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Liu L, Li Y, Wang Q, Xu X, Yan J, Wang Y, Wang Y, Shah SMA, Peng Y, Zhu Z, Xu Z, Chen G. Constructed Rice Tracers Identify the Major Virulent Transcription Activator-Like Effectors of the Bacterial Leaf Blight Pathogen. RICE (NEW YORK, N.Y.) 2024; 17:30. [PMID: 38656724 PMCID: PMC11043257 DOI: 10.1186/s12284-024-00704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) injects major transcription activator-like effectors (TALEs) into plant cells to activate susceptibility (S) genes for promoting bacterial leaf blight in rice. Numerous resistance (R) genes have been used to construct differential cultivars of rice to identify races of Xoo, but the S genes were rarely considered. Different edited lines of rice cv. Kitaake were constructed using CRISPR/Cas9 gene-editing, including single, double and triple edits in the effector-binding elements (EBEs) located in the promoters of rice S genes OsSWEET11a, OsSWEET13 and OsSWEET14. The near-isogenic lines (NILs) were used as tracers to detect major TALEs (PthXo1, PthXo2, PthXo3 and their variants) in 50 Xoo strains. The pathotypes produced on the tracers determined six major TALE types in the 50 Xoo strains. The presence of the major TALEs in Xoo strains was consistent with the expression of S genes in the tracers, and it was also by known genome sequences. The EBE editing had little effect on agronomic traits, which was conducive to balancing yield and resistance. The rice-tracers generated here provide a valuable tool to track major TALEs of Xoo in Asia which then shows what rice cultivars are needed to combat Xoo in the field.
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Affiliation(s)
- Linlin Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiali Yan
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yijie Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongzheng Peng
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhangfei Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhu X, Chen L, Zhang Z, Li J, Zhang H, Li Z, Pan Y, Wang X. Genetic-based dissection of resistance to bacterial leaf streak in rice by GWAS. BMC PLANT BIOLOGY 2023; 23:396. [PMID: 37596557 PMCID: PMC10436437 DOI: 10.1186/s12870-023-04412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Rice is the second-largest food crop in the world and vulnerable to bacterial leaf streak disease. A thorough comprehension of the genetic foundation of agronomic traits was essential for effective implementation of molecular marker-assisted selection. RESULTS Our study aimed to evaluate the vulnerability of rice to bacterial leaf streak disease (BLS) induced by the gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc). In order to accomplish this, we first analyzed the population structure of 747 accessions and subsequently assessed their phenotypes 20 days after inoculation with a strain of Xoc, GX01. We conducted genome-wide association studies (GWAS) on a population of 747 rice accessions, consisting of both indica and japonica subpopulations, utilizing phenotypic data on resistance to bacterial leaf streak (RBLS) and sequence data. We identified a total of 20 QTLs associated with RBLS in our analysis. Through the integration of linkage mapping, sequence analysis, haplotype analysis, and transcriptome analysis, we were able to identify five potential candidate genes (OsRBLS1-OsRBLS5) that possess the potential to regulate RBLS in rice. In order to gain a more comprehensive understanding of the genetic mechanism behind resistance to bacterial leaf streak, we conducted tests on these genes in both the indica and japonica subpopulations, ultimately identifying superior haplotypes that suggest the potential utilization of these genes in breeding disease-resistant rice varieties. CONCLUSIONS The findings of our study broaden our comprehension of the genetic mechanisms underlying RBLS in rice and offer significant insights that can be applied towards genetic improvement and breeding of disease-resistant rice in rapidly evolving environmental conditions.
