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Zafar H, Saier MH. An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes. Microb Physiol 2024; 34:133-141. [PMID: 38636461 DOI: 10.1159/000538779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community. SUMMARY This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut. KEY MESSAGES Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Milton H Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, La Jolla, California, USA
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Goettelmann F, Koebnik R, Roman-Reyna V, Studer B, Kölliker R. High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences. BMC Genomics 2023; 24:741. [PMID: 38053038 DOI: 10.1186/s12864-023-09855-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Xanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity. RESULTS In this study, we produced high-quality, complete genome sequences of four strains of Xtg, complementing the recently obtained complete genome sequence of the Xtg pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related. A high number of transposases were exclusively found in Xtg and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 plant cell wall degradative enzymes. CONCLUSION These results suggest a high adaptability of Xtg, conferred by the abundance of mobile genetic elements, which could play a crucial role in pathogen adaptation. The large amount of such elements in Xtg compared to other pathovars of the species could, at least partially, explain its high virulence and broad host range. Conserved features that were specific to Xtg were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of Xtg.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
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Osdaghi E, Taghavi SM, Aliabadi AA, Khojasteh M, Abachi H, Moallem M, Mohammadikhah S, Shah SMA, Chen G, Liu Z. Detection and Diagnosis of Bacterial Leaf Streak on Small Grain Cereals: From Laboratory to Field. PHYTOPATHOLOGY 2023; 113:2024-2036. [PMID: 37069135 DOI: 10.1094/phyto-09-22-0343-sa] [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: 06/19/2023]
Abstract
Bacterial leaf streak of small-grain cereals is an economically important disease of wheat and barley crops. The disease occurs in many countries across the globe, with particular importance in regions characterized by high precipitation or areas in which sprinkler irrigation is used. Three genetically distinct lineages of the Gram-negative bacterium Xanthomonas translucens (X. translucens pv. undulosa, X. translucens pv. translucens, and X. translucens pv. cerealis) are responsible for most of the bacterial leaf streak infections on wheat and barley crops. Considering the seedborne nature of the pathogens, they are included in the A2 (high-risk) list of quarantine organisms for some European countries; hence, they are under strict quarantine control and zero tolerance. Due to the taxonomic complexities within X. translucens, the exact geographic distribution of each pathovar has not yet been determined. In this mini review, we provide an updated overview of the detection and diagnosis of the bacterial leaf streak pathogens. First, a short history of the leaf streak pathogens is provided, followed by the symptomology and host range of the causal agents. Then, the utility of conventional methods and high-throughput molecular approaches in the precise detection and identification of the pathogens is explained. Finally, we highlight the role of quarantine inspections and early detection of the pathogen in combating the risk of bacterial leaf streak in the 21st century's small-grains cereals' industry.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Alizadeh Aliabadi
- Plant Pathology Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Moein Khojasteh
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Hamid Abachi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Mahsa Moallem
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Sedighe Mohammadikhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
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Shah SMA, Khojasteh M, Wang Q, Haq F, Xu X, Li Y, Zou L, Osdaghi E, Chen G. Comparative Transcriptomic Analysis of Wheat Cultivars in Response to Xanthomonas translucens pv. cerealis and Its T2SS, T3SS, and TALEs Deficient Strains. PHYTOPATHOLOGY 2023; 113:2073-2082. [PMID: 37414408 DOI: 10.1094/phyto-02-23-0049-sa] [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: 07/08/2023]
Abstract
Xanthomonas translucens pv. cerealis causes bacterial leaf streak disease on small grain cereals. Type II and III secretion systems (T2SS and T3SS) play a pivotal role in the pathogenicity of the bacterium, while no data are available on the transcriptomic profile of wheat cultivars infected with either wild type (WT) or mutants of the pathogen. In this study, WT, TAL-effector mutants, and T2SS/T3SS mutants of X. translucens pv. cerealis strain NXtc01 were evaluated for their effect on the transcriptomic profile of two wheat cultivars, 'Chinese Spring' and 'Yangmai-158', using Illumina RNA-sequencing technology. RNA-Seq data showed that the number of differentially expressed genes (DEGs) was higher in Yangmai-158 than in Chinese Spring, suggesting higher susceptibility of Yangmai-158 to the pathogen. In T2SS, most suppressed DEGs were related to transferase, synthase, oxidase, WRKY, and bHLH transcription factors. The gspD mutants showed significantly decreased disease development in wheat, suggesting an active contribution of T2SS in virulence. Moreover, the gspD mutant restored full virulence and its multiplication in planta by addition of gspD in trans. In the T3SS-deficient strain, downregulated DEGs were associated with cytochrome, peroxidases, kinases, phosphatases, WRKY, and ethylene-responsive transcription factors. In contrast, upregulated DEGs were trypsin inhibitors, cell number regulators, and calcium transporter. Transcriptomic analyses coupled with quantitative real-time-PCR indicated that some genes are upregulated in Δtal1/Δtal2 compared with the tal-free strain, but no direct interaction was observed. These results provide novel insight into wheat transcriptomes in response to X. translucens infection and pave the way for understanding host-pathogen interactions.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, 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
