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Warsi ZI, Khatoon K, Singh P, Rahman LU. Enhancing drought resistance in Pogostemon cablin (Blanco) Benth. through overexpression of ACC deaminase gene using thin cell layer regeneration system. FRONTIERS IN PLANT SCIENCE 2023; 14:1238838. [PMID: 37636084 PMCID: PMC10452012 DOI: 10.3389/fpls.2023.1238838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023]
Abstract
Pogostemon cablin cultivation faces massive constraints because of its susceptability to drought stress that reduces patchouli propagation and oil yield. The present study has achieved an efficient and rapid direct regeneration system for the transgenic production of P. cablin using Agrobacterium-mediated genetic transformation. To establish an efficient regeneration protocol for fast in-vitro multiplication of patchouli plants, leaf, petiole, and transverse thin cell layer (tTCL) explants were used and inoculated on an MS medium supplemented with different combinations of phytohormones. A comparative study showed a maximum regeneration frequency of 93.30 ± 0.56% per explant was obtained from leaf segments on optimal MS medium fortified with 0.2mg/L BAP and 0.1mg/L NAA. Leaf and petiole explants took 25-35 days to regenerate while tTCL section showed regeneration in just 15-20 days on the same medium. Subsequently, productive genetic transformation protocol OD600 0.6, AS 200µM, 30mg/L kanamycin, and infection time 5 min. was standardized and best-suited explants were infected at optimum conditions from the Agrobacterium tumefaciens (LBA 4404) strain harboring ACC deaminase to generate transgenic P. cablin Benth. (CIM-Samarth) plants. The investigation suggested that the optimized protocol provides a maximum transformation frequency of 42 ± 1.9% in 15-20 days from tTCL. The transgenic plants were shifted to the greenhouse with a 52.0 ± 0.8% survival frequency. A molecular docking study confirmed significant binding affinity of ligand ACC with ACC deaminase at the catalytic site, and ligand interactions showed four H-bonds at the binding pocket with amino acids Cys-196, Val-198, Thr-199, and Gly-200 that validate gene relative expression in transgenic plants. Among all transgenic acclimatized greenhouse-grown patchouli plants, line PT4 showed improved drought resistance under severe water stress as its RWC was 71.7 ± 2.3% to 75.7 ± 2.1% which is greater than the RWC of the control plant, 58.30 ± 0.21%. Analysis of the other physiological indicators, H2O2, chlorophyll content, and ROS result support drought resistance ability. Our study concluded that the first report on P. cablin, tTCL direct regeneration, and standardized transformation protocol created a new opportunity for genetic manipulation to achieve drought-resistant patchouli plants for cultivation in all seasons at the commercial level.
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Affiliation(s)
| | | | | | - Laiq Ur Rahman
- Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research (CSIR), Lucknow, India
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Fang C, Sun X, Fan F, Zhang X, Wang O, Zheng H, Peng Z, Luo X, Chen A, Zhang W, Drmanac R, Peters BA, Song Z, Kristiansen K. High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities. CELL REPORTS METHODS 2023; 3:100437. [PMID: 37056375 PMCID: PMC10088238 DOI: 10.1016/j.crmeth.2023.100437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
Sequencing of hypervariable regions as well as internal transcribed spacer regions of ribosomal RNA genes (rDNA) is broadly used to identify bacteria and fungi, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length using high throughput, cost-efficient second-generation sequencing. We developed a method to obtain nearly full-length rDNA by assembling single DNA molecules combining DNA co-barcoding with single-tube long fragment read technology and second-generation sequencing. Benchmarking was performed using mock bacterial and fungal communities as well as two forest soil samples. All mock species rDNA were successfully recovered with identities above 99.5% compared to the reference sequences. From the soil samples we obtained good coverage with identification of more than 20,000 unknown species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.
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Affiliation(s)
- Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Fei Fan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Ou Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China
- Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhuobing Peng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Radoje Drmanac
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Brock A. Peters
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450 Copenhagen, Denmark
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Sun Y, Su Y, Hussain A, Xiong L, Li C, Zhang J, Meng Z, Dong Z, Yu G. Complete genome sequence of the Pogostemon cablin bacterial wilt pathogen Ralstonia solanacearum strain SY1. Genes Genomics 2023; 45:123-134. [PMID: 35670995 PMCID: PMC9171469 DOI: 10.1007/s13258-022-01270-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Ralstonia solanacearum causes bacterial wilt of Pogostemon cablin which is an important aromatic herb and also the main materials of COVID-19 therapeutic traditional drugs. However, we are lacking the information on the genomic sequences of R. solanacearum isolated from P. cablin. OBJECTIVE The acquisition and analysis of this whole-genome sequence of the P. cablin bacterial wilt pathogen. METHODS An R. solanacearum strain, named SY1, was isolated from infected P. cablin plants, and the complete genome sequence was sequenced and analyzed. RESULTS The SY1 strain contains a 3.70-Mb chromosome and a 2.18-Mb megaplasmid, with GC contents of 67.57% and 67.41%, respectively. A total of 3308 predicted genes were located on the chromosome and 1657 genes were located in the megaplasmid. SY1 strain has 273 unique genes compared with five representative R. solanacearum strains, and these genes were enriched in the plant-pathogen interaction pathway. SY1 possessed a higher syntenic relationship with phylotype I strains, and the arsenal of type III effectors predicted in SY1 were also more closely related to those of phylotype I strains. SY1 contained 14 and 5 genomic islands in its chromosome and megaplasmid, respectively, and two prophage sequences in its chromosome. In addition, 215 and 130 genes were annotated as carbohydrate-active enzymes and antibiotic resistance genes, respectively. CONCLUSION This is the first genome-scale assembly and annotation for R. solanacearum which isolated from infected P. cablin plants. The arsenal of virulence and antibiotic resistance may as the determinants in SY1 for infection of P. cablin plants.