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Affiliation(s)
- Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lei Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yinghua Pan
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Xueqiang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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3
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Ectopic Expression of Executor Gene Xa23 Enhances Resistance to Both Bacterial and Fungal Diseases in Rice. Int J Mol Sci 2022; 23:ijms23126545. [PMID: 35742990 PMCID: PMC9224217 DOI: 10.3390/ijms23126545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial blight (BB) and bacterial leaf streak (BLS), caused by phytopathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are the most serious bacterial diseases of rice, while blast, caused by Magnaporthe oryzae (M. oryzae), is the most devastating fungal disease in rice. Generating broad-spectrum resistance to these diseases is one of the key approaches for the sustainable production of rice. Executor (E) genes are a unique type of plant resistance (R) genes, which can specifically trap transcription activator-like effectors (TALEs) of pathogens and trigger an intense defense reaction characterized by a hypersensitive response in the host. This strong resistance is a result of programed cell death induced by the E gene expression that is only activated upon the binding of a TALE to the effector-binding element (EBE) located in the E gene promoter during the pathogen infection. Our previous studies revealed that the E gene Xa23 has the broadest and highest resistance to BB. To investigate whether the Xa23-mediated resistance is efficient against Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of BLS, we generated a new version of Xa23, designated as Xa23p1.0, to specifically trap the conserved TALEs from multiple Xoc strains. The results showed that the Xa23p1.0 confers broad resistance against both BB and BLS in rice. Moreover, our further experiment on the Xa23p1.0 transgenic plants firstly demonstrated that the E-gene-mediated defensive reaction is also effective against M. oryzae, the causal agent of the most devastating fungal disease in rice. Our current work provides a new strategy to exploit the full potential of the E-gene-mediated disease resistance in rice.
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Diversity of transcription activator-like effectors and pathogenicity in strains of Xanthomonas oryzae pv. oryzicola from Yunnan. World J Microbiol Biotechnol 2022; 38:71. [PMID: 35258706 DOI: 10.1007/s11274-022-03230-7] [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: 03/21/2021] [Accepted: 01/07/2022] [Indexed: 10/18/2022]
Abstract
The present study aimed to evaluate transcriptional activator-like effector (TALE) genes in 86 Xanthomonas oryzae pv. oryzicola strains collected from 8 rice-growing regions in Yunnan, and to examine the relationship between TALE genotypes and virulence in 6 differential rice lines. Besides, the geographical areas, distribution of these genotypes were studied in detail. Genetic diversity was analyzed through the number and size of putative TALE genes based on TALE gene avrXa3 as a probe. We found that X. oryzae pv. oryzicola strains consist of variable number (13-27) of avrXa3-hybridizing fragments (putative TALE genes). Test strains were classified into 8 genotypes (G1-G8) with major genotypes G3 and G7 widely distributed in Yunnan. Pathogenicity of X. oryzae pv. oryzicola was evaluated by inoculating 6 differential rice lines with a single resistance gene into 9 pathotypes clusters (I-IX), the dominant Genotypes G3 and G7 consist of pathotypes I, II, and IV. Furthermore, we also detected the known TALE target genes expression in susceptible rice cultivar (cv. nipponbare) after inoculating 8 genotypes-representative X. oryzae pv. oryzicola strain. Correlation between the numbers of putative TALE genes of X. oryzae pv. oryzicola and relevant target genes in nipponbare confirmed up-regulation. Altogether, this study has given insights into the population structure of X. oryzae pv. oryzicola that may inform strategies to control BLS in rice.
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Ji Z, Guo W, Chen X, Wang C, Zhao K. Plant Executor Genes. Int J Mol Sci 2022; 23:ijms23031524. [PMID: 35163443 PMCID: PMC8835739 DOI: 10.3390/ijms23031524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/14/2022] [Accepted: 01/26/2022] [Indexed: 12/28/2022] Open
Abstract
Executor (E) genes comprise a new type of plant resistance (R) genes, identified from host-Xanthomonas interactions. The Xanthomonas-secreted transcription activation-like effectors (TALEs) usually function as major virulence factors, which activate the expression of the so-called "susceptibility" (S) genes for disease development. This activation is achieved via the binding of the TALEs to the effector-binding element (EBE) in the S gene promoter. However, host plants have evolved EBEs in the promoters of some otherwise silent R genes, whose expression directly causes a host cell death that is characterized by a hypersensitive response (HR). Such R genes are called E genes because they trap the pathogen TALEs in order to activate expression, and the resulting HR prevents pathogen growth and disease development. Currently, deploying E gene resistance is becoming a major component in disease resistance breeding, especially for rice bacterial blight resistance. Currently, the biochemical mechanisms, or the working pathways of the E proteins, are still fuzzy. There is no significant nucleotide sequence homology among E genes, although E proteins share some structural motifs that are probably associated with the signal transduction in the effector-triggered immunity. Here, we summarize the current knowledge regarding TALE-type avirulence proteins, E gene activation, the E protein structural traits, and the classification of E genes, in order to sharpen our understanding of the plant E genes.
