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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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2
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Ángel C. CA, Marín-Ramírez GA, Maldonado CE. Genome sequence of Hemileia vastatrix Berk. and Br. (Race I), the causal agent of coffee leaf rust, isolate from Risaralda, Colombia. Microbiol Resour Announc 2023; 12:e0044423. [PMID: 37791781 PMCID: PMC10652848 DOI: 10.1128/mra.00444-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023] Open
Abstract
Coffee leaf rust, caused by the fungus Hemileia vastatrix (Basidiomycota; Pucciniomycota), is a devastating disease spread worldwide. To improve the available genomes, we use PacBio HiFi sequencing enhanced by Dovetail Omni-C chromatin conformation capture to assemble a highly contiguous 747.98 Mb genome of an isolate collected from Coffea arabica.
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Affiliation(s)
- Carlos A. Ángel C.
- Plant Pathology, Colombian National Coffee Federation (FNC)/National Coffee Research Center (CENICAFE), Chinchiná, Colombia
| | - Gustavo A. Marín-Ramírez
- Plant Pathology, Colombian National Coffee Federation (FNC)/National Coffee Research Center (CENICAFE), Chinchiná, Colombia
| | - Carlos E. Maldonado
- Plant Breeding, Colombian National Coffee Federation (FNC)/National Coffee Research Center (CENICAFE), Chinchiná, Colombia
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3
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Degnan RM, McTaggart AR, Shuey LS, Pame LJS, Smith GR, Gardiner DM, Nock V, Soffe R, Sale S, Garrill A, Carroll BJ, Mitter N, Sawyer A. Exogenous double-stranded RNA inhibits the infection physiology of rust fungi to reduce symptoms in planta. MOLECULAR PLANT PATHOLOGY 2023; 24:191-207. [PMID: 36528383 PMCID: PMC9923395 DOI: 10.1111/mpp.13286] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 06/01/2023]
Abstract
Rust fungi (Pucciniales) are a diverse group of plant pathogens in natural and agricultural systems. They pose ongoing threats to the diversity of native flora and cause annual crop yield losses. Agricultural rusts are predominantly managed with fungicides and breeding for resistance, but new control strategies are needed on non-agricultural plants and in fragile ecosystems. RNA interference (RNAi) induced by exogenous double-stranded RNA (dsRNA) has promise as a sustainable approach for managing plant-pathogenic fungi, including rust fungi. We investigated the mechanisms and impact of exogenous dsRNA on rust fungi through in vitro and whole-plant assays using two species as models, Austropuccinia psidii (the cause of myrtle rust) and Coleosporium plumeriae (the cause of frangipani rust). In vitro, dsRNA either associates externally or is internalized by urediniospores during the early stages of germination. The impact of dsRNA on rust infection architecture was examined on artificial leaf surfaces. dsRNA targeting predicted essential genes significantly reduced germination and inhibited development of infection structures, namely appressoria and penetration pegs. Exogenous dsRNA sprayed onto 1-year-old trees significantly reduced myrtle rust symptoms. Furthermore, we used comparative genomics to assess the wide-scale amenability of dsRNA to control rust fungi. We sequenced genomes of six species of rust fungi, including three new families (Araucariomyceaceae, Phragmidiaceae, and Skierkaceae) and identified key genes of the RNAi pathway across 15 species in eight families of Pucciniales. Together, these findings indicate that dsRNA targeting essential genes has potential for broad-use management of rust fungi across natural and agricultural systems.
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Affiliation(s)
- Rebecca M. Degnan
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alistair R. McTaggart
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Louise S. Shuey
- Queensland Department of Agriculture and FisheriesEcosciences PrecinctDutton ParkQueenslandAustralia
| | - Leny Jane S. Pame
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Grant R. Smith
- The New Zealand Institute for Plant and Food Research LimitedLincolnNew Zealand
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Volker Nock
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
| | - Rebecca Soffe
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- Present address:
School of EngineeringRMIT UniversityMelbourneVictoriaAustralia
| | - Sarah Sale
- Department of Electrical and Computer EngineeringUniversity of CanterburyChristchurchNew Zealand
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Ashley Garrill
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Bernard J. Carroll
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | - Anne Sawyer
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQueenslandAustralia
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural ScienceThe University of QueenslandSt LuciaQueenslandAustralia
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4
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Rodrigues ASB, Silva DN, Várzea V, Paulo OS, Batista D. Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History. PHYTOPATHOLOGY 2022; 112:1998-2011. [PMID: 35322716 DOI: 10.1094/phyto-09-21-0376-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.
