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Arndell T, Chen J, Sperschneider J, Upadhyaya NM, Blundell C, Niesner N, Outram MA, Wang A, Swain S, Luo M, Ayliffe MA, Figueroa M, Vanhercke T, Dodds PN. Pooled effector library screening in protoplasts rapidly identifies novel Avr genes. Nat Plants 2024; 10:572-580. [PMID: 38409291 PMCID: PMC11035141 DOI: 10.1038/s41477-024-01641-y] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.
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Affiliation(s)
- Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Nathalie Niesner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Steve Swain
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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2
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Figueroa M, Coaker G, Kanyuka K. Focus on the Effectors at the Interface of Plant-Microbe Interactions. Mol Plant Microbe Interact 2024; 37:168-170. [PMID: 38573845 DOI: 10.1094/mpmi-02-24-0010-cm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT 2600, Australia
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), Cambridge, CB3 0LE, U.K
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3
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Lubega J, Figueroa M, Dodds PN, Kanyuka K. Comparative Analysis of the Avirulence Effectors Produced by the Fungal Stem Rust Pathogen of Wheat. Mol Plant Microbe Interact 2024; 37:171-178. [PMID: 38170736 DOI: 10.1094/mpmi-10-23-0169-fi] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Crops are constantly exposed to pathogenic microbes. Rust fungi are examples of these harmful microorganisms, which have a major economic impact on wheat production. To protect themselves from pathogens like rust fungi, plants employ a multilayered immune system that includes immunoreceptors encoded by resistance genes. Significant efforts have led to the isolation of numerous resistance genes against rust fungi in cereals, especially in wheat. However, the evolution of virulence of rust fungi hinders the durability of resistance genes as a strategy for crop protection. Rust fungi, like other biotrophic pathogens, secrete an arsenal of effectors to facilitate infection, and these are the molecules that plant immunoreceptors target for pathogen recognition and mounting defense responses. When recognized, these effector proteins are referred to as avirulence (Avr) effectors. Despite the many predicted effectors in wheat rust fungi, only five Avr genes have been identified, all from wheat stem rust. Knowledge of the Avr genes and their variation in the fungal population will inform deployment of the most appropriate wheat disease-resistance genes for breeding and farming. The review provides an overview of methodologies as well as the validation techniques that have been used to characterize Avr effectors from wheat stem rust. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Jibril Lubega
- National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, U.K
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra 2601, Australia
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, U.K
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4
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Hewitt TC, Henningsen EC, Pereira D, McElroy K, Nazareno ES, Dugyala S, Nguyen-Phuc H, Li F, Miller ME, Visser B, Pretorius ZA, Boshoff WHP, Sperschneider J, Stukenbrock EH, Kianian SF, Dodds PN, Figueroa M. Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae. Mol Plant Microbe Interact 2024; 37:290-303. [PMID: 37955552 DOI: 10.1094/mpmi-09-23-0126-fi] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Tim C Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva C Henningsen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Danilo Pereira
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva H Stukenbrock
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
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5
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Henningsen E, Lewis D, Nguyen D, Sperschneider J, Kianian SF, Stone EA, Dodds P, Figueroa M. Virulence patterns of oat crown rust in Australia - season 2022. Plant Dis 2024. [PMID: 38277650 DOI: 10.1094/pdis-09-23-1973-sc] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48 Pca isolates derived from different locations in Australia was characterised using a collection of oat lines often utilised in rust surveys in the USA and Australia. This analysis indicates that Pca populations in Eastern Australia are broadly virulent, in contrast to the population in Western Australia (WA). Several oat lines/Pc genes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the USA oat differential set that display disease resistance to Pca in WA, some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the USA. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes for Pca in Australia. Nevertheless, the Pca population in the USA is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection with Pca supports hypotheses of allelism or redundancy among Pc genes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.
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Affiliation(s)
- Eva Henningsen
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Australian National University, 2219, Research School of Biology, Canberra, Australian Capital Territory, Australia;
| | - David Lewis
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Duong Nguyen
- CSIRO, 2221, Agriculture and Food, Adelaide, South Australia, Australia;
| | - Jana Sperschneider
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Shahryar F Kianian
- USDA ARS, 17123, Cereal Disease Laboratory, St. Paul, Minnesota, United States;
| | - Eric A Stone
- Australian National University, 2219, Research School of Biology, Canberra, Australian Capital Territory, Australia
- Australian National University, 2219, Biological Data Science Institute, Canberra, Australian Capital Territory, Australia;
| | - Peter Dodds
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Melania Figueroa
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
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6
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Nguyen DT, Henningsen EC, Lewis D, Mago R, McNeil M, Suchecki R, Boden S, Sperschneider J, Kianian S, Dodds P, Figueroa M. Genotypic and resistance profile analysis of two oat crown rust differential sets urge coordination and standardisation. Phytopathology 2023. [PMID: 38114076 DOI: 10.1094/phyto-10-23-0353-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is the causal agent of the disease known as crown rust which represents a bottleneck in oat production worldwide. Characterisation of pathogen populations often involves race (pathotype) assignments using differential sets, which are not uniform across countries. This study compared virulence profiles of 25 Pca isolates from Australia using two host differential sets, one from Australia and one from the USA. These differential sets were also genotyped using DArT sequencing technology. Phenotypic and genotypic discrepancies were detected on eight out of 29 common lines between the two sets, indicating that pathogen race assignments based on those lines are not comparable. To further investigate molecular markers that could assist in the stacking of rust resistance genes important for Australia, four published Pc91-linked markers were validated across the differential sets and then screened across a collection of 150 oat cultivars. Drover, Aladdin, and Volta were identified as putative carriers of the Pc91 locus. This is the first report to confirm that the cultivar 'Volta' carries Pc91 and demonstrates the value of implementing molecular markers to characterise materials in breeding pools of oat. Overall, our findings highlight the necessity of examining seed stocks using pedigree and molecular markers to ensure seed uniformity and bring robustness to surveillance methodologies.