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Affiliation(s)
- Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China;
- Correspondence: (Z.J.); (K.Z.); Tel.: +86-10-82108751 (Z.J. & K.Z.)
| | - Wei Guo
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (W.G.); (X.C.)
| | - Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (W.G.); (X.C.)
| | - Chunlian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China;
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China;
- Correspondence: (Z.J.); (K.Z.); Tel.: +86-10-82108751 (Z.J. & K.Z.)
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6
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Yang R, Li S, Li Y, Yan Y, Fang Y, Zou L, Chen G. Bactericidal Effect of Pseudomonas oryziphila sp. nov., a Novel Pseudomonas Species Against Xanthomonas oryzae Reduces Disease Severity of Bacterial Leaf Streak of Rice. Front Microbiol 2021; 12:759536. [PMID: 34803984 PMCID: PMC8600968 DOI: 10.3389/fmicb.2021.759536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas is a diverse genus of Gammaproteobacteria with increasing novel species exhibiting versatile trains including antimicrobial and insecticidal activity, as well as plant growth-promoting, which make them well suited as biocontrol agents of some pathogens. Here we isolated strain 1257 that exhibited strong antagonistic activity against two pathovars of Xanthomonas oryzae, especially X. oryzae pv. oryzicola (Xoc) responsible for the bacterial leaf streak (BLS) in rice. The phylogenetic, genomic, physiological, and biochemical characteristics support that strain 1257 is a representative of a novel Pseudomonas species that is most closely related to the entomopathogenic bacterium Pseudomonas entomophila. We propose to name it Pseudomonas oryziphila sp. nov. Comparative genomics analyses showed that P. oryziphila 1257 possesses most of the central metabolic genes of two closely related strains P. entomophila L48 and Pseudomonas mosselii CFML 90-83, as well as a set of genes encoding the type IV pilus system, suggesting its versatile metabolism and motility properties. Some features, such as insecticidal toxins, phosphate solubilization, indole-3-acetic acid, and phenylacetic acid degradation, were disclosed. Genome-wide random mutagenesis revealed that the non-ribosomal peptide catalyzed by LgrD may be a major active compound of P. oryziphila 1257 against Xoc RS105, as well as the critical role of the carbamoyl phosphate and the pentose phosphate pathway that control the biosynthesis of this target compound. Our findings demonstrate that 1257 could effectively inhibit the growth and migration of Xoc in rice tissue to prevent the BLS disease. To our knowledge, this is the first report of a novel Pseudomonas species that displays a strong antibacterial activity against Xoc. The results suggest that the P. oryziphila strain could be a promising biological control agent for BLS.
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Affiliation(s)
- Ruihuan Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shengzhang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yilang Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yichao Yan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Fang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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7
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Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen Xanthomonas citri pv. glycines. Microorganisms 2021; 9:microorganisms9102065. [PMID: 34683386 PMCID: PMC8538872 DOI: 10.3390/microorganisms9102065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas citri pv. glycines is a major pathogen of soybean in Korea. Here, we analyzed pathogenicity genes based on a comparative genome analysis of five Korean strains and one strain from the United States, 8ra. Whereas all six strains had nearly identical profiles of carbohydrate-active enzymes, they varied in diversity and number of candidate type III secretion system effector (T3SE) genes. The five Korean strains were similar in their effectors, but differed from the 8ra strain. Across the six strains, transcription activator-like effectors (TALEs) showed diverse repeat sizes and at least six forms of the repeat variable di-residue (RVD) sequences, with differences not correlated with the origin of the strains. However, a phylogenetic tree based on the alignment of RVD sequences showed two distinct clusters with 17.5 repeats, suggesting that two distinct 17.5 RVD clusters have evolved, potentially to adapt Xcg to growth on distinct soybean cultivars. The predicted effector binding elements of the TALEs fell into six groups and were strongly overlapping in sequence, suggesting evolving target specificity of the binding domains in soybean cultivars. Our findings reveal the variability and adaptability of T3SEs in the Xcg strains and enhance our understanding of Xcg pathogenicity in soybean.