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Affiliation(s)
- Ana Sofia B Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Diogo Nuno Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Vitor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
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5
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:ijms23179629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
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6
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Ramírez-Camejo LA, Eamvijarn A, Díaz-Valderrama JR, Karlsen-Ayala E, Koch RA, Johnson E, Pruvot-Woehl S, Mejía LC, Montagnon C, Maldonado-Fuentes C, Aime MC. Global Analysis of Hemileia vastatrix Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range. PHYTOPATHOLOGY 2022; 112:643-652. [PMID: 34428920 DOI: 10.1094/phyto-06-21-0255-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.
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Affiliation(s)
- Luis A Ramírez-Camejo
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
- Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton, Panama, Republic of Panama
| | - Amnat Eamvijarn
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- Department of Agriculture, Chatuchak, Bangkok, Thailand
| | - Jorge R Díaz-Valderrama
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elena Karlsen-Ayala
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
- University of Florida, Department of Plant Pathology, Gainesville, FL, U.S.A
| | - Rachel A Koch
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
| | - Elizabeth Johnson
- Inter-American Institute for Cooperation on Agriculture, Hope Gardens, Kingston, Jamaica
| | | | - Luis C Mejía
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Ancón, Republic of Panama
| | | | | | - M Catherine Aime
- Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, U.S.A
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7
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Quispe-Apaza C, Mansilla-Samaniego R, Espejo-Joya R, Bernacchia G, Yabar-Larios M, López-Bonilla C. Spatial and Temporal Genetic Diversity and Population Structure of Hemileia vastatrix from Peruvian Coffee Plantations. THE PLANT PATHOLOGY JOURNAL 2021; 37:280-290. [PMID: 34111917 PMCID: PMC8200579 DOI: 10.5423/ppj.oa.10.2020.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity (Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years (FST = 0.00180, P = 0.20053 and FST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.
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Affiliation(s)
- Cinthia Quispe-Apaza
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
| | | | - Rosa Espejo-Joya
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
| | - Giovanni Bernacchia
- Università degli Studi di Ferrara, Dip Scienze della Vita e Biotecnologie, Via Borsari 46, 44121 Ferrara, Italy
| | - Marisela Yabar-Larios
- Servicio Nacional de Sanidad Agraria, Av. La Molina 1915, La Molina, 15024 Lima, Perú
| | - César López-Bonilla
- Universidad Nacional Agraria La Molina, Av. La Molina s/n, La Molina, 15024 Lima, Perú
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Talhinhas P, Carvalho R, Loureiro J. The use of flow cytometry for fungal nuclear DNA quantification. Cytometry A 2021; 99:343-347. [PMID: 33704904 DOI: 10.1002/cyto.a.24335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/08/2022]
Abstract
Genome size information is sparse across fungi, with information being available for less than 2000 species. So far, most records have been obtained using static, microscope-based cytometry methods or derived from genome sequencing projects. Flow cytometry is now considered the state-of-the-art method for obtaining genome size measurements, and appropriate methods and DNA standards are available, enabling the analysis of most genome size ranges in a rapid, robust and inexpensive way. The average fungal genome size is 60 Mbp, but sizes vary across phylogeny, ranging from 2.2 (Encephalitozoon romaleae) to 3706 Mbp (Jafnea semitosta). In several fungal clades, genome size expansion seems to accompany evolution either to plant mutualism or to plant parasitism (particularly biotrophy), and fungi that interact with plants seem to have larger genomes than saprobes and those that interact with animals. Whereas flow cytometry for nuclear DNA quantification is routinely employed in plant sciences for genome size and ploidy studies, its use in fungal biology is still infrequent. Appropriate standards, methods and best practices are described here, with the aim of stimulating a more generalized and widespread use of flow cytometry for fungal genome size measurement.
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Affiliation(s)
- Pedro Talhinhas
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Carvalho
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
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Barka GD, Caixeta ET, Ferreira SS, Zambolim L. In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach. PLoS One 2020; 15:e0222747. [PMID: 32639982 PMCID: PMC7343155 DOI: 10.1371/journal.pone.0222747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/19/2020] [Indexed: 11/19/2022] Open
Abstract
Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.
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Affiliation(s)
- Geleta Dugassa Barka
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
- Applied Biology Department, Adama Science and Technology University (ASTU), Adama, Oromia, Ethiopia
| | - Eveline Teixeira Caixeta
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
- Embrapa Café, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil
- * E-mail:
| | - Sávio Siqueira Ferreira
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
| | - Laércio Zambolim
- Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
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10
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Abstract
It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor.