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Affiliation(s)
- Duong T Nguyen
- CSIRO, 2221, Agriculture and Food, Adelaide, South Australia, Australia;
| | - Eva Celeste Henningsen
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Australian National University, 2219, Research School of Biology, Canberra, Australian Capital Territory, Australia;
| | - Dave Lewis
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Rohit Mago
- CSIRO, 2221, Agriculture & Food, GPO Box 1700, Canberra, Australian Capital Territory, Australia, 2601;
| | - Meredith McNeil
- CSIRO, 2221, Agriculture and Food, 306 Carmody Road, St Lucia , Queensland, Australia, 4067;
| | | | - Scott Boden
- The University of Adelaide, 1066, School of Food, Agriculture, and Wine, Adelaide, South Australia, Australia;
| | - Jana Sperschneider
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Shahryar Kianian
- USDA-ARS Cereal Disease Laboratory, 57840, 1551 Lindig Street, Saint Paul, Minnesota, United States, 55108;
| | - Peter Dodds
- CSIRO, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, 2221, Agriculture and Food, Canberra, Australian Capital Territory, Australia;
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Sperschneider J, Hewitt T, Lewis DC, Periyannan S, Milgate AW, Hickey LT, Mago R, Dodds PN, Figueroa M. Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina. Nat Microbiol 2023; 8:2130-2141. [PMID: 37884814 PMCID: PMC10627818 DOI: 10.1038/s41564-023-01494-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - David C Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Sambasivam Periyannan
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
- School of Agriculture and Environmental Science, Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, New South Wales, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
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Sandoval-Caballero C, Luarte L, Jiménez Y, Jaque C, Cifuentes F, Arenas GA, Figueroa M, Jara J, Olszewski PK, Teske JA, Pérez-Leighton CE. Meta-analysis of pre-clinical studies on the effects of opioid receptor ligands on food intake, motivation, and choice. Neurosci Biobehav Rev 2023; 152:105288. [PMID: 37331611 DOI: 10.1016/j.neubiorev.2023.105288] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
The opioid receptors (OR) regulate food intake. Still, despite extensive pre-clinical research, the overall effects and individual contribution of the mu (MOR), kappa (KOR), and delta (DOR) OR subtypes to feeding behaviors and food intake remain unclear. To address this, we conducted a pre-registered systematic search and meta-analysis of rodent dose-response studies to evaluate the impact of central and peripheral administration of non-selective and selective OR ligands on intake, motivation, and choice of food. All studies had a high bias risk. Still, the meta-analysis confirmed the overall orexigenic and anorexigenic effects of OR agonists and antagonists, respectively. Our results support a larger orexigenic role for central MOR agonists among OR subtypes and that peripheral OR antagonists reduce motivation for and intake of preferred foods. In binary food choice studies, peripheral OR agonists selectively increase the intake of fat-preferred foods; in contrast, they did not increase the intake of sweet carbohydrate-preferred foods. Overall, these data support that OR regulation of intake, motivation, and choice is influenced by food macronutrient composition.
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Affiliation(s)
- C Sandoval-Caballero
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - L Luarte
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - Y Jiménez
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - C Jaque
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - F Cifuentes
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - G A Arenas
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Libertador Bernardo O'Higgins #611, Rancagua 2841959, Region del Libertador Bernardo O'Higgins, Chile
| | - M Figueroa
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - J Jara
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile
| | - P K Olszewski
- Faculty of Science and Engineering, University of Waikato, Hamilton, Private Bag 3105, Hamilton 3240, New Zealand
| | - J A Teske
- School of Nutritional Sciences and Wellness and the Graduate Interdisciplinary Programs in Physiological Sciences and Neuroscience at the University of Arizona, 1177 E 4th Street Shantz 332, Tucson, AZ 85721, USA
| | - C E Pérez-Leighton
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago 8331150, Region Metropolitana, Chile.
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Nazareno ES, Fiedler JD, Ardayfio NK, Miller ME, Figueroa M, Kianian SF. Genetic Analysis and Physical Mapping of Oat Adult Plant Resistance Loci Against Puccinia coronata f. sp. avenae. Phytopathology 2023; 113:1307-1316. [PMID: 36721375 DOI: 10.1094/phyto-10-22-0395-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Six quantitative trait loci (QTLs) for adult plant resistance against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations. Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTLs were mapped on six different chromosomes: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTLs for coefficient of infection range from 12.2 to 46.9%, whereas heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking single-nucleotide polymorphism markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTLs in each population were determined using single-nucleotide polymorphism haplotype data, which showed a significantly lower coefficient of infection in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, polymerase chain reaction allelic competitive extension (PACE) markers for the adult plant resistance loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Jason D Fiedler
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Naa Korkoi Ardayfio
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Pairwise Plants, LLC, 807 East Main Street, Suite 4-100, Durham, NC, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, U.S.A
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Mata R, Flores-Bocanegra L, Ovalle-Magallanes B, Figueroa M. Natural products from plants targeting key enzymes for the future development of antidiabetic agents. Nat Prod Rep 2023. [PMID: 37283232 DOI: 10.1039/d3np00007a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Covering: 2000 to January 2023Diabetes is a metabolic disease of serious concern nowadays, with a negative economic impact. In 2021, the International Diabetes Federation estimated that more than 537 million adults live with diabetes, causing over 6.7 million deaths in that year. Intensive scientific research on medicinal plants in the last 100 years reveals that herbal drugs have been an essential source of products for developing antidiabetic agents acting on different physiological targets. This review summarizes recent research from 2000 to 2022 on plant natural compounds affecting selected crucial enzymes (dipeptidyl peptidase IV, diacylglycerol acyltransferase, fructose 1,6-biphosphatase, glucokinase, and fructokinase) involved in glucose homeostasis. Enzyme-aimed treatments usually induce reversible inhibition, irreversible by covalent changes of the objective enzymes, or bind non-covalently but so tightly that their inhibition is irreversible. Depending on the binding site, these inhibitors could be orthosteric or allosteric; in any case, the desired pharmacological action is achieved. One crucial advantage of targeting enzymes in drug discovery is that the required assays are usually simple, using biochemical experiments capable of analyzing enzyme activity.