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Li
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture and Biology/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai Jiao Tong University, Shanghai 200240, China
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Alvandi H, Taghavi SM, Khojasteh M, Rahimi T, Dutrieux C, Taghouti G, Jacques MA, Portier P, Osdaghi E. Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa. PLANT DISEASE 2023; 107:2279-2287. [PMID: 36611242 DOI: 10.1094/pdis-11-22-2677-sr] [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
Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. Thus far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa because the expected 229-bp DNA fragment was not amplified in the closely related pathovars or in other xanthomonads, wheat-pathogenic bacteria, and other plant-pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/μl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 CFU/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 CFU/g while a culture-plate method was able to detect the pathogen at a concentration of 50 × 105 CFU/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.
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Affiliation(s)
- Hosna Alvandi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Touraj Rahimi
- Department of Plant Production and Genetics, Agriculture Faculty, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Cecile Dutrieux
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Geraldine Taghouti
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Jung H, Kim HS, Han G, Park J, Seo YS. Comparative Analyses of Four Complete Genomes in Pseudomonas amygdali Revealed Differential Adaptation to Hostile Environments and Secretion Systems. THE PLANT PATHOLOGY JOURNAL 2022; 38:167-174. [PMID: 35385921 PMCID: PMC9343901 DOI: 10.5423/ppj.nt.11.2021.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/03/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.
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Affiliation(s)
- Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Hong-Seop Kim
- Korea Seed & Variety Service, Pyeongchang 25343, Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
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7
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Goettelmann F, Roman-Reyna V, Cunnac S, Jacobs JM, Bragard C, Studer B, Koebnik R, Kölliker R. Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades. Front Microbiol 2022; 12:817815. [PMID: 35310401 PMCID: PMC8924669 DOI: 10.3389/fmicb.2021.817815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Claude Bragard
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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Te Molder D, Poncheewin W, Schaap PJ, Koehorst JJ. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. BMC Genomics 2021; 22:848. [PMID: 34814827 PMCID: PMC8612006 DOI: 10.1186/s12864-021-08093-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.
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Affiliation(s)
- Dennie Te Molder
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Wasin Poncheewin
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- UNLOCK, Wageningen University, Wageningen, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands.
- UNLOCK, Wageningen University, Wageningen, the Netherlands.
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Ledman KE, Curland RD, Ishimaru CA, Dill-Macky R. Xanthomonas translucens pv. undulosa Identified on Common Weedy Grasses in Naturally Infected Wheat Fields in Minnesota. PHYTOPATHOLOGY 2021; 111:1114-1121. [PMID: 33225830 DOI: 10.1094/phyto-08-20-0337-r] [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: 06/11/2023]
Abstract
Bacterial leaf streak (BLS) of wheat, caused by Xanthomonas translucens pv. undulosa, has been a notable disease in Minnesota wheat fields over the past decade. Potential sources of the pathogen include infested seed and crop debris. Perennial weeds are also considered a possible inoculum source, but no surveys have been conducted to evaluate which X. translucens pathovars are present on weedy grasses that are common in Minnesota wheat fields. Multilocus sequence analysis (MLSA) of four housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to identify 77 strains isolated from six weedy grass species, wheat, and barley in and around naturally infected wheat fields in Minnesota. The MLSA phylogeny identified all strains originating from weedy grass species, except smooth brome, as X. translucens pv. undulosa, whereas strains isolated from smooth brome were determined to be X. translucens pv. cerealis. In planta character states corroborated these identifications on a subset of 41 strains, as all strains from weedy grasses caused water-soaking on wheat and barley in greenhouse assays. Multilocus sequence typing was used to evaluate genetic diversity and revealed that sequence types of X. translucens pv. undulosa originating from weedy grass hosts are similar to those found on wheat. This study identifies both annual and perennial poaceous weeds common in Minnesota that harbor X. translucens pv. undulosa and expands our understanding of the diversity of the pathogen population.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Wu G, Zhang Y, Wang B, Li K, Lou Y, Zhao Y, Liu F. Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. RICE (NEW YORK, N.Y.) 2021; 14:57. [PMID: 34176023 PMCID: PMC8236019 DOI: 10.1186/s12284-021-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. RESULTS Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. CONCLUSION Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.
