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Baysal Ö, Studholme DJ, Jimenez-Quiros C, Tör M. Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07. Access Microbiol 2024; 6:000762.v3. [PMID: 38868377 PMCID: PMC11165630 DOI: 10.1099/acmi.0.000762.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/17/2024] [Indexed: 06/14/2024] Open
Abstract
Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here, we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713, but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for EU07's beneficial properties.
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Affiliation(s)
- Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, 48000 Menteşe, Turkey
- Department of Biological Sciences, University of Worcester, Worcester, UK
| | | | | | - Mahmut Tör
- Department of Biological Sciences, University of Worcester, Worcester, UK
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Genome analysis uncovers the prolific antagonistic and plant growth-promoting potential of endophyte Bacillus velezensis K1. Gene 2022; 836:146671. [PMID: 35714801 DOI: 10.1016/j.gene.2022.146671] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022]
Abstract
Insights into the application of endophytic bacilli in sustainable agricultural practices have opened up new avenues for the inhibition of soil-borne pathogens and the improvement of plant health. Bacillus subtilis K1, an endophytic bacterium originally isolated from aerial roots of Ficus benghalensis is a potential biocontrol agent secreting a mixture of surfactins, iturins and fengycins. The current study extends the characterization of this bacterium through genomic and comparative genomics approaches. The sequencing of the bacterial genome at Illumina MiSeq platform revealed that it possessed a 4,103,502-bp circular chromosome with 45.98% GC content and 4325 predicted protein-coding sequences. Based on phylogenomics and whole-genome average nucleotide identity, the B. subtilis K1 was taxonomically classified as Bacillus velezensis. The formerly evaluated phenotypic traits viz. C-source utilization and lipopeptide-mediated fungal antagonism were correlated to their molecular determinants. The genome also harbored several genes associated with induced systemic resistance and plant growth promotion i.e, phytohormone production, nitrogen assimilation and reduction, siderophore production, phosphate solubilization, biofilm formation, swarming motility, acetoin and butanediol synthesis. The production of antifungal volatile organic compounds and plant growth promotion was experimentally demonstrated by volatile compound assay and seed germination assay on cumin and groundnut. The isolate also holds great prospects for application as a soil inoculant as indicated by enhancement in the growth of groundnut via in planta pot studies. Bacterial pan-genome analysis based on a comparison of whole genomes with eighteen other Bacillus strains was also conducted. Comparative examination of biosynthetic gene clusters across all genomes indicated that the largest number of gene clusters were harbored by the K1 genome. Based on the findings, we propose K1 as a model for scrutinizing non-ribosomally synthesized peptide synthetase and polyketide synthetase derived molecules.
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Guo X, Chen F, Liu J, Shao Y, Wang X, Zhou Y. Genome Mining and Analysis of PKS Genes in Eurotium cristatum E1 Isolated from Fuzhuan Brick Tea. J Fungi (Basel) 2022; 8:jof8020193. [PMID: 35205947 PMCID: PMC8874483 DOI: 10.3390/jof8020193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/04/2022] Open
Abstract
Eurotium cristatum as the dominant fungi species of Fuzhuan brick tea in China, can produce multitudinous secondary metabolites (SMs) with various bioactivities. Polyketides are a very important class of SMs found in E. cristatum and have gained extensive attention in recent years due to their remarkable diversity of structures and multiple functions. Therefore, it is necessary to explore the polyketides produced by E. cristatum at the genomic level to enhance its application value. In this paper, 12 polyketide synthase (PKS) genes were found in the whole genome of E. cristatum E1 isolated from Fuzhuan brick tea. In addition, the qRT-PCR results further demonstrated that these genes were expressed. Moreover, metabolic analysis demonstrated E. cristatum E1 can produce a variety of polyketides, including citreorosein, emodin, physcion, isoaspergin, dihydroauroglaucin, iso-dihydroauroglaucin, aspergin, flavoglaucin and auroglaucin. Furthermore, based on genomic analysis, the putative secondary metabolites clusters for emodin and flavoglaucin were proposed. The results reported here will lay a good basis for systematically mining SMs resources of E. cristatum and broadening its application fields.
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Affiliation(s)
- Xiaoxiao Guo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Liu
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro Products, Wuhan 430064, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.G.); (F.C.); (Y.S.)
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.W.); (Y.Z.); Tel./Fax: +86-27-87282111 (X.W.); +86-27-87389465 (Y.Z.)
| | - Youxiang Zhou
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro Products, Wuhan 430064, China
- Correspondence: (X.W.); (Y.Z.); Tel./Fax: +86-27-87282111 (X.W.); +86-27-87389465 (Y.Z.)
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Liang L, Fu Y, Deng S, Wu Y, Gao M. Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus. Microorganisms 2021; 10:microorganisms10010063. [PMID: 35056513 PMCID: PMC8778260 DOI: 10.3390/microorganisms10010063] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
Ginger rhizome rot disease, caused by the pathogen Bacilluspumilus GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new Bacillus velezensis strain, designated ATR2. Genome analysis revealed B. velezensis ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, B. velezensis ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. B. velezensis ATR2 was also efficacious in control of aphids. The antagonistic compound from B. velezensis ATR2 against B.pumilus GR8 was purified and identified as bacillomycin D. In addition, B. velezensis ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of B. velezensis ATR2 as a biocontrol agent in agricultural diseases and pests management.
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Affiliation(s)
- Leiqin Liang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (L.L.); (Y.F.); (S.D.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (L.L.); (Y.F.); (S.D.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (L.L.); (Y.F.); (S.D.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (L.L.); (Y.F.); (S.D.); (Y.W.)