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Affiliation(s)
- R Mata
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
| | - L Flores-Bocanegra
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
| | - B Ovalle-Magallanes
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
| | - M Figueroa
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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11
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Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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12
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Nazareno ES, Fiedler J, Miller ME, Figueroa M, Kianian SF. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). Theor Appl Genet 2022; 135:3307-3321. [PMID: 36029319 DOI: 10.1007/s00122-022-04128-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
We mapped three adult plant resistance (APR) loci on oat chromosomes 4D and 6C and developed flanking KASP/PACE markers for marker-assisted selection and gene pyramiding. Using sequence orthology search and the available oat genomic and transcriptomic data, we surveyed these genomic regions for genes that may control disease resistance. Sources of durable disease resistance are needed to minimize yield losses in cultivated oat caused by crown rust (Puccinia coronata f. sp. avenae). In this study, we developed five oat recombinant inbred line mapping populations to identify sources of adult plant resistance from crosses between five APR donors and Otana, a susceptible variety. The preliminary bulk segregant mapping based on allele frequencies showed two regions in linkage group Mrg21 (Chr4D) that are associated with the APR phenotype in all five populations. Six markers from these regions in Chr4D were converted to high-throughput allele specific PCR assays and were used to genotype all individuals in each population. Simple interval mapping showed two peaks in Chr4D, named QPc.APR-4D.1 and QPc.APR-4D.2, which were detected in the OtanaA/CI4706-2 and OtanaA/CI9416-2 and in the Otana/PI189733, OtanaD/PI260616, and OtanaA/CI8000-4 populations, respectively. These results were validated by mapping two entire populations, Otana/PI189733 and OtanaA/CI9416, genotyped using Illumina HiSeq, in which polymorphisms were called against the OT3098 oat reference genome. Composite interval mapping results confirmed the presence of the two quantitative trait loci (QTL) located on oat chromosome 4D and an additional QTL with a smaller effect located on chromosome 6C. This mapping approach also narrowed down the physical intervals to between 5 and 19 Mb, and indicated that QPc.APR-4D.1, QPc.APR-4D.2, and QPc.APR-6C explained 43.4%, 38.5%, and 21.5% of the phenotypic variation, respectively. In a survey of the gene content of each QTL, several clusters of disease resistance genes that may contribute to APR were found. The allele specific PCR markers developed for these QTL regions would be beneficial for marker-assisted breeding, gene pyramiding, and future cloning of resistance genes from oat.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Jason Fiedler
- US Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, USA
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Pairwise Plants, LLC. 807 East Main Street, Suite 4-100, Durham, NC, USA
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
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13
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Henningsen EC, Hewitt T, Dugyala S, Nazareno ES, Gilbert E, Li F, Kianian SF, Steffenson BJ, Dodds PN, Sperschneider J, Figueroa M. A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts. G3 (Bethesda) 2022; 12:6613142. [PMID: 35731221 PMCID: PMC9339303 DOI: 10.1093/g3journal/jkac149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022]
Abstract
Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
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Affiliation(s)
- Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Feng Li
- eGenesis Inc., Cambridge, MA 02139, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
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14
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. Front Plant Sci 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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15
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Outram MA, Figueroa M, Sperschneider J, Williams SJ, Dodds PN. Seeing is believing: Exploiting advances in structural biology to understand and engineer plant immunity. Curr Opin Plant Biol 2022; 67:102210. [PMID: 35461025 DOI: 10.1016/j.pbi.2022.102210] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/27/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Filamentous plant pathogens cause disease in numerous economically important crops. These pathogens secrete virulence proteins, termed effectors, that modulate host cellular processes and promote infection. Plants have evolved immunity receptors that detect effectors and activate defence pathways, resulting in resistance to the invading pathogen. This leads to an evolutionary arms race between pathogen and host that is characterised by highly diverse effector repertoires in plant pathogens. Here, we review the recent advances in understanding host-pathogen co-evolution provided by the structural determination of effectors alone, and in complex with immunity receptors. We highlight the use of recent advances in structural prediction within this field and its role for future development of designer resistance proteins.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.
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16
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Duan H, Jones AW, Hewitt T, Mackenzie A, Hu Y, Sharp A, Lewis D, Mago R, Upadhyaya NM, Rathjen JP, Stone EA, Schwessinger B, Figueroa M, Dodds PN, Periyannan S, Sperschneider J. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biol 2022; 23:84. [PMID: 35337367 PMCID: PMC8957140 DOI: 10.1186/s13059-022-02658-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Background Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false-positive signals. Results We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false-positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30–40 times using HiFi sequencing is required for phasing of the leaf rust genome, with 0.7% heterozygosity, and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. Conclusions This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02658-2.
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Affiliation(s)
- Hongyu Duan
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Amy Mackenzie
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Anna Sharp
- Research School of Biology, The Australian National University, Canberra, Australia.,Current Address: John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | | | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Sambasivam Periyannan
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Current Address: Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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17
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Muñoz-Diaz P, Jiménez K, Luraschi R, Cornejo F, Figueroa M, Vera C, Rivas-Pardo A, Sandoval JM, Vásquez C, Arenas F. Anaerobic RSH-dependent tellurite reduction contributes to Escherichia coli tolerance against tellurite. Biol Res 2022; 55:13. [PMID: 35313991 PMCID: PMC8935827 DOI: 10.1186/s40659-022-00383-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tellurium is a rare metalloid that exerts high toxicity on cells, especially on bacteria, partly due to reactive oxygen species (ROS) generation. Moreover, it has also been observed that tellurite can target free cell thiols groups (RSH) (i.e. reduced glutathione (GSH)), enhancing the cellular redox imbalance. Additionally, in vitro experiments have suggested that several enzymes can reduce tellurite (IV) to its elemental form (0); where RSH present on their active sites may be responsible for the process. Nevertheless, the mechanisms implemented by bacteria for tellurite reduction and its role in resistance have not been evaluated in vivo. RESULTS This work shows that tellurite reduction to elemental tellurium is increased under anaerobic conditions in E. coli cells. The in vivo tellurite reduction is related to the intracellular concentration of total RSH, in the presence and absence of oxygen. This metabolization of tellurite directly contributes to the resistance of the bacteria to the oxyanion. CONCLUSIONS We demonstrated that in vivo tellurite reduction is related to the intracellular thiol concentration, i.e. large availability of cellular RSH groups, results in a more significant reduction of tellurite. Furthermore, we observed that, when the bacterium exhibits less resistance to the oxyanion, a decreased tellurite reduction was seen, affecting the growth fitness. Together, these results let us propose that tellurite reduction and the intracellular RSH content are related to the oxyanion bacterial resistance, this tripartite mechanism in an oxygen-independent anaerobic process.
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Affiliation(s)
- P Muñoz-Diaz
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - K Jiménez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - R Luraschi
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - F Cornejo
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - M Figueroa
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C Vera
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - A Rivas-Pardo
- Laboratorio de Genómica Microbiana, Centro de Genómica Y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J M Sandoval
- Facultad de Ciencias, Universidad Arturo Prat, Iquique, Chile
| | - C Vásquez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - F Arenas
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química Y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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18
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Sperschneider J, Jones AW, Nasim J, Xu B, Jacques S, Zhong C, Upadhyaya NM, Mago R, Hu Y, Figueroa M, Singh KB, Stone EA, Schwessinger B, Wang MB, Taylor JM, Dodds PN. The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation. BMC Biol 2021; 19:203. [PMID: 34526021 PMCID: PMC8444563 DOI: 10.1186/s12915-021-01123-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. Results We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5′ uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5′ adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. Conclusions We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01123-z.