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Affiliation(s)
- Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yutong Su
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ansar Hussain
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Lina Xiong
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jie Zhang
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhen Meng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
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Zheng X, Xiao R, Chen M, Wu H, Gao X, Wang J. An avirulent Ralstonia solanacearum strain FJAT1458 outcompetes with virulent strain and induces tomato plant resistance against bacterial wilt. PEST MANAGEMENT SCIENCE 2022; 78:5002-5013. [PMID: 36053816 DOI: 10.1002/ps.7123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/22/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bacterial wilt (BW) caused by Ralstonia solanacearum (RS) is considered as one of the most destructive plant diseases. An avirulent strain of RS, FJAT1458, is a potential biocontrol agent of BW. In this study, the mechanism of FJAT1458 against BW was evaluated. RESULTS FJAT1458 was tagged with the red fluorescent protein gene, and the resulting strain was named as FJAT1458-RFP. When FJAT1458-RFP and FJAT91-GFP (a virulent strain of RS labelled with the green fluorescent protein gene), were co-inoculated in potted tomato plants, the colonization of FJAT91-GFP reached an almost undetectable level at 7 days post-inoculation (dpi) in the roots and at 9 dpi in rhizosphere soil. When they were co-inoculated in a hydroponic tomato growing system, numbers of the two strains were similar at 3 dpi in the root tissues; however, FJAT91-GFP was not detected at 9 dpi while FJAT1458-RFP maintained 1.77 × 105 CFU g-1 . The inoculation of FJAT1458-RFP alone or combination with FJAT91-GFP significantly increased tomato root activity. Moreover, expression levels of the defense-related genes PR-1a, GLUA, and CHI3 in tomato roots were significantly up-regulated by FJAT1458-RFP and co-inoculation of FJAT1458-RFP and FJAT91-GFP at 5 dpi, compared to the control (water, CK) treatment. Noteworthy, expression levels of GLUA in the treatments of FJAT1458-RFP and FJAT1458-RFP + FJAT91-GFP were 12.22- and 12.05-fold higher than that in the CK at 5 dpi, respectively. CONCLUSIONS The results suggested that the avirulent strain FJAT1458-RFP could suppress colonization of the virulent strain in tomato roots, and induce tomato plant resistance against BW. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xuefang Zheng
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, China
| | - Rongfeng Xiao
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, China
| | - Meichun Chen
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, China
| | - Huijun Wu
- Key Laboratory of Integrated and Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuewen Gao
- Key Laboratory of Integrated and Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jieping Wang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, China
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Identification and characterization of virulence-attenuated mutants in Ralstonia solanacearum as potential biocontrol agents against bacterial wilt of Pogostemon cablin. Microb Pathog 2020; 147:104418. [PMID: 32739402 DOI: 10.1016/j.micpath.2020.104418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/30/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022]
Abstract
Ralstonia solanacearum is a soil-borne pathogen that causes bacterial wilt worldwide. The virulence-attenuated mutants were able to combat the soil-borne plant diseases. In this study, we screened the virulence-attenuated mutant PRS-84-4-49 of Ralstonia solanacearum and demonstrated that this strain showed a significant biocontrol effect against patchouli bacterial wilt. Three putative virulence-attenuated mutants obtained in our previous preliminary screen were individually tested for their pathogenicity to patchouli plants. Mutant PRS-84-4-49 showed significantly less virulence to patchouli plants than the other investigated mutants. The virulence-attenuated mutant PRS-84-4-49 was then evaluated for its potential to control patchouli bacterial wilt. The results revealed that the biocontrol treatment significantly reduced disease severity compared with the inoculated control plants, their highest disease incidence were 33% and 63%, respectively, at 5 days post-inoculation. Mutant PRS-84-4-49 exhibited less motility and produced fewer biofilms than the wild-type strain. Therefore, our results demonstrate that virulence-attenuated mutant of Ralstonia solanacearum has potential as biological control agent capable of suppressing patchouli bacterial wilt.
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