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Rodriguez-Algaba J, Hovmøller MS, Schulz P, Hansen JG, Lezáun JA, Joaquim J, Randazzo B, Czembor P, Zemeca L, Slikova S, Hanzalová A, Holdgate S, Wilderspin S, Mascher F, Suffert F, Leconte M, Flath K, Justesen AF. Stem rust on barberry species in Europe: Host specificities and genetic diversity. Front Genet 2022; 13:988031. [PMID: 36246643 PMCID: PMC9554944 DOI: 10.3389/fgene.2022.988031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The increased emergence of cereal stem rust in southern and western Europe, caused by the pathogen Puccinia graminis, and the prevalence of alternate (sexual) host, Berberis species, have regained attention as the sexual host may serve as source of novel pathogen variability that may pose a threat to cereal supply. The main objective of the present study was to investigate the functional role of Berberis species in the current epidemiological situation of cereal stem rust in Europe. Surveys in 11 European countries were carried out from 2018 to 2020, where aecial infections from five barberry species were collected. Phylogenetic analysis of 121 single aecial clusters of diverse origin using the elongation factor 1-α gene indicated the presence of different special forms (aka formae speciales) of P. graminis adapted to different cereal and grass species. Inoculation studies using aecial clusters from Spain, United Kingdom, and Switzerland resulted in 533 stem rust isolates sampled from wheat, barley, rye, and oat, which confirmed the presence of multiple special forms of P. graminis. Microsatellite marker analysis of a subset of 192 sexually-derived isolates recovered on wheat, barley and rye from the three populations confirmed the generation of novel genetic diversity revealed by the detection of 135 multilocus genotypes. Discriminant analysis of principal components resulted in four genetic clusters, which grouped at both local and country level. Here, we demonstrated that a variety of Berberis species may serve as functional alternate hosts for cereal stem rust fungi and highlights the increased risks that the sexual cycle may pose to cereal production in Europe, which calls for new initiatives within rust surveillance, epidemiological research and resistance breeding.
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Affiliation(s)
- Julian Rodriguez-Algaba
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
- *Correspondence: Julian Rodriguez-Algaba,
| | - Mogens S. Hovmøller
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Philipp Schulz
- Federal Research Centre for Cultivated Plants, Julius Kühn-Institut, Institute for Plant Protection in Field Crops and Grassland, Kleinmachnow, Germany
| | - Jens G. Hansen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | - Juan Antonio Lezáun
- INTIA, Institute for Agrifood Technology and Infrastructures of Navarra, Villava, Navarra, Spain
| | - Jessica Joaquim
- Agroscope, Crop Plant Breeding and Genetic Ressources, Nyon, Switzerland
| | | | - Paweł Czembor
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
| | - Liga Zemeca
- Institute of Plant Protection Research “Agrihorts”, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | | | - Alena Hanzalová
- Crop Research Institute, Department of Genetics and Plant Breeding Methods, Prague, Czech Republic
| | - Sarah Holdgate
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Sarah Wilderspin
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Fabio Mascher
- Agroscope, Crop Plant Breeding and Genetic Ressources, Nyon, Switzerland
| | - Frederic Suffert
- INRAE (French National Institute for Agriculture Food and Environment), Université Paris-Saclay, Thiverval-Grignon, France
| | - Marc Leconte
- INRAE (French National Institute for Agriculture Food and Environment), Université Paris-Saclay, Thiverval-Grignon, France
| | - Kerstin Flath
- Federal Research Centre for Cultivated Plants, Julius Kühn-Institut, Institute for Plant Protection in Field Crops and Grassland, Kleinmachnow, Germany
| | - Annemarie F. Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
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van der Merwe M, Ericson L, Walker J, Thrall PH, Burdon JJ. Evolutionary relationships among species of Puccinia and Uromyces (Pucciniaceae, Uredinales) inferred from partial protein coding gene phylogenies. ACTA ACUST UNITED AC 2007; 111:163-75. [PMID: 17324755 DOI: 10.1016/j.mycres.2006.09.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 09/15/2006] [Accepted: 09/18/2006] [Indexed: 11/23/2022]
Abstract
The two rust genera with the largest number of species are Puccinia Pers. ex Pers. and Uromyces (Link) Unger in the family Pucciniaceae (Uredinales). The hosts of these pathogens include representatives from almost all major angiosperm orders. Despite their ecological and economic importance, the status of Puccinia and Uromyces as distinct genera has been disputed, and little is known about relationships within and among these groups. Here we present phylogenetic analyses based on sequence data from the translation elongation factor 1alpha gene for over 60 species in the family Pucciniaceae. In particular, we investigate evolutionary relationships between Puccinia and Uromyces. A relatively smaller phylogeny using the beta-tubulin 1 gene was generated to test support for this phylogeny. Two main phylogenetic clades were identified and indicate at least two radiations within the Pucciniaceae. As expected neither Puccinia s. lat. nor Uromyces s. lat. are supported as monophyletic groups by either of the protein coding genes. However, both Puccinia sensu stricto (type P. graminis), and Uromyces sensu stricto (type U. appendiculatus) constitute distinct clades. In general, members of Uromyces spp. occurred scattered throughout the phylogeny suggesting that they represent more recent radiations. Several host families are found in both of the two main clades while two families, Poaceae and Cyperaceae, are separated, with one in each of the two main clades.