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Affiliation(s)
- Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Jamila Nasim
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Bo Xu
- Thermo Fisher Scientific, 5 Caribbean Drive, Scoresby, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia
| | - Chengcheng Zhong
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Karam B Singh
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia.,Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Ming-Bo Wang
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jennifer M Taylor
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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19
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Upadhyaya NM, Mago R, Panwar V, Hewitt T, Luo M, Chen J, Sperschneider J, Nguyen-Phuc H, Wang A, Ortiz D, Hac L, Bhatt D, Li F, Zhang J, Ayliffe M, Figueroa M, Kanyuka K, Ellis JG, Dodds PN. Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair. Nat Plants 2021; 7:1220-1228. [PMID: 34294906 DOI: 10.1038/s41477-021-00971-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.
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Affiliation(s)
- Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Vinay Panwar
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hoa Nguyen-Phuc
- Department of Ecology and Evolutionary Biology, Vietnam National University, Ho Chi Minh, Vietnam
| | - Aihua Wang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Génétique et Amélioration des Fruits et Légumes, INRA, Montfavet Cedex, France
| | - Luch Hac
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Feng Li
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jianping Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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20
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Brogi A, Yang Q, Masala E, Figueroa M, Santini V. Topic: AS04-MDS Biology and Pathogenesis/AS04g-Epigenetic deregulation. Leuk Res 2021. [DOI: 10.1016/j.leukres.2021.106681.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Abstract
Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
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Affiliation(s)
- Sebastien Duplessis
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Cecile Lorrain
- Plant Pathology Group, ETH Zurich, 8092 Zurich, Switzerland;
| | - Benjamin Petre
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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22
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Figueroa M, Ortiz D, Henningsen EC. Tactics of host manipulation by intracellular effectors from plant pathogenic fungi. Curr Opin Plant Biol 2021; 62:102054. [PMID: 33992840 DOI: 10.1016/j.pbi.2021.102054] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Diana Ortiz
- National Research Institute for Agriculture, Food and Environment, Unit of Genetics and Breeding of Fruit and Vegetables, Domaine St Maurice, CS 60094, F-84143 Montfavet, France
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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23
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Henningsen EC, Omidvar V, Della Coletta R, Michno JM, Gilbert E, Li F, Miller ME, Myers CL, Gordon SP, Vogel JP, Steffenson BJ, Kianian SF, Hirsch CD, Figueroa M. Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. Front Plant Sci 2021; 12:657796. [PMID: 33968112 PMCID: PMC8097158 DOI: 10.3389/fpls.2021.657796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 05/30/2023]
Abstract
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
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Affiliation(s)
- Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Jean-Michel Michno
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
| | - Erin Gilbert
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Chad L. Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | | | - John P. Vogel
- Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, United States
| | - Cory D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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24
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Henningsen E, Sallam AH, Matny O, Szinyei T, Figueroa M, Steffenson BJ. Rpg7: A New Gene for Stem Rust Resistance from Hordeum vulgare ssp. spontaneum. Phytopathology 2021; 111:548-558. [PMID: 32880513 DOI: 10.1094/phyto-08-20-0325-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wheat stem rust (causal organism: Puccinia graminis f. sp. tritici) is an important fungal disease that causes significant yield losses in barley. The deployment of resistant cultivars is the most effective means of controlling this disease. Stem rust evaluations of a diverse collection of wild barley (Hordeum vulgare ssp. spontaneum) identified two Jordanian accessions (WBDC094 and WBDC238) with resistance to a virulent pathotype (P. graminis f. sp. tritici HKHJC) from the United States. To elucidate the genetics of stem rust resistance, both accessions were crossed to the susceptible landrace Hiproly. Segregation ratios of F2 and F3 progeny indicated that a single dominant gene confers resistance to P. graminis f. sp. tritici HKHJC. Molecular mapping of the resistance locus was performed in the Hiproly/WBDC238 F2 population based on 3,329 single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Quantitative trait locus analysis positioned the resistance gene to the long arm of chromosome 3H between the physical/genetic positions of 683.8 Mbp/172.9 cM and 693.7 Mbp/176.0 cM. Because this resistance gene is novel, it was assigned the new gene locus symbol of Rpg7 with a corresponding allele symbol of Rpg7.i. At the seedling stage, Rpg7 confers resistance against a number of other important P. graminis f. sp. tritici pathotypes from the United States (MCCFC, QCCJB, and TTTTF) and Africa (TTKSK) as well as an isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis) from Minnesota. The resistance conferred by Rpg7 can be readily transferred into breeding programs because of its simple inheritance and clear phenotypic expression.
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Affiliation(s)
- Eva Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN 55108, U.S.A
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25
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Miller ME, Nazareno ES, Rottschaefer SM, Riddle J, Dos Santos Pereira D, Li F, Nguyen-Phuc H, Henningsen EC, Persoons A, Saunders DGO, Stukenbrock E, Dodds PN, Kianian SF, Figueroa M. Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci. PLoS Genet 2020; 16:e1009291. [PMID: 33370783 PMCID: PMC7793281 DOI: 10.1371/journal.pgen.1009291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/08/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae (Pca), which causes crown rust disease in oat (Avena sativa) sampled from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide diversity patterns at a single Avr locus corresponding to Pc38, Pc39, Pc55, Pc63, Pc70, and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
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Affiliation(s)
- Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric S. Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Susan M. Rottschaefer
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jakob Riddle
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Danilo Dos Santos Pereira
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Antoine Persoons
- INRA/Universite de Lorraine Interactions Abres/Microorganismes, Champenoux, France
| | | | - Eva Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plon, Germany
- Christian-Albrechts University of Kiel, Kiel Germany
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australia
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26
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Figueroa M, Dodds PN, Henningsen EC. Evolution of virulence in rust fungi - multiple solutions to one problem. Curr Opin Plant Biol 2020; 56:20-27. [PMID: 32244171 DOI: 10.1016/j.pbi.2020.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 05/18/2023]
Abstract
Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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27
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Muñoz-Villagrán C, Contreras F, Cornejo F, Figueroa M, Valenzuela-Bezanilla D, Luraschi R, Reinoso C, Rivas-Pardo J, Vásquez C, Castro M, Arenas F. Understanding gold toxicity in aerobically-grown Escherichia coli. Biol Res 2020; 53:26. [PMID: 32513271 PMCID: PMC7278051 DOI: 10.1186/s40659-020-00292-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/16/2020] [Indexed: 12/03/2022] Open
Abstract
Background There is an emerging field to put into practice new strategies for developing molecules with antimicrobial properties. In this line, several metals and metalloids are currently being used for these purposes, although their cellular effect(s) or target(s) in a particular organism are still unknown. Here we aimed to investigate and analyze Au3+ toxicity through a combination of biochemical and molecular approaches. Results We found that Au3+ triggers a major oxidative unbalance in Escherichia coli, characterized by decreased intracellular thiol levels, increased superoxide concentration, as well as by an augmented production of the antioxidant enzymes superoxide dismutase and catalase. Because ROS production is, in some cases, associated with metal reduction and the concomitant generation of gold-containing nanostructures (AuNS), this possibility was evaluated in vivo and in vitro. Conclusions Au3+ is toxic for E. coli because it triggers an unbalance of the bacterium’s oxidative status. This was demonstrated by using oxidative stress dyes and antioxidant chemicals as well as gene reporters, RSH concentrations and AuNS generation.