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11
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Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1190 I. Introduction 1190 II. Rust fungi: a diverse and serious threat to agriculture 1191 III. The different facets of rust life cycles and unresolved questions about their evolution 1191 IV. The biology of rust infection 1192 V. Rusts in the genomics era: the ever-expanding list of candidate effector genes 1195 VI. Functional characterization of rust effectors 1197 VII. Putting rusts to sleep: Pucciniales research outlooks 1201 Acknowledgements 1202 References 1202 SUMMARY: Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure, largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts. Thousands of genes encoding secreted proteins highly expressed during host infection have been reported for different rust species, which represents significant potential towards understanding rust effector function. Recent high-throughput in planta expression screen approaches (effectoromics) have pushed the field ahead even further towards predicting high-priority effectors and identifying avirulence genes. These new insights into rust effector biology promise to inform future research and spur the development of effective and sustainable strategies for managing rust diseases.
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Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
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12
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Porto BN, Caixeta ET, Mathioni SM, Vidigal PMP, Zambolim L, Zambolim EM, Donofrio N, Polson SW, Maia TA, Chen C, Adetunji M, Kingham B, Dalio RJD, de Resende MLV. Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility. PLoS One 2019; 14:e0215598. [PMID: 30998802 PMCID: PMC6472787 DOI: 10.1371/journal.pone.0215598] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/04/2019] [Indexed: 12/17/2022] Open
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is one of the most important leaf diseases of coffee plantations worldwide. Current knowledge of the H. vastatrix genome is limited and only a small fraction of the total fungal secretome has been identified. In order to obtain a more comprehensive understanding of its secretome, we aimed to sequence and assemble the entire H. vastatrix genome using two next-generation sequencing platforms and a hybrid assembly strategy. This resulted in a 547 Mb genome of H. vastatrix race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034 putative proteins with transcriptomic support. Based on this proteome, 615 proteins contain putative secretion peptides, and lack transmembrane domains. From this putative secretome, 111 proteins were identified as candidate effectors (EHv33) unique to H. vastatrix, and a subset consisting of 17 EHv33 genes was selected for a temporal gene expression analysis during infection. Five genes were significantly induced early during an incompatible interaction, indicating their potential role as pre-haustorial effectors possibly recognized by the resistant coffee genotype. Another nine genes were significantly induced after haustorium formation in the compatible interaction. Overall, we suggest that this fungus is able to selectively mount its survival strategy with effectors that depend on the host genotype involved in the infection process.
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Affiliation(s)
- Brenda Neves Porto
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Sandra Marisa Mathioni
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Laércio Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Eunize Maciel Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Thiago Andrade Maia
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Modupe Adetunji
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Brewster Kingham
- Sequencing and Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Ronaldo José Durigan Dalio
- Instituto Agronômico de Campinas, Centro de Citricultura “Sylvio Moreira”, Cordeirópolis, São Paulo, Brazil
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13
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Silva DN, Várzea V, Paulo OS, Batista D. Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust. MOLECULAR PLANT PATHOLOGY 2018; 19:1742-1753. [PMID: 29328532 PMCID: PMC6638104 DOI: 10.1111/mpp.12657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 05/30/2023]
Abstract
Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.
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Affiliation(s)
- Diogo Nuno Silva
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Vítor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio Salgueiro Paulo
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Dora Batista
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
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14
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Florez JC, Mofatto LS, do Livramento Freitas-Lopes R, Ferreira SS, Zambolim EM, Carazzolle MF, Zambolim L, Caixeta ET. High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection. PLANT MOLECULAR BIOLOGY 2017; 95:607-623. [PMID: 29094279 DOI: 10.1007/s11103-017-0676-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/21/2017] [Indexed: 06/07/2023]
Abstract
We provide a transcriptional profile of coffee rust interaction and identified putative up regulated resistant genes Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome and de novo assembly, we obtained 43,159 transcripts. At early infection events (12 and 24 h after infection), HdT responded to the attack of H. vastatrix with a larger number of up-regulated genes than Caturra, which was related to prehaustorial resistance. The genes found in HdT at early hours were involved in receptor-like kinases, response ion fluxes, production of reactive oxygen species, protein phosphorylation, ethylene biosynthesis and callose deposition. We selected 13 up-regulated HdT-exclusive genes to validate by real-time qPCR, which most of them confirmed their higher expression in HdT than in Caturra at early stage of infection. These genes have the potential to assist the development of new coffee rust control strategies. Collectively, our results provide understanding of expression profiles in coffee-H. vastatrix interaction over a time course in susceptible and resistant coffee plants.