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Affiliation(s)
- Guichun Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yuqiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, P. R. China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Kaihuai Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Yuanlai Lou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
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11
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Tambong JT, Xu R, Gerdis S, Daniels GC, Chabot D, Hubbard K, Harding MW. Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. Front Microbiol 2021; 12:666689. [PMID: 34093484 PMCID: PMC8170138 DOI: 10.3389/fmicb.2021.666689] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3CT = DOAB 1063T = CECT 30248T = LMG 32139T), Pseudomonas triticumensis sp. nov. (type strain 32L3AT = DOAB 1067T = CECT 30249T = LMG 32140T) and Pseudomonas foliumensis sp. nov. (type strain 10L4BT = DOAB 1069T = CECT 30250T = LMG 32142T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Greg C Daniels
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael W Harding
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
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12
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Fernandes C, Martins L, Teixeira M, Blom J, Pothier JF, Fonseca NA, Tavares F. Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree. Microorganisms 2021; 9:microorganisms9030624. [PMID: 33803052 PMCID: PMC8003016 DOI: 10.3390/microorganisms9030624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/20/2022] Open
Abstract
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424T, and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.
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Affiliation(s)
- Camila Fernandes
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, INIAV, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Correspondence: (C.F.); (F.T.)
| | - Leonor Martins
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Miguel Teixeira
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Ludwigstraße 23, 35390 Giessen, Germany;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland;
| | - Nuno A. Fonseca
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
| | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (C.F.); (F.T.)
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13
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Li T, Mann R, Sawbridge T, Kaur J, Auer D, Spangenberg G. Novel Xanthomonas Species From the Perennial Ryegrass Seed Microbiome - Assessing the Bioprotection Activity of Non-pathogenic Relatives of Pathogens. Front Microbiol 2020; 11:1991. [PMID: 32983016 PMCID: PMC7479056 DOI: 10.3389/fmicb.2020.01991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
The productivity of the Australian dairy industry is underpinned by pasture grasses, and importantly perennial ryegrass. The performance of these pasture grasses is supported by the fungal endophyte Epichloë spp. that has bioprotection activities, however, the broader microbiome is not well characterized. In this study, we characterized a novel bioprotectant Xanthomonas species isolated from perennial ryegrass (Lolium perenne L. cv. Alto). In vitro and in planta bioassays against key fungal pathogens of grasses (Sclerotium rolfsii, Drechslera brizae and Microdochium nivale) indicated strong bioprotection activities. A complete circular chromosome of ∼5.2 Mb was generated for three strains of the novel Xanthomonas sp. Based on the 16S ribosomal RNA gene, the strains were closely related to the plant pathogen Xanthomonas translucens, however, comparative genomics of 22 closely related xanthomonad strains indicated that these strains were a novel species. The comparative genomics analysis also identified two unique gene clusters associated with the production of bioprotectant secondary metabolites including one associated with a novel nonribosomal peptide synthetase and another with a siderophore. The analysis also identified genes associated with an endophytic lifestyle (e.g., Type VI secretion system), while no genes associated with pathogenicity were identified (e.g., Type III secretion system and effectors). Overall, these results indicate that these strains represent a novel, bioactive, non-pathogenic species of the genus Xanthomonas. Strain GW was the designated type strain of this novel Xanthomonas sp.
