs T3), respectively, whereas 8677 and 5081 DEGs were detected in HAJS. Gene expression pattern analysis suggested a delay of Cd responded transcriptional changes in LAJK compared to HAJS. DEG functional enrichments proposed genotype-specific biological processes coped with Cd stress. Cell wall biosynthesis and glutathione (GSH) metabolism were found to involve in Cd resistance in HAJS, whereas DNA repair and abscisic acid (ABA) signal transduction pathways played important roles in LAJK. Furthermore, the genes participating in Cd efflux such as PDR8 were overexpressed in LAJK, whereas those responsible for Cd transport such as YSL1 were more enhanced in HAJS, exhibiting different Cd transport processes between two genotypes. These novel findings should be useful for molecular assisted screening and breeding of low-Cd-accumulating genotypes for pakchoi.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Jing-Jie Guo
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Chun-Tao He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Chuang Shen
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Ying-Ying Huang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Jing-Xin Chen
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Jian-Hua Guo
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Jian-Gang Yuan
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
| | - Zhong-Yi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University , Xingang Xi Road 135, Guangzhou 510275, China
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10
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Liu T, Zhu S, Tang Q, Tang S. Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. Gene 2014; 558:131-7. [PMID: 25550046 DOI: 10.1016/j.gene.2014.12.057] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 12/15/2022]
Abstract
Cadmium (Cd) contamination in agricultural soils has become a major environmental problem in China. Ramie, a fiber crop, has frequently been proposed for use as a phytoremediation crop for the restoration of Cd-contaminated farmlands. However, high levels of Cd can greatly inhibit stem growth in ramie, which reduces its economic value as a crop. To understand the potential mechanisms behind this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing on two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2). Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequence reads were generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, and de novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels in CO and CdS ramie revealed 155 differentially expressed genes (DEGs) between treatment and control conditions. Sixteen DEGs were further analyzed for expression differences by using real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase (a major enzyme for deactivating bioactive gibberellins [GAs]) showed markedly up-regulated expression in Cd stressed ramie. This might be responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that the cutin, suberine and wax biosynthesis pathway was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful in further understanding the mechanism of Cd-stress response and improving Cd stress tolerance in ramie.
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Affiliation(s)
- Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Qingming Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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11
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Zimmermann P, Bleuler S, Laule O, Martin F, Ivanov NV, Campanoni P, Oishi K, Lugon-Moulin N, Wyss M, Hruz T, Gruissem W. ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions. BioData Min 2014; 7:18. [PMID: 25228922 PMCID: PMC4165432 DOI: 10.1186/1756-0381-7-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/13/2014] [Indexed: 11/18/2022] Open
Abstract
Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. Here, we describe a new type of standardized datasets representative for the spatial and temporal dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments. Expression data is aggregated by anatomical part or stage of development to yield a representative transcriptome for each category. For example, we created a genome-wide expression dataset representing the FDA tissue panel across 35 tissue types. The proposed datasets were created for human and several model organisms and are publicly available at http://www.expressiondata.org.
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Affiliation(s)
| | | | - Oliver Laule
- NEBION AG, Hohlstrasse 515, 8048 Zurich, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Prisca Campanoni
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | - Karen Oishi
- Philip Morris International R&D, Quai Jeanrenaud 5, 2003 Neuchatel, Switzerland
| | | | - Markus Wyss
- NEBION AG, Hohlstrasse 515, 8048 Zurich, Switzerland
| | - Tomas Hruz
- Institute of Theoretical Computer Science, ETH Zurich, 8092 Zurich, Switzerland
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12
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Sierro N, Battey JN, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV. The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 2014; 5:3833. [PMID: 24807620 PMCID: PMC4024737 DOI: 10.1038/ncomms4833] [Citation(s) in RCA: 330] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
The allotetraploid plant Nicotiana tabacum (common tobacco) is a major crop species and a model organism, for which only very fragmented genomic sequences are currently available. Here we report high-quality draft genomes for three main tobacco varieties. These genomes show both the low divergence of tobacco from its ancestors and microsynteny with other Solanaceae species. We identify over 90,000 gene models and determine the ancestral origin of tobacco mosaic virus and potyvirus disease resistance in tobacco. We anticipate that the draft genomes will strengthen the use of N. tabacum as a versatile model organism for functional genomics and biotechnology applications.
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Affiliation(s)
- Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - James N.D. Battey
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Nicolas Bakaher
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Lucien Bovet
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Adrian Willig
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
- Present address: 25b Quai Charles-Page, CH-1205 Genève, Switzerland
| | - Simon Goepfert
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Nikolai V. Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
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13
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Meskauskiene R, Laule O, Ivanov NV, Martin F, Wyss M, Gruissem W, Zimmermann P. Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies. PLANT METHODS 2013; 9:33. [PMID: 23958387 PMCID: PMC3751485 DOI: 10.1186/1746-4811-9-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/13/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a particular purpose. In most cases, the practical application of these ontologies has been limited to systematically storing experimental data. Due to technical constraints, complex data structures and term redundancies, it has been difficult to apply them directly into analysis tools. RESULTS Here, we describe a simplified and cross-species compatible set of controlled vocabularies for plant anatomy, focussing mainly on monocotypledonous and dicotyledonous crop and model plants. Their content was designed primarily for their direct use in graphical visualization tools. Specifically, we created annotation vocabularies that can be understood by non-specialists, are minimally redundant, simply structured, have low tree depth, and we tested them practically in the frame of Genevestigator. CONCLUSIONS The application of the proposed ontologies enabled the aggregation of data from hundreds of experiments to visualize gene expression across tissue types. It also facilitated the comparison of expression across species. The described controlled vocabularies are maintained by a dedicated curation team and are available upon request.
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Affiliation(s)
| | - Oliver Laule
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
- NEBION AG, Hohlstrasse 515, Zurich 8048, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Quai Jeanrenaud 5, Neuchatel 2003, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Quai Jeanrenaud 5, Neuchatel 2003, Switzerland
| | - Markus Wyss
- NEBION AG, Hohlstrasse 515, Zurich 8048, Switzerland
| | | | - Philip Zimmermann
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
- NEBION AG, Hohlstrasse 515, Zurich 8048, Switzerland
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14
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Sierro N, Battey JND, Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch MC, Ivanov NV. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 2013; 14:R60. [PMID: 23773524 PMCID: PMC3707018 DOI: 10.1186/gb-2013-14-6-r60] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 05/10/2013] [Accepted: 06/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species. RESULTS Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis. CONCLUSIONS The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution.
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Affiliation(s)
- Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - James ND Battey
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Lucien Bovet
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Simon Goepfert
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nicolas Bakaher
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
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