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Affiliation(s)
- Juan Carlos Florez
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil
| | - Luciana Souto Mofatto
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Distrito de Barão Geraldo, Campinas, SP, 13083-970, Brazil
| | - Rejane do Livramento Freitas-Lopes
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil
| | - Sávio Siqueira Ferreira
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil
| | - Eunize Maciel Zambolim
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Distrito de Barão Geraldo, Campinas, SP, 13083-970, Brazil
| | - Laércio Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil
| | - Eveline Teixeira Caixeta
- Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), BioCafé, Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil.
- Embrapa Café, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Campus Universitário, Avenida P.H. Rolfs, s/n, Viçosa, MG, Brazil.
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15
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Talhinhas P, Batista D, Diniz I, Vieira A, Silva DN, Loureiro A, Tavares S, Pereira AP, Azinheira HG, Guerra‐Guimarães L, Várzea V, Silva MDC. The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. MOLECULAR PLANT PATHOLOGY 2017; 18:1039-1051. [PMID: 27885775 PMCID: PMC6638270 DOI: 10.1111/mpp.12512] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/09/2016] [Accepted: 11/12/2016] [Indexed: 05/22/2023]
Abstract
TAXONOMY AND HISTORY Hemileia vastatrix Berk. and Broome (Basidiomycota, Pucciniales) was described in 1869 in eastern Africa and Ceylon as the agent of coffee leaf rust and has spread to all coffee cultivation areas worldwide. Major disease outbreaks in Asia, Africa and America caused and continue to cause severe yield losses, making this the most important disease of Arabica coffee, a cash crop for many tropical and sub-tropical countries. LIFE CYCLE AND DISEASE SYMPTOMS Hemileia vastatrix is a hemicyclic fungus with the urediniosporic life cycle as its most important (if not only) source of inoculum. Chlorotic spots are the first macroscopic symptoms, preceding the differentiation of suprastomatal, bouquet-shaped, orange-coloured uredinia. The disease can cause yield losses of up to 35% and have a polyetic epidemiological impact on subsequent years. DISEASE CONTROL Although the use of fungicides is one of the preferred immediate control measures, the use of resistant cultivars is considered to be the most effective and durable disease control strategy. The discovery of 'Híbrido de Timor' provided sources of resistance that have been used in several breeding programmes and that have been proven to be effective and durable, as some have been in use for more than 30 years. GENETIC DIVERSITY AND MOLECULAR PATHOGENICITY Although exhibiting limited genetic polymorphism, the very large genome of H. vastatrix (c. 797 Mbp) conceals great pathological diversity, with more than 50 physiological races. Gene expression studies have revealed a very precocious activation of signalling pathways and production of putative effectors, suggesting that the plant-fungus dialogue starts as early as at the germ tube stage, and have provided clues for the identification of avr genes.
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Affiliation(s)
- Pedro Talhinhas
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Dora Batista
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
- Computational Biology and Population Genomics Group, cE3c – Centre for EcologyEvolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaCampo GrandeLisbon1749‐016Portugal
| | - Inês Diniz
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Ana Vieira
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- Computational Biology and Population Genomics Group, cE3c – Centre for EcologyEvolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaCampo GrandeLisbon1749‐016Portugal
| | - Diogo N. Silva
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- Computational Biology and Population Genomics Group, cE3c – Centre for EcologyEvolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaCampo GrandeLisbon1749‐016Portugal
| | - Andreia Loureiro
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Sílvia Tavares
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
| | - Ana Paula Pereira
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
| | - Helena G. Azinheira
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Leonor Guerra‐Guimarães
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Vítor Várzea
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
| | - Maria do Céu Silva
- CIFC, Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaQuinta do MarquêsOeiras2784‐505Portugal
- LEAF, Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaTapada da AjudaLisbon1349‐017Portugal
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Maia T, Badel JL, Marin‐Ramirez G, Rocha CDM, Fernandes MB, da Silva JCF, de Azevedo‐Junior GM, Brommonschenkel SH. The Hemileia vastatrix effector HvEC-016 suppresses bacterial blight symptoms in coffee genotypes with the S H 1 rust resistance gene. THE NEW PHYTOLOGIST 2017; 213:1315-1329. [PMID: 27918080 PMCID: PMC6079635 DOI: 10.1111/nph.14334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/16/2016] [Indexed: 05/03/2023]
Abstract
A number of genes that confer resistance to coffee leaf rust (SH 1-SH 9) have been identified within the genus Coffea, but despite many years of research on this pathosystem, the complementary avirulence genes of Hemileia vastatrix have not been reported. After identification of H. vastatrix effector candidate genes (HvECs) expressed at different stages of its lifecycle, we established an assay to characterize HvEC proteins by delivering them into coffee cells via the type-three secretion system (T3SS) of Pseudomonas syringae pv. garcae (Psgc). Employing a calmodulin-dependent adenylate cyclase assay, we demonstrate that Psgc recognizes a heterologous P. syringae T3SS secretion signal which enables us to translocate HvECs into the cytoplasm of coffee cells. Using this Psgc-adapted effector detector vector (EDV) system, we found that HvEC-016 suppresses the growth of Psgc on coffee genotypes with the SH 1 resistance gene. Suppression of bacterial blight symptoms in SH 1 plants was associated with reduced bacterial multiplication. By contrast, HvEC-016 enhanced bacterial multiplication in SH 1-lacking plants. Our findings suggest that HvEC-016 may be recognized by the plant immune system in a SH 1-dependent manner. Thus, our experimental approach is an effective tool for the characterization of effector/avirulence proteins of this important pathogen.