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Affiliation(s)
- Tongda Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Ross Mann
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Timothy Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Jatinder Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Desmond Auer
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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14
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Sapkota S, Mergoum M, Liu Z. The translucens group of Xanthomonas translucens: Complicated and important pathogens causing bacterial leaf streak on cereals. MOLECULAR PLANT PATHOLOGY 2020; 21:291-302. [PMID: 31967397 PMCID: PMC7036361 DOI: 10.1111/mpp.12909] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 12/21/2019] [Indexed: 05/31/2023]
Abstract
UNLABELLED Xanthomonas translucens is a group of gram-negative bacteria that can cause important diseases in cereal crops and forage grasses. Different pathovars have been defined according to their host ranges, and molecular and biochemical characteristics. Pathovars have been placed into two major groups: translucens and graminis. The translucens group contains the pathovars causing bacterial leaf streak (BLS) on cereal crops such as wheat, barley, triticale, rye, and oat. In recent years, BLS has re-emerged as a major problem for many wheat- and barley-producing areas worldwide. The biology of the pathogens and the host-pathogen interactions in cereal BLS diseases were poorly understood. However, recent genome sequence data have provided an insight into the bacterial phylogeny and identification and pathogenicity/virulence. Furthermore, identification of sources of resistance to BLS and mapping of the resistance genes have been initiated. TAXONOMY Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. translucens; translucens group pathovars: undulosa, translucens, cerealis, hordei, and secalis; graminis group pathovars: arrhenatheri, graminis, poae, phlei; newly established pathovar: pistaciae. HOST RANGE X. translucens mainly infects plant species in the Poaceae with the translucens group on cereal crop species and the graminis group on forage grass species. However, some strains have been isolated from, and are able to infect, ornamental asparagus and pistachio trees. Most pathovars have a narrow host range, while a few can infect a broad range of hosts. GENOME The complete genome sequence is available for two X. translucens pv. undulosa strains and one pv. translucens strain. A draft genome sequence is also available for at least one strain from each pathovar. The X. translucens pv. undulosa strain Xt4699 was the first to have its complete genome sequenced, which consists of 4,561,137 bp with total GC content approximately at 68% and 3,528 predicted genes. VIRULENCE MECHANISMS Like most xanthomonads, X. translucens utilizes a type III secretion system (T3SS) to deliver a suite of T3SS effectors (T3Es) inside plant cells. Transcription activator-like effectors, a special group of T3Es, have been identified in most of the X. translucens genomes, some of which have been implicated in virulence. Genetic factors determining host range virulence have also been identified.
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Affiliation(s)
- Suraj Sapkota
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
- Department of Crop and Soil SciencesUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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15
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Curland RD, Gao L, Hirsch CD, Ishimaru CA. Localized Genetic and Phenotypic Diversity of Xanthomonas translucens Associated With Bacterial Leaf Streak on Wheat and Barley in Minnesota. PHYTOPATHOLOGY 2020; 110:257-266. [PMID: 31448998 DOI: 10.1094/phyto-04-19-0134-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley has been a disease of increasing concern in the Upper Midwest over the past decade. In this study, intra- and interfield genetic and pathogenic diversity of bacteria causing BLS in Minnesota was evaluated. In 2015, 89 strains were isolated from 100 leaf samples collected from two wheat and two barley fields naturally infected with BLS. Virulence assays and multilocus sequence alignments of four housekeeping genes supported pathovar identifications. All wheat strains were pathogenic on wheat and barley and belonged to the same lineage as the Xanthomonas translucens pv. undulosa-type strain. All barley strains were pathogenic on barley but not on wheat. Three lineages of barley strains were detected. The frequency and number of sequence types of each pathovar varied within and between fields. A significant population variance was detected between populations of X. translucens pv. undulosa collected from different wheat fields. Population stratification of X. translucens pv. translucens was not detected. Significant differences in virulence were detected among three dominant sequence types of X. translucens pv. undulosa but not those of X. translucens pv. translucens. Field trials with wheat and barley plants inoculated with strains of known sequence type and virulence did not detect significant race structures within either pathovar. Knowledge of virulence, sequence types, and population structures of X. translucens on wheat and barley can support studies on plant-bacterial interactions and breeding for BLS disease resistance.
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Affiliation(s)
- Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Liangliang Gao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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16
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Knorst V, Byrne S, Yates S, Asp T, Widmer F, Studer B, Kölliker R. Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:947-958. [PMID: 30506318 PMCID: PMC6449324 DOI: 10.1007/s00122-018-3250-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/23/2018] [Indexed: 05/27/2023]
Abstract
SNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F1 progeny of a segregating population. Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
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Affiliation(s)
- Verena Knorst
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Stephen Byrne
- Crops Science Department, Teagasc, Oak Park, Carlow, R93 XE12, Ireland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Torben Asp
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Franco Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland.
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland.
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17
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Kale SD. PenSeq: coverage you can count on. THE NEW PHYTOLOGIST 2019; 221:1177-1179. [PMID: 30644579 DOI: 10.1111/nph.15608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Shiv D Kale
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24060, USA
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18
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Chen NWG, Serres-Giardi L, Ruh M, Briand M, Bonneau S, Darrasse A, Barbe V, Gagnevin L, Koebnik R, Jacques MA. Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean. BMC Genomics 2018; 19:606. [PMID: 30103675 PMCID: PMC6090828 DOI: 10.1186/s12864-018-4975-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. RESULTS To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. CONCLUSIONS Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.