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8
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Xu X, Xu Z, Li Z, Zakria M, Zou L, Chen G. Increasing resistance to bacterial leaf streak in rice by editing the promoter of susceptibility gene OsSULRT3;6. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1101-1103. [PMID: 33942463 PMCID: PMC8196642 DOI: 10.1111/pbi.13602] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/09/2021] [Indexed: 05/09/2023]
Affiliation(s)
- Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina
| | - Ziyang Li
- School of Agriculture and Biology/State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina
| | - Muhammad Zakria
- National Agricultural Research CenterCrop Diseases Research InstituteIslamabadPakistan
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghaiChina
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9
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Sattayachiti W, Wanchana S, Arikit S, Nubankoh P, Patarapuwadol S, Vanavichit A, Darwell CT, Toojinda T. Genome-Wide Association Analysis Identifies Resistance Loci for Bacterial Leaf Streak Resistance in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1673. [PMID: 33260392 PMCID: PMC7761455 DOI: 10.3390/plants9121673] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/14/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022]
Abstract
Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating diseases in rice production areas, especially in humid tropical and subtropical zones throughout Asia and worldwide. A genome-wide association study (GWAS) analysis conducted on a collection of 236 diverse rice accessions, mainly indica varieties, identified 12 quantitative trait loci (QTLs) on chromosomes 1, 2, 3, 4, 5, 8, 9 and 11, conferring resistance to five representative isolates of Thai Xoc. Of these, five QTLs conferred resistance to more than one Xoc isolates. Two QTLs, qBLS5.1 and qBLS2.3, were considered promising QTLs for broad-spectrum resistance to BLS. The xa5 gene was proposed as a potential candidate gene for qBLS5.1 and three genes, encoding pectinesterase inhibitor (OsPEI), eukaryotic zinc-binding protein (OsRAR1), and NDP epimerase function, were proposed as candidate genes for qBLS2.3. Results from this study provide an insight into the potential QTLs and candidate genes for BLS resistance in rice. The recessive xa5 gene is suggested as a potential candidate for strong influence on broad-spectrum resistance and as a focal target in rice breeding programs for BLS resistance.
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Affiliation(s)
- Wannapa Sattayachiti
- Plant Breeding Program, Faculty of Agriculture at Kamphaeng Saen, Kesetsart University, Nakhon Pathom 73140, Thailand;
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand; (S.W.); (P.N.); (C.T.D.)
| | - Siwaret Arikit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; (S.A.); (A.V.)
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
- Center of Excellence on Rice Precision Breeding for Food Security, Quality, and Nutrition, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Phakchana Nubankoh
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand; (S.W.); (P.N.); (C.T.D.)
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
| | - Apichart Vanavichit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; (S.A.); (A.V.)
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
- Center of Excellence on Rice Precision Breeding for Food Security, Quality, and Nutrition, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Clive T. Darwell
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand; (S.W.); (P.N.); (C.T.D.)
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand; (S.W.); (P.N.); (C.T.D.)
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10
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Haq F, Xie S, Huang K, Shah SMA, Ma W, Cai L, Xu X, Xu Z, Wang S, Zou L, Zhu B, Chen G. Identification of a virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V 2-18. BMC Microbiol 2020; 20:91. [PMID: 32293266 PMCID: PMC7160923 DOI: 10.1186/s12866-020-01783-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/05/2020] [Indexed: 01/22/2023] Open
Abstract
Background Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8–12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions. Results In this study, we identified six tal genes in Xss-V2–18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2–18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2–18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2–18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2–18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2–18. Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2–18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.