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Affiliation(s)
- C Muñoz-Villagrán
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - F Contreras
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - F Cornejo
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - M Figueroa
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - D Valenzuela-Bezanilla
- Laboratorio de Microbiología Aplicada, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Sede Santiago, Chile
| | - R Luraschi
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - C Reinoso
- Laboratorio de Microbiología Aplicada, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Sede Santiago, Chile
| | - J Rivas-Pardo
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Laboratorio de Biología estructural, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - C Vásquez
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - M Castro
- Laboratorio de Microbiología Aplicada, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Sede Santiago, Chile.
| | - F Arenas
- Laboratorio Microbiología Molecular, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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Kangara N, Kurowski TJ, Radhakrishnan GV, Ghosh S, Cook NM, Yu G, Arora S, Steffenson BJ, Figueroa M, Mohareb F, Saunders DGO, Wulff BBH. Mutagenesis of Puccinia graminis f. sp. tritici and Selection of Gain-of-Virulence Mutants. Front Plant Sci 2020; 11:570180. [PMID: 33072145 PMCID: PMC7533539 DOI: 10.3389/fpls.2020.570180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/19/2020] [Indexed: 05/08/2023]
Abstract
Wheat stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is regaining prominence due to the recent emergence of virulent isolates and epidemics in Africa, Europe and Central Asia. The development and deployment of wheat cultivars with multiple stem rust resistance (Sr) genes stacked together will provide durable resistance. However, certain disease resistance genes can suppress each other or fail in particular genetic backgrounds. Therefore, the function of each Sr gene must be confirmed after incorporation into an Sr-gene stack. This is difficult when using pathogen disease assays due to epistasis from recognition of multiple avirulence (Avr) effectors. Heterologous delivery of single Avr effectors can circumvent this limitation, but this strategy is currently limited by the paucity of cloned Pgt Avrs. To accelerate Avr gene cloning, we outline a procedure to develop a mutant population of Pgt spores and select for gain-of-virulence mutants. We used ethyl methanesulphonate (EMS) to mutagenize urediniospores and create a library of > 10,000 independent mutant isolates that were combined into 16 bulks of ~658 pustules each. We sequenced random mutants and determined the average mutation density to be 1 single nucleotide variant (SNV) per 258 kb. From this, we calculated that a minimum of three independently derived gain-of-virulence mutants is required to identify a given Avr gene. We inoculated the mutant library onto plants containing Sr43, Sr44, or Sr45 and obtained 9, 4, and 14 mutants with virulence toward Sr43, Sr44, or Sr45, respectively. However, only mutants identified on Sr43 and Sr45 maintained their virulence when reinolculated onto the lines from which they were identified. We further characterized 8 mutants with virulence toward Sr43. These also maintained their virulence profile on the stem rust international differential set containing 20 Sr genes, indicating that they were most likely not accidental contaminants. In conclusion, our method allows selecting for virulent mutants toward targeted resistance (R) genes. The development of a mutant library from as little as 320 mg spores creates a resource that enables screening against several R genes without the need for multiple rounds of spore multiplication and mutagenesis.
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Affiliation(s)
| | - Tomasz J. Kurowski
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Bedford, United Kingdom
| | | | - Sreya Ghosh
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
| | - Nicola M. Cook
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
| | - Guotai Yu
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
| | - Sanu Arora
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, NSW, Australia
| | - Fady Mohareb
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Bedford, United Kingdom
- *Correspondence: Brande B. H. Wulff, ; Diane G. O. Saunders, ; Fady Mohareb,
| | - Diane G. O. Saunders
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
- *Correspondence: Brande B. H. Wulff, ; Diane G. O. Saunders, ; Fady Mohareb,
| | - Brande B. H. Wulff
- Crop Genetics Department, John Innes Centre, Norwich, United Kingdom
- *Correspondence: Brande B. H. Wulff, ; Diane G. O. Saunders, ; Fady Mohareb,
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. Phytopathology 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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Figueroa M, Hammond‐Kosack KE, Solomon PS. A review of wheat diseases-a field perspective. Mol Plant Pathol 2018; 19:1523-1536. [PMID: 29045052 PMCID: PMC6638159 DOI: 10.1111/mpp.12618] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [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: 07/27/2017] [Revised: 09/10/2017] [Accepted: 09/22/2017] [Indexed: 05/19/2023]
Abstract
Wheat is one of the primary staple foods throughout the planet. Significant yield gains in wheat production over the past 40 years have resulted in a steady balance of supply versus demand. However, predicted global population growth rates and dietary changes mean that substantial yield gains over the next several decades will be needed to meet this escalating demand. A key component to meeting this challenge is better management of fungal incited diseases, which can be responsible for 15%-20% yield losses per annum. Prominent diseases of wheat that currently contribute to these losses include the rusts, blotches and head blight/scab. Other recently emerged or relatively unnoticed diseases, such as wheat blast and spot blotch, respectively, also threaten grain production. This review seeks to provide an overview of the impact, distribution and management strategies of these diseases. In addition, the biology of the pathogens and the molecular basis of their interaction with wheat are discussed.