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Broeker K, Bernard F, Moerschbacher BM. An EST library from Puccinia graminis f. sp. tritici reveals genes potentially involved in fungal differentiation. FEMS Microbiol Lett 2006; 256:273-81. [PMID: 16499617 DOI: 10.1111/j.1574-6968.2006.00127.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The rust fungus Puccinia graminis f. sp. tritici is an obligately biotrophic pathogen on wheat plants and thus difficult to investigate. Hence, little is known about this fungus at the molecular level. We constructed a differential suppression subtractive hybridization cDNA-library from rust-infected vs. healthy wheat plants. The majority of expressed sequence tags (ESTs) showed similarities to fungal sequences. Semiquantitative RT-PCR using mRNA from rust-infected leaves, and from axenically grown, differentiating and nondifferentiating young rust colonies as well as sporulating and nonsporulating mature mycelia revealed rather diverse expression patterns for different ESTs, shedding new light on their potential involvement in differentiation and host-pathogen interaction.
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Affiliation(s)
- Katja Broeker
- Institut für Biochemie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Münster, Germany
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Yergeau E, Filion M, Vujanovic V, St-Arnaud M. A PCR-denaturing gradient gel electrophoresis approach to assess Fusarium diversity in asparagus. J Microbiol Methods 2005; 60:143-54. [PMID: 15590089 DOI: 10.1016/j.mimet.2004.09.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 09/09/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
In North America, asparagus (Asparagus officinalis) production suffers from a crown and root rot disease mainly caused by Fusarium oxysporum f. sp. asparagi and F. proliferatum. Many other Fusarium species are also found in asparagus fields, whereas accurate detection and identification of these organisms, especially when processing numerous samples, is usually difficult and time consuming. In this study, a PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess Fusarium species diversity in asparagus plant samples. Fusarium-specific PCR primers targeting a partial region of the translation elongation factor-1 alpha (EF-1 alpha) gene were designed, and their specificity was tested against genomic DNA extracted from a large collection of closely and distantly related organisms isolated from multiple environments. Amplicons of 450 bp were obtained from all Fusarium isolates, while no PCR product was obtained from non-Fusarium organisms. The ability of DGGE to discriminate between Fusarium taxa was tested over 19 different Fusarium species represented by 39 isolates, including most species previously reported from asparagus fields worldwide. The technique was effective to visually discriminate between the majority of Fusarium species and/or isolates tested in pure culture, while a further sequencing step permitted to distinguish between the few species showing similar migration patterns. Total genomic DNA was extracted from field-grown asparagus plants naturally infested with different Fusarium species, submitted to PCR amplification, DGGE analysis and sequencing. The two to four bands observed for each plant sample were all affiliated with F. oxysporum, F. proliferatum or F. solani, clearly supporting the reliability, sensitivity and specificity of this approach for the study of Fusarium diversity from asparagus plants samples.
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Affiliation(s)
- E Yergeau
- Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, Canada H1X 2B2
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Sirand-Pugnet P, Santos C, Labarère J. The Aa-Pri4 gene, specifically expressed during fruiting initiation in the Agrocybe aegerita complex, contains an unusual CT-rich leader intron within the 5' uncoding region. Curr Genet 2003; 44:124-31. [PMID: 13680153 DOI: 10.1007/s00294-003-0435-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Revised: 07/02/2003] [Accepted: 07/15/2003] [Indexed: 10/26/2022]
Abstract
The Aa1-Pri4 gene was cloned from the edible mushroom Agrocybe aegerita. The gene, specifically expressed during fruiting initiation, encodes a glycine-rich protein of 116 amino acids, with no homology to already known proteins. Homologous genes were amplified from two other strains belonging to the Agr. aegerita complex and originating from South-East Asia; and a comparison of the three genes revealed a high conservation of the coding sequences (72.8-97.8%). The PRI4 putative protein sequences were highly similar (87.5-100.0%); and all of them contained two protein kinase C sites, suggesting a potential supplementary regulation by phosphorylation at the protein level. The 5' uncoding regions all presented a leader intron, very variable in sequence (45.7% identity), but with a high C+T content (74.5-79.0%). The presence of such CT-rich sequences previously described in the promoter of highly expressed fungal genes suggests that the leader intron of the Aa1-Pri4 gene could be involved in the high-level, stage-specific expression.
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Affiliation(s)
- Pascal Sirand-Pugnet
- Laboratoire de Génétique et d'Amélioration des Champignons Cultivés, University Victor Segalen, Bordeaux 2 INRA, C.R.A. de Bordeaux, B.P. 81, 33883 Villenave d'Ornon Cedex, France
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