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Affiliation(s)
- Fazal Haq
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiwang Xie
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Kunxuan Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lulu Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sai Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Lifang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China. .,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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11
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Khojasteh M, Shah SMA, Haq F, Xu X, Taghavi SM, Osdaghi E, Chen G. Transcription Activator-Like Effectors Diversity in Iranian Strains of Xanthomonas translucens. PHYTOPATHOLOGY 2020; 110:758-767. [PMID: 31868568 DOI: 10.1094/phyto-11-19-0428-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak caused by different pathovars of Xanthomonas translucens is the most important seedborne bacterial disease of small grain cereals. However, variations in the virulence-associated genomic areas of the pathogen remain uninvestigated. In this study, the diversity of transcription activator-like effectors (TALE) was investigated using the Southern blotting of BamHI-digested genomic DNAs in the Iranian strains of X. translucens. All 65 X. translucens strains were assigned into 13 genotypes, where 57 X. translucens pv. undulosa strains were placed in genotypes 1 to 8, and seven X. translucens pv. translucens strains were placed in genotypes 9 to 12. Interestingly, we did not find any TALE genes in the strain XtKm7 (genotype 13), which showed to be pathogenic only on barley. Virulence and aggressiveness of these strains in greenhouse conditions were in agreement with the TALE-based clustering of the strains in the pathovar level, though variations were observed in the aggressiveness of X. translucens pv. undulosa strains. In general, strains containing higher numbers of putative TALE genes were more virulent on wheat and barley than strains containing fewer. This is the first TALE-based genetic diversity analysis on X. translucens strains and provides novel insights into the virulence repertories and genomic characteristics of the pathogen. Further investigations using TALE mutagenesis and complementation analysis are warranted to precisely elucidate the role of each detected X. translucens TALE in bacterial virulence and aggressiveness either on wheat or barley.
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Affiliation(s)
- Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
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12
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Chen X, Wei S, Yan Q, Huang F, Ma Z, Li R, Cen Z, Yan W, Li K. Virulence and DNA fingerprinting analysis of Xanthomonas oryzae pv. oryzae identify a new pathotype in Guangxi, South China. J Basic Microbiol 2019; 59:1082-1091. [PMID: 31544274 DOI: 10.1002/jobm.201900354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/02/2019] [Accepted: 08/25/2019] [Indexed: 12/15/2022]
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases affecting rice worldwide. However, little is known about the population structure of this organism in Guangxi Zhuang Autonomous Region, South China. Here, pathotypic and DNA fingerprint analyses were conducted to characterize the isolates of Xoo collected from rice leaves in five districts of the region from 2013 to 2016. Their pathogenicity was tested by leaf clipping, and the DNA fingerprints were analyzed by repetitive sequence-based polymerase chain reaction and endogenous insertion sequence element-based polymerase chain reaction assays using the repetitive extragenic palindromic sequence and enterobacterial repetitive intergenic consensus primers, respectively. Pathogenicity assays of 70 representative isolates were conducted using a series of near-isogenic lines and two new pathotypes were identified. All the pathotypes were found to be incompatible with xa5 and Xa7. One pathotype was virulent to Xa14, Xa21, and Xa23, whereas another virulent to Xa21 and Xa23, but incompatible with Xa14. A dendrogram generated for the data sets obtained from DNA fingerprinting suggested the prevalence of high genetic diversity of Xoo throughout Guangxi, and no association between the molecular haplotypes and pathotypes was identified.
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Affiliation(s)
- Xiaolin Chen
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Shanfu Wei
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Qun Yan
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Fengkuan Huang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Zengfeng Ma
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ruifang Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Zhenlu Cen
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Weihong Yan
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Kunhua Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
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13
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Niu XN, Wei ZQ, Zou HF, Xie GG, Wu F, Li KJ, Jiang W, Tang JL, He YQ. Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola. BMC Microbiol 2015; 15:233. [PMID: 26498126 PMCID: PMC4619425 DOI: 10.1186/s12866-015-0562-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. METHODS The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. RESULTS The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. CONCLUSIONS pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.
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Affiliation(s)
- Xiang-Na Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Zhi-Qiong Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Hai-Fan Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Gui-Gang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Feng Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Kang-Jia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
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14
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Booher NJ, Carpenter SCD, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microb Genom 2015; 1. [PMID: 27148456 PMCID: PMC4853030 DOI: 10.1099/mgen.0.000032] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33–35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.
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Affiliation(s)
- Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert P Sebra
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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15
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Booher NJ, Carpenter SCD, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microb Genom 2015. [PMID: 27148456 DOI: 10.1099/mgen.000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33-35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.
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Affiliation(s)
- Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert P Sebra
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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