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Affiliation(s)
- Melania Figueroa
- Department of Plant PathologyStakman‐Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. PaulMN 55108USA
| | - Kim E. Hammond‐Kosack
- Department of Biointeractions and Crop ProtectionRothamsted Research, West CommonHarpendenHertfordshire AL5 2JQUK
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of BiologyThe Australian National UniversityCanberraACT 2601Australia
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31
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Nazareno ES, Li F, Smith M, Park RF, Kianian SF, Figueroa M. Puccinia coronata f. sp. avenae: a threat to global oat production. Mol Plant Pathol 2018; 19:1047-1060. [PMID: 28846186 PMCID: PMC6638059 DOI: 10.1111/mpp.12608] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 05/20/2023]
Abstract
UNLABELLED Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. CONTROL Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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Affiliation(s)
- Eric S. Nazareno
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Feng Li
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Madeleine Smith
- Department of Plant PathologyUniversity of Minnesota‐Northwest Research and Outreach CenterCrookstonMN 56716USA
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyNarellanNSW2567Australia
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, US Department of Agriculture‐Agricultural Research ServiceSt. PaulMN 55108USA
| | - Melania Figueroa
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
- Stakman‐Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMN 55108USA
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32
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Sehgal NKR, Sullivan C, Figueroa M, Pencak JA, Einstadter D, Thornton JD. A Standardized Donor Designation Ratio to Assess the Performance of Driver's License Agencies. Transplant Proc 2018; 49:1211-1214. [PMID: 28735982 DOI: 10.1016/j.transproceed.2017.01.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
Abstract
Evaluating Department of Motor Vehicles (DMV) locations based on the percent of patrons who register as donors does not account for individual characteristics that may influence willingness to donate. We reviewed the driver's licenses of 2997 randomly selected patients at an urban medical system to obtain donor designation, age, gender, and DMV location and linked patient addresses with census tract data on race, ethnicity, income, and education. We then developed a Standardized Donor Designation Ratio (SDDR) (ie, the observed number of donors at each DMV divided by the expected number of donors based on patient demographic characteristics). Overall, 1355 (45%) patients were designated as donors. Donor designation was independently associated with younger age, female gender, nonblack race, and higher income. Across 18 DMVs, the proportion of patients who were donors ranged from 30% to 68% and SDDRs ranged from 0.82 to 1.17. Among the 6 facilities in the lowest tertile by SDDR, 3 were in the lowest tertile by percent donation. In conclusion, there is a great deal of variation across DMVs in rates of organ donor designation. SDDRs that adjust for DMV patron characteristics are distinct measures that may more accurately describe the performance of DMVs in promoting organ donation.
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Affiliation(s)
| | - C Sullivan
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA
| | - M Figueroa
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA
| | - J A Pencak
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA
| | - D Einstadter
- Center for Health Care Research and Policy, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA; Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of Internal Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA
| | - J D Thornton
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA; Department of Internal Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA; Division of Pulmonary, Critical Care, and Sleep Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, USA.
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33
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Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, Mago R, Newell K, Xia X, Bernoux M, Taylor JM, Steffenson B, Jin Y, Zhang P, Kanyuka K, Figueroa M, Ellis JG, Park RF, Dodds PN. Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Science 2018; 358:1607-1610. [PMID: 29269475 DOI: 10.1126/science.aao4810] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023]
Abstract
Race-specific resistance genes protect the global wheat crop from stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) but are often overcome owing to evolution of new virulent races of the pathogen. To understand virulence evolution in Pgt, we identified the protein ligand (AvrSr50) recognized by the Sr50 resistance protein. A spontaneous mutant of Pgt virulent to Sr50 contained a 2.5 mega-base pair loss-of-heterozygosity event. A haustorial secreted protein from this region triggers Sr50-dependent defense responses in planta and interacts directly with the Sr50 protein. Virulence alleles of AvrSr50 have arisen through DNA insertion and sequence divergence, and our data provide molecular evidence that in addition to sexual recombination, somatic exchange can play a role in the emergence of new virulence traits in Pgt.
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Affiliation(s)
- Jiapeng Chen
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.,Judith and David Coffey Life Lab, Charles Perkins Centre, University of Sydney
| | - Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Perth, WA, Australia
| | - Feng Li
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Clement Bouton
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Susan Breen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Bo Xu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Kim Newell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Brian Steffenson
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Yue Jin
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA.,United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
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35
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Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust. mBio 2018; 9:e01650-17. [PMID: 29463655 PMCID: PMC5821079 DOI: 10.1128/mbio.01650-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/09/2018] [Indexed: 01/18/2023] Open
Abstract
Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenaeIMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae.
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Affiliation(s)
- Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Ying Zhang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Perth, WA, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Castle Raley
- Leidos Biomedical Research, Frederick, Maryland, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, Wisconsin, USA
| | - Diana Garnica
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Narayana Upadhyaya
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
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Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, The Australian National University, Canberra Australian Capital Territory, Australia
| | - Ricky J. Milne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- * E-mail:
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Santini V, Allione B, Zini G, Gioia D, Lunghi M, Poloni A, Cilloni D, Sanna A, Masiera E, Ceccarelli M, Abdel-Wahab O, Terenzi A, Angelucci E, Finelli C, Onida F, Pelizzari A, Ferrero D, Saglio G, Figueroa M, Levis A. A phase II, multicentre trial of decitabine in higher-risk chronic myelomonocytic leukemia. Leukemia 2017; 32:413-418. [PMID: 28607470 PMCID: PMC5808077 DOI: 10.1038/leu.2017.186] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/21/2017] [Accepted: 05/24/2017] [Indexed: 12/30/2022]
Abstract
Chronic myelomonocytic leukemia (CMML) is a complex clonal hematological disorder classified among myelodysplastic (MDS)/myeloproliferative neoplasms. Prognosis is poor and there is a lack of effective treatments. The hypomethylating agent decitabine has shown activity against MDS and elderly acute myeloid leukemia, but there is little data focusing specifically on its efficacy in CMML. In this prospective, phase 2 Italian study, CMML patients received intravenous decitabine 20 mg/m2 per day on Days 1–5 of a 28-day treatment cycle. Response was evaluated after four and six cycles; patients responding at the end of six cycles could continue treatment with decitabine. Forty-three patients were enrolled; >50% were high-risk according to four CMML-specific scoring systems. In the intent-to-treat population (n=42), the overall response rate after six cycles was 47.6%, with seven complete responses (16.6%), eight marrow responses (19%), one partial response (2.4%) and four hematological improvements (9.5%). After a median follow-up of 51.5 months (range: 44.4–57.2), median overall survival was 17 months, with responders having a significantly longer survival than non-responders (P=0.02). Grade 3/4 anemia, neutropenia and thrombocytopenia occurred in 28.6%, 50% and 38% of patients, respectively. Decitabine appears to be an effective and well-tolerated treatment for patients with high-risk CMML.