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Affiliation(s)
- Nicolas W. G. Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Laurana Serres-Giardi
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion France
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
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19
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Curland RD, Gao L, Bull CT, Vinatzer BA, Dill-Macky R, Van Eck L, Ishimaru CA. Genetic Diversity and Virulence of Wheat and Barley Strains of Xanthomonas translucens from the Upper Midwestern United States. PHYTOPATHOLOGY 2018; 108:443-453. [PMID: 29165007 DOI: 10.1094/phyto-08-17-0271-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley, caused by Xanthomonas translucens pv. undulosa and X. translucens pv. translucens, has been of growing concern in small grains production in the Upper Midwestern United States. To optimize disease resistance breeding, a greater awareness is needed of the pathovars and genetic diversity within the pathogens causing BLS in the region. Multilocus sequencing typing (MLST) and analysis (MLSA) of four common housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to evaluate the genetic diversity of 82 strains of X. translucens isolated between 2006 and 2013 from wheat, barley, rye, and intermediate wheatgrass. In addition, in planta disease assays were conducted on 75 strains to measure relative virulence in wheat and barley. All strains were determined by MLSA to be related to X. translucens pv. undulosa and X. translucens pv. translucens. Clustering of strains based on Bayesian, network, and minimum spanning trees correlated with relative virulence levels in inoculated wheat and barley. Thus, phylogeny based on rpoD, dnaK, fyuA, and gyrB correlated with host of isolation and was an effective means for predicting virulence of strains belonging to X. translucens pv. translucens and X. translucens pv. undulosa.
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Affiliation(s)
- Rebecca D Curland
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Liangliang Gao
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carolee T Bull
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Boris A Vinatzer
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Ruth Dill-Macky
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Leon Van Eck
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carol A Ishimaru
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
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Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. J Biotechnol 2017; 253:55-61. [DOI: 10.1016/j.jbiotec.2017.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 11/18/2022]
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Pesce C, Jacobs JM, Berthelot E, Perret M, Vancheva T, Bragard C, Koebnik R. Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF. Front Microbiol 2017; 8:1177. [PMID: 28694803 PMCID: PMC5483457 DOI: 10.3389/fmicb.2017.01177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023] Open
Abstract
Xanthomonas translucens is the causal agent of bacterial leaf streak, the most common bacterial disease of wheat and barley. To cause disease, most xanthomonads depend on a highly conserved type III secretion system, which translocates type III effectors into host plant cells. Mutagenesis of the conserved type III secretion gene hrcT confirmed that the X. translucens type III secretion system is required to cause disease on the host plant barley and to trigger a non-host hypersensitive response (HR) in pepper leaves. Type III effectors are delivered to the host cell by a surface appendage, the Hrp pilus, and a translocon protein complex that inserts into the plant cell plasma membrane. Homologs of the Xanthomonas HrpF protein, including PopF from Ralstonia solanacearum and NolX from rhizobia, are thought to act as a translocon protein. Comparative genomics revealed that X. translucens strains harbor a noncanonical hrp gene cluster, which rather shares features with type III secretion systems from Ralstonia solanacearum, Paraburkholderia andropogonis, Collimonas fungivorans, and Uliginosibacterium gangwonense than other Xanthomonas spp. Surprisingly, none of these bacteria, except R. solanacearum, encode a homolog of the HrpF translocon. Here, we aimed at identifying a candidate translocon from X. translucens. Notably, genomes from strains that lacked hrpF/popF/nolX instead encode another gene, called hpaT, adjacent to and co-regulated with the type III secretion system gene cluster. An insertional mutant in the X. translucens hpaT gene, which is the first gene of a two-gene operon, hpaT-hpaH, was non-pathogenic on barley and did not cause the HR or programmed cell death in non-host pepper similar to the hrcT mutant. The hpaT mutant phenotypes were partially complemented by either hpaT or the downstream gene, hpaH, which has been described as a facilitator of translocation in Xanthomonas oryzae. Interestingly, the hpaT mutant was also complemented by the hrpF gene from Xanthomonas euvesicatoria. These findings reveal that both HpaT and HpaH contribute to the injection of type III effectors into plant cells.
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Affiliation(s)
- Céline Pesce
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Jonathan M. Jacobs
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Edwige Berthelot
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Marion Perret
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Taca Vancheva
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Claude Bragard
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Ralf Koebnik
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
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