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van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, Chavarro-Carrero E, Meijer HJG, Feurtey A, Maryani N, Ordóñez N, Schneiders H, Nijbroek K, Wittenberg AHJ, Hofstede R, García-Bastidas F, Sørensen A, Swennen R, Drenth A, Stukenbrock EH, Kema GHJ, Seidl MF. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. New Phytol 2024; 242:610-625. [PMID: 38402521 DOI: 10.1111/nph.19604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.
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Affiliation(s)
- Anouk C van Westerhoven
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Carolina Aguilera-Galvez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Giuliana Nakasato-Tagami
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Einar Martinez de la Parte
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Edgar Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department Biointeractions and Plant Health, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alice Feurtey
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
- Plant Pathology, Eidgenössische Technische Hochschule Zürich, Rämistrasse 101, 8092, Zürich, Switzerland
| | - Nani Maryani
- Biology Education, Universitas Sultan Ageng Tirtayasa, Jalan Raya Palka No.Km 3, 42163, Banten, Indonesia
| | - Nadia Ordóñez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harrie Schneiders
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Rene Hofstede
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Anker Sørensen
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Ronny Swennen
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Catholic University of Leuven, Oude Markt 13, 3000, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15 Naguru E Rd, Kampala, PO Box 7878, Uganda
| | - Andre Drenth
- The University of Queensland, St Lucia, 4072, Brisbane, Queensland, Australia
| | - Eva H Stukenbrock
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michael F Seidl
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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García-Bastidas FA, Van der Veen AJT, Nakasato-Tagami G, Meijer HJG, Arango-Isaza RE, Kema GHJ. An Improved Phenotyping Protocol for Panama Disease in Banana. Front Plant Sci 2019; 10:1006. [PMID: 31447871 PMCID: PMC6691145 DOI: 10.3389/fpls.2019.01006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/18/2019] [Indexed: 05/06/2023]
Abstract
Fusarium oxysporum (Fo) belongs to a group of soil-borne hyphomycetes that are taxonomically collated in the Fusarium oxysporum Species Complex (FOSC). Hitherto, those infecting bananas were placed in the forma specialis cubense (Foc). Recently, however, these genetically different Foc lineages were recognized as new Fusarium spp. placed in the Fusarium of Banana Complex (FOBC). A member of this complex F. odoratissimum II-5 that uniquely comprises the so-called Tropical Race 4 (TR4), is a major problem sweeping through production zones of Cavendish banana in several regions of the world. Because of this, there is an urgent need for a phenotyping method that allows the screening for resistance to TR4 of large numbers of banana genotypes. Most Fusarium species produce three types of spores: macroconidia, microconidia and the persistent chlamydospores that can contaminate soils for many years. Inoculum production has been an important bottleneck for efficient phenotyping due to the low or variable number of conidia and the elaborate laboratory procedures requiring specific infrastructure. Here, we report a rapid, simple and high-yielding spore production method for nine F. oxysporum formae speciales as well as the biocontrol species Fo47 and Fo618-12. For Fusarium spp. causing Fusarium wilt or Panama disease of banana, we used the protocol for four species comprising the recognized physiological races, including Tropical Race 4 (TR4). We subsequently tested the produced inoculum in comparative inoculation trials on banana plants to evaluate their efficiency. All assays resulted in typical symptoms within 10 weeks; significant differences in final disease ratings were observed, depending on inoculum concentration. Pouring inoculum directly onto banana plants showed the most consistent and reproducible results, as expressed in external wilting, internal discoloration and determined by real-time PCR assays on entire rhizomes. Moreover, this method allows the inoculation of 250 plants per hour by one individual thereby facilitating the phenotyping of large mutant and breeding populations.
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Affiliation(s)
| | | | | | - Harold J. G. Meijer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Gert H. J. Kema
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands
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