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Affiliation(s)
- V Santini
- Department of Hematology, AOU Careggi, University of Florence, Florence, Italy
| | - B Allione
- AOU Citta della Salute e della Scienza, Torino, Italy
| | - G Zini
- Department of Oncology and Hematology, Hematology Institute, Fondazion e Policlinico Gemelli, UCSC, Rome, Italy
| | | | - M Lunghi
- Division of Haematology, Department of Translational Medicine, UPO, Novara, Italy
| | - A Poloni
- Department of Hematology, AOU Ospedali Riuniti, Università Politecnica Marche, Ancona, Italy
| | - D Cilloni
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Turin, Italy
| | - A Sanna
- Università degli studi di Firenze, Dipartimento di medicina sperimentale e Clinica, Firenze, Italy
| | | | - M Ceccarelli
- AOU Città della salute e della scienza di Torino, Torino, Italy
| | - O Abdel-Wahab
- Human Oncology and Pathogenesis Program, and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Terenzi
- BMT Centre of Perugia, Department of Hematology, Perugia, Italy
| | - E Angelucci
- Hematology and Transplant Unit, Ospedale Oncologico di Riferimento Regionale Armando Businco, Cagliari, Italy
| | - C Finelli
- Institute of Hematology, S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - F Onida
- Oncohematology Unit, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico-Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - A Pelizzari
- Spedali Civili Brescia Hematology Unit, Brescia, Italy
| | - D Ferrero
- Hematology Division, Università degli Studi di Torino, Torino, Italy
| | - G Saglio
- Department of Clinical and Biological Sciences, University of Turin, Torino, Italy
| | - M Figueroa
- Department of Human Genetics and, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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Sehgal NKR, Sullivan C, Scallan C, Figueroa M, Pencak JA, Kirkland J, Scott K, Thornton JD. Is Signature Size Associated With Organ Donor Designation on Driver's Licenses? Transplant Proc 2017; 48:1911-5. [PMID: 27569921 DOI: 10.1016/j.transproceed.2016.02.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/16/2016] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Previous studies suggest that large signature size is associated with narcissistic characteristics. By contrast, organ donation is an indicator of altruism. Because altruism and narcissism may be viewed as opposites, we sought to determine if smaller signature size is associated with willingness to be an organ donor. METHODS Using a cross-sectional study design, we reviewed the health records of 571 randomly selected primary care patients at a large urban safety-net medical system to obtain their demographic and medical characteristics. We also examined driver's licenses that were scanned into electronic health records as part of the patient registration process. We measured signature sizes and obtained the organ donor designation from these driver's licenses. RESULTS Overall, 256 (45%) patients were designated as donors on their driver's licenses. Signature size averaged 113.3 mm(2) but varied greatly across patients (10th percentile 49.1 mm(2), 90th percentile 226.1 mm(2)). On multivariate analysis, donor designation was positively associated with age 18-34 years, non-black race, having private insurance, and not having any comorbid conditions. However, signature size was not associated with organ donor designation. CONCLUSIONS Signature size is not associated with verified organ donor designation. Further work is needed to understand the relationship between personality types and willingness to be an organ donor.
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Affiliation(s)
- N K R Sehgal
- University School, Chagrin Falls, Ohio, United States
| | - C Sullivan
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States
| | - C Scallan
- Department of Internal Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States
| | - M Figueroa
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States
| | - J A Pencak
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States
| | - J Kirkland
- Case Western Reserve University, Cleveland, Ohio, United States
| | - K Scott
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States
| | - J D Thornton
- Center for Reducing Health Disparities, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States; Department of Internal Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States; Division of Pulmonary, Critical Care, and Sleep Medicine, MetroHealth Campus of Case Western Reserve University, Cleveland, Ohio, United States.
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Verdín-Betancourt F, López-González M, Cruz-Hurtado M, Cerda C, Figueroa M, Sierra-Santoyo A. Chemical characterization of vinclozoline M5 metabolite. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.07.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zhang J, Presley GN, Hammel KE, Ryu JS, Menke JR, Figueroa M, Hu D, Orr G, Schilling JS. Localizing gene regulation reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta. Proc Natl Acad Sci U S A 2016; 113:10968-73. [PMID: 27621450 PMCID: PMC5047196 DOI: 10.1073/pnas.1608454113] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation (LOX) by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and nonselective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that LOX components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole-transcriptome shotgun sequencing (RNA-seq) and assayed relevant enzyme activities. We found a marked pattern of LOX up-regulation in a narrow (5-mm, 48-h) zone at the hyphal front, which included many genes likely involved in ROS generation. Up-regulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with the notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization.
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Affiliation(s)
- Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108
| | - Gerald N Presley
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108
| | - Kenneth E Hammel
- Institute for Microbial and Biochemical Technology, US Forest Products Laboratory, Madison, WI 53726; Department of Bacteriology, University of Wisconsin, Madison, WI 53706
| | - Jae-San Ryu
- Eco-Friendliness Research Department, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju 660-360, Republic of Korea
| | - Jon R Menke
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108
| | - Dehong Hu
- Chemical and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Galya Orr
- Chemical and Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jonathan S Schilling
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108;
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Fra-Vázquez A, Morales N, Figueroa M, Val del Río A, Regueiro L, Campos J, Mosquera-Corral A. Bacterial community dynamics in long-term operation of a pilot plant using aerobic granular sludge to treat pig slurry. Biotechnol Prog 2016; 32:1212-1221. [DOI: 10.1002/btpr.2314] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/22/2016] [Indexed: 12/22/2022]
Affiliation(s)
- A. Fra-Vázquez
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - N. Morales
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - M. Figueroa
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - A. Val del Río
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - L. Regueiro
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
| | - J.L. Campos
- Faculty of Engineering and Science; Universidad Adolfo Ibáñez; Avda. Padre Hurtado 750 Viña del Mar Chile
| | - A. Mosquera-Corral
- Dept. of Chemical Engineering, Group of Environmental Engineering and Bioprocesses; Inst. of Technology, University of Santiago de Compostela; Santiago de Compostela 15705 Spain
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Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN. Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici. Front Plant Sci 2016; 7:205. [PMID: 26941766 PMCID: PMC4764693 DOI: 10.3389/fpls.2016.00205] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/06/2016] [Indexed: 05/03/2023]
Abstract
The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Narayana M. Upadhyaya
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Jana Sperschneider
- Agriculture, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research OrganisationPerth, WA, Australia
| | - Robert F. Park
- Faculty of Agriculture and Environment, Plant Breeding Institute, The University of SydneyNarellan, NSW, Australia
| | - Les J. Szabo
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research ServiceSt. Paul, MN, USA
| | - Brian Steffenson
- Department of Plant Pathology and the Stakman-Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. Paul, MN, USA
| | - Jeff G. Ellis
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Peter N. Dodds
- Agriculture, Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
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Abstract
The necrotrophic fungus Pyrenophora tritici-repentis is responsible for the disease tan spot of wheat. Ptr ToxB (ToxB), a proteinaceous host-selective toxin, is one of the effectors secreted by P. tritici-repentis. ToxB induces chlorosis in toxin-sensitive wheat cultivars and displays characteristics common to apoplastic effectors. We addressed the hypothesis that ToxB exerts its activity extracellularly. Our data indicate that hydraulic pressure applied in the apoplast following ToxB infiltration can displace ToxB-induced symptoms. In addition, treatment with a proteolytic cocktail following toxin infiltration results in reduction of symptom development and indicates that ToxB requires at least 8 h in planta to induce maximum symptom development. In vitro assays demonstrate that apoplastic fluids extracted from toxin-sensitive and -insensitive wheat cultivars cannot degrade ToxB. Additionally, ToxB can be reisolated from apoplastic fluid after toxin infiltration. Furthermore, localization studies of fluorescently labeled ToxB indicate that the toxin remains in the apoplast in toxin-sensitive and -insensitive wheat cultivars. Our findings support the hypothesis that ToxB acts as an extracellular effector.
