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Peduzzi C, Sagia A, Burokienė D, Nagy IK, Fischer-Le Saux M, Portier P, Dereeper A, Cunnac S, Roman-Reyna V, Jacobs JM, Bragard C, Koebnik R. Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas. PHYTOPATHOLOGY 2023; 113:1185-1191. [PMID: 36611232 DOI: 10.1094/phyto-10-22-0373-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
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Affiliation(s)
- Chloé Peduzzi
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Angeliki Sagia
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Daiva Burokienė
- Nature Research Centre, Institute of Botany, Laboratory of Plant Pathology, Vilnius, Lithuania
| | | | | | - Perrine Portier
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Alexis Dereeper
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Claude Bragard
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
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Sha G, Sun P, Kong X, Han X, Sun Q, Fouillen L, Zhao J, Li Y, Yang L, Wang Y, Gong Q, Zhou Y, Zhou W, Jain R, Gao J, Huang R, Chen X, Zheng L, Zhang W, Qin Z, Zhou Q, Zeng Q, Xie K, Xu J, Chiu TY, Guo L, Mortimer JC, Boutté Y, Li Q, Kang Z, Ronald PC, Li G. Genome editing of a rice CDP-DAG synthase confers multipathogen resistance. Nature 2023; 618:1017-1023. [PMID: 37316672 DOI: 10.1038/s41586-023-06205-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
The discovery and application of genome editing introduced a new era of plant breeding by giving researchers efficient tools for the precise engineering of crop genomes1. Here we demonstrate the power of genome editing for engineering broad-spectrum disease resistance in rice (Oryza sativa). We first isolated a lesion mimic mutant (LMM) from a mutagenized rice population. We then demonstrated that a 29-base-pair deletion in a gene we named RESISTANCE TO BLAST1 (RBL1) caused broad-spectrum disease resistance and showed that this mutation caused an approximately 20-fold reduction in yield. RBL1 encodes a cytidine diphosphate diacylglycerol synthase that is required for phospholipid biosynthesis2. Mutation of RBL1 results in reduced levels of phosphatidylinositol and its derivative phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). In rice, PtdIns(4,5)P2 is enriched in cellular structures that are specifically associated with effector secretion and fungal infection, suggesting that it has a role as a disease-susceptibility factor3. By using targeted genome editing, we obtained an allele of RBL1, named RBL1Δ12, which confers broad-spectrum disease resistance but does not decrease yield in a model rice variety, as assessed in small-scale field trials. Our study has demonstrated the benefits of editing an LMM gene, a strategy relevant to diverse LMM genes and crops.
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Affiliation(s)
- Gan Sha
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Peng Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Kong
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Han
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Qiping Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Laetitia Fouillen
- Laboratoire de Biogenèse Membranaire, Université de Bordeaux, CNRS, Villenave-d'Ornon, France
| | - Juan Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Yun Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Lei Yang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Yin Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Qiuwen Gong
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Yaru Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Wenqing Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA, USA
- Feedstocks Division, The Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Xiaoyang Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
- College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Lu Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Wanying Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Ziting Qin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China
| | - Qi Zhou
- BGI-Shenzhen, Shenzhen, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiandi Xu
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan, China
| | | | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jenny C Mortimer
- Feedstocks Division, The Joint BioEnergy Institute, Emeryville, CA, USA
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire, Université de Bordeaux, CNRS, Villenave-d'Ornon, France
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA, USA.
- Feedstocks Division, The Joint BioEnergy Institute, Emeryville, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China.
- The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, China.
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA, USA.
- Feedstocks Division, The Joint BioEnergy Institute, Emeryville, CA, USA.
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