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (L.L.); (Y.F.); (S.D.); (Y.W.)
- Correspondence:
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Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules 2021; 11:1111. [PMID: 34439777 PMCID: PMC8393538 DOI: 10.3390/biom11081111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
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Affiliation(s)
- Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain
| | - Sergio Gálvez
- Dep. Lenguajes y Ciencias de la Computación, Boulevard Louis Pasteur 35, Universidad de Málaga, 29071 Málaga, Spain;
| | - Teresa E. Rosales
- Laboratorio de Arqueobiología, Avda. Universitaria s/n, Universidad Nacional de Trujillo, 13011 Trujillo, Peru;
| | - Víctor F. Vásquez
- Centro de Investigaciones Arqueobiológicas y Paleoecológicas Andinas Arqueobios, Martínez de Companón 430-Bajo 100, Urbanización San Andres, 13088 Trujillo, Peru;
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain;
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Vairagkar U, Nipanikar-Gokhale P, Mirza Y. Genomic insights into biocontrol potential of edible seaweed-associated Bacillus velezensis MTCC 10456 from Gulf of Mannar. Arch Microbiol 2021; 203:2941-2952. [PMID: 33770230 DOI: 10.1007/s00203-021-02244-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Bacillus velezensis MTCC 10456, is a marine mesophilic heterotrophic bacterium, isolated from edible red seaweed, Laurenciae papillosa, with a potential for plant growth promotion and biocontrol activity. We report the genome sequence analysis of strain MTCC 10456, which has a genome size of 4.19 Mb with an average G + C content of 45.9%, 4077 coding sequences and 94 RNAs. Comparative genome analysis of MTCC 10456 with 76 other land plant-based strains with complete information on the source of their isolation, was carried out. This study provided evidence that multiple gene clusters that contributed to the seaweed colonization, growth promotion, immunity and hyperosmotic stress tolerance are conserved in different B. velezensis strains. A unique methyltransferase gene that can cause global alterations in DNA methylation patterns affecting gene expression and regulation of transcription in MTCC 10456 genome was identified. The genome provides insights into multiple gene clusters encoding antagonistic metabolites, such as non-ribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs), unidentified metabolites and genes for antimicrobial resistance. Overall, findings from this study indicate the application of B. velezensis MTCC 10456 in the aquaculture industry as a biocontrol agent and may also contribute in understanding the ecological adaptations of plant-associated B. velezensis strains in different habitats.
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Affiliation(s)
- Uttara Vairagkar
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India.,Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Padmaja Nipanikar-Gokhale
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India
| | - Yasmin Mirza
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India.
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Cortese IJ, Castrillo ML, Onetto AL, Bich GÁ, Zapata PD, Laczeski ME. De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate). PLoS One 2021; 16:e0248274. [PMID: 33705487 PMCID: PMC7954119 DOI: 10.1371/journal.pone.0248274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/23/2021] [Indexed: 11/18/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo. The purposes of this work were to assemble the genomes of B. altitudinis 19RS3 and T5S-T4, using different assemblers available for Windows and Linux and to select the best assembly for each strain. Both genomes were also automatically annotated to detect PGP genes and compare sequences with other genomes reported. Library construction and draft genome sequencing were performed by Macrogen services. Raw reads were filtered using the Trimmomatic tool. Genomes were assembled using SPAdes, ABySS, Velvet, and SOAPdenovo2 assemblers for Linux, and Geneious and CLC Genomics Workbench assemblers for Windows. Assembly evaluation was done by the QUAST tool. The parameters evaluated were the number of contigs ≥ 500 bp and ≥ 1000 bp, the length of the longest contig, and the N50 value. For genome annotation PROKKA, RAST, and KAAS tools were used. The best assembly for both genomes was obtained using Velvet. The B. altitudinis 19RS3 genome was assembled into 15 contigs with an N50 value of 1,943,801 bp. The B. altitudinis T5S-T4 genome was assembled into 24 contigs with an N50 of 344,151 bp. Both genomes comprise several genes related to PGP mechanisms, such as those for nitrogen fixation, iron metabolism, phosphate metabolism, and auxin biosynthesis. The results obtained offer the basis for a better understanding of B. altitudinis 19RS3 and T5S-T4 and make them promissory for bioinoculant development.
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Affiliation(s)
- Iliana Julieta Cortese
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Andrea Liliana Onetto
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
| | - Margarita Ester Laczeski
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología
Misiones “Dra. María Ebe Reca” (InBioMis), CONICET, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
- Cátedra de Bacteriología, Dpto. de Microbiología, Facultad de Ciencias
Exactas, Químicas y Naturales/FCEQyN, Universidad Nacional de Misiones/UNaM,
Posadas, Misiones, Argentina
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Li C, Cheng P, Zheng L, Li Y, Chen Y, Wen S, Yu G. Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait. Genomics 2021; 113:900-909. [PMID: 33592313 DOI: 10.1016/j.ygeno.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 01/27/2023]
Abstract
Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.
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Affiliation(s)
- 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 510225, People's Republic of China.
| | - Ping Cheng
- 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 510225, People's Republic of China.
| | - Li Zheng
- 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 510225, People's Republic of China
| | - Yongjian Li
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Yanhong Chen
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Shuheng Wen
- Guangdong Geolong Biotechnology Co., Ltd., Zhuhai 519050, People's Republic of 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 510225, People's Republic of China.
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