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Affiliation(s)
- Melania Figueroa
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Viola A Manning
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Iovanna Pandelova
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Lynda M Ciuffetti
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
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Figueroa M, Castell-Miller CV, Li F, Hulbert SH, Bradeen JM. Pushing the boundaries of resistance: insights from Brachypodium-rust interactions. Front Plant Sci 2015; 6:558. [PMID: 26284085 PMCID: PMC4519692 DOI: 10.3389/fpls.2015.00558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant-microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Claudia V. Castell-Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
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Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, Zhao Z, Kang D, Underwood J, Grigoriev IV, Figueroa M, Schilling JS, Chen F, Wang Z. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing. PLoS One 2015; 10:e0132628. [PMID: 26177194 PMCID: PMC4503453 DOI: 10.1371/journal.pone.0132628] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/16/2015] [Indexed: 12/27/2022] Open
Abstract
Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.
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Affiliation(s)
- Sean P. Gordon
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Elizabeth Tseng
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jiwei Zhang
- Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Xiandong Meng
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Zhiying Zhao
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dongwan Kang
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jason Underwood
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jonathan S. Schilling
- Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Feng Chen
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- School of Natural Sciences, University of California at Merced, Merced, California, United States of America
- * E-mail:
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47
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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48
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Nyarko A, Singarapu KK, Figueroa M, Manning VA, Pandelova I, Wolpert TJ, Ciuffetti LM, Barbar E. Solution NMR structures of Pyrenophora tritici-repentis ToxB and its inactive homolog reveal potential determinants of toxin activity. J Biol Chem 2014; 289:25946-56. [PMID: 25063993 DOI: 10.1074/jbc.m114.569103] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyrenophora tritici-repentis Ptr ToxB (ToxB) is a proteinaceous host-selective toxin produced by Pyrenophora tritici-repentis (P. tritici-repentis), a plant pathogenic fungus that causes the disease tan spot of wheat. One feature that distinguishes ToxB from other host-selective toxins is that it has naturally occurring homologs in non-pathogenic P. tritici-repentis isolates that lack toxic activity. There are no high-resolution structures for any of the ToxB homologs, or for any protein with >30% sequence identity, and therefore what underlies activity remains an open question. Here, we present the NMR structures of ToxB and its inactive homolog Ptr toxb. Both proteins adopt a β-sandwich fold comprising three strands in each half that are bridged together by two disulfide bonds. The inactive toxb, however, shows higher flexibility localized to the sequence-divergent β-sandwich half. The absence of toxic activity is attributed to a more open structure in the vicinity of one disulfide bond, higher flexibility, and residue differences in an exposed loop that likely impacts interaction with putative targets. We propose that activity is regulated by perturbations in a putative active site loop and changes in dynamics distant from the site of activity. Interestingly, the new structures identify AvrPiz-t, a secreted avirulence protein produced by the rice blast fungus, as a structural homolog to ToxB. This homology suggests that fungal proteins involved in either disease susceptibility such as ToxB or resistance such as AvrPiz-t may have a common evolutionary origin.
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Affiliation(s)
- Afua Nyarko
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Kiran K Singarapu
- the Center for NMR and Structural Chemistry, Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India, and
| | - Melania Figueroa
- the Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Viola A Manning
- the Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Iovanna Pandelova
- the Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Thomas J Wolpert
- the Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Lynda M Ciuffetti
- the Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Elisar Barbar
- From the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331,
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49
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Arranz-Marquez E, Fatela-Cantillo B, Figueroa M, Teus MÁ. [Late onset lens particle glaucoma in Marfan syndrome]. ACTA ACUST UNITED AC 2014; 90:40-3. [PMID: 24388607 DOI: 10.1016/j.oftal.2013.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 11/07/2013] [Accepted: 11/18/2013] [Indexed: 12/01/2022]
Abstract
CASE REPORT A case is presented of an acute onset lens particle glaucoma originating from a crystalline lens spontaneously dislocated into the vitreous for more than 20 years in a patient diagnosed with Marfan syndrome. DISCUSSION Marfan syndrome is a connective tissue disorder with autosomal dominant inheritance caused by fibrillin gene mutation. Ectopia lentis is the predominant ocular abnormality and a major diagnostic criterion. An association between Marfan syndrome and glaucoma has also been demonstrated. The reported case is unusual in that a complete spontaneous lens dislocation to vitreous was present and progressed to secondary lens particle open angle glaucoma.
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Affiliation(s)
- E Arranz-Marquez
- Hospital Rey Juan Carlos, Madrid, España; Novovision, Madrid, España
| | | | - M Figueroa
- Vissum Corporación, Madrid, España; Hospital Universitario Ramón y Cajal, Madrid, España
| | - M Á Teus
- Novovision, Madrid, España; Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Madrid, España; Departamento de Ciencias Morfológicas y Cirugía, Facultad de Medicina, Universidad de Alcalá, Alcalá de Henares, Madrid, España
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50
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Riera F, Medeot M, Sartori L, Bergallo C, Minoli J, Vilchez V, Sánchez P, Abiega C, Pincheira C, Correa S, Bartoli C, Figueroa M, Montamat M, Spitale N, Minguez A, Caeiro JP. [Candidemia epidemiology in Córdoba Argentina. Surveillance study of five institutions]. Rev Fac Cien Med Univ Nac Cordoba 2014; 71:89-93. [PMID: 25365194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
UNLABELLED The incidence rate of invasive infections due to Candida species has increased drastically in the last 20 years, causing a 40% mortality rate in hospitalized patients. In order to comprehend the epidemiology of Candida bloodstream infection, the study was carried out. MATERIALS AND METHODS A retrospective study was done based on microbiology laboratory reports from five terciary care hospitals from the city of Cordoba between January 2010 and August 2012. RESULTS 158 patients had candidemia, the average age was 55,8 years, and 54% of patients were in the intensive care unit. Candida albicans (44%), Candida parapsilosis (22%) and Candida tropicalis (12%) were the main fungi isolated. Candida parapsilosis was commonly associated with catether infections. CONCLUSIONS The data from the city of Cordoba showed that C. albicans, C. parapsilosis y C. tropicalis were the more frequent species isolated from blood cultures. This is similar to what is seen in other series published from Argentina and Latinamerica. This study may have implications when it comes to deciding which empiric antifugal agent is best for the treatment of candidemia.
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