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Affiliation(s)
- Thiago Maia
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Jorge L. Badel
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Gustavo Marin‐Ramirez
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Cynthia de M. Rocha
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Michelle B. Fernandes
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - José C. F. da Silva
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Gilson M. de Azevedo‐Junior
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
| | - Sérgio H. Brommonschenkel
- Departamento de Fitopatologia and National Institute for Plant‐Pest Interactions/Instituto de Biotecnologia Aplicada a Agropecuária‐BIOAGROUniversidade Federal de ViçosaViçosaMG 36570‐000Brazil
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17
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Anderson C, Khan MA, Catanzariti AM, Jack CA, Nemri A, Lawrence GJ, Upadhyaya NM, Hardham AR, Ellis JG, Dodds PN, Jones DA. Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini. BMC Genomics 2016; 17:667. [PMID: 27550217 PMCID: PMC4994203 DOI: 10.1186/s12864-016-3011-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/11/2016] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. RESULTS To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. CONCLUSIONS The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.
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Affiliation(s)
- Claire Anderson
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Muhammad Adil Khan
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
- Current address: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Ann-Maree Catanzariti
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Cameron A. Jack
- ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia
| | - Adnane Nemri
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
- Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574 Germany
| | | | | | - Adrienne R. Hardham
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | | | - Peter N. Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
| | - David A. Jones
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
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19
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Latest Developments in the Research of Rust Fungi and Their Allies (Pucciniomycotina). ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-29137-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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20
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Lorrain C, Hecker A, Duplessis S. Effector-Mining in the Poplar Rust Fungus Melampsora larici-populina Secretome. FRONTIERS IN PLANT SCIENCE 2015; 6:1051. [PMID: 26697026 PMCID: PMC4678189 DOI: 10.3389/fpls.2015.01051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/11/2015] [Indexed: 05/24/2023]
Abstract
The poplar leaf rust fungus, Melampsora larici-populina has been established as a tree-microbe interaction model. Understanding the molecular mechanisms controlling infection by pathogens appears essential for durable management of tree plantations. In biotrophic plant-parasites, effectors are known to condition host cell colonization. Thus, investigation of candidate secreted effector proteins (CSEPs) is a major goal in the poplar-poplar rust interaction. Unlike oomycetes, fungal effectors do not share conserved motifs and candidate prediction relies on a set of a priori criteria established from reported bona fide effectors. Secretome prediction, genome-wide analysis of gene families and transcriptomics of M. larici-populina have led to catalogs of more than a thousand secreted proteins. Automatized effector-mining pipelines hold great promise for rapid and systematic identification and prioritization of CSEPs for functional characterization. In this review, we report on and discuss the current status of the poplar rust fungus secretome and prediction of candidate effectors from this species.
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Affiliation(s)
- Cécile Lorrain
- INRA, UMR 1136 Interactions Arbres/Microorganismes INRA/Université de Lorraine, Centre INRA Nancy Lorraine, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes Université de Lorraine/INRA, Faculté des Sciences et Technologies, Vandoeuvre-lès-Nancy, France
| | - Arnaud Hecker
- INRA, UMR 1136 Interactions Arbres/Microorganismes INRA/Université de Lorraine, Centre INRA Nancy Lorraine, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes Université de Lorraine/INRA, Faculté des Sciences et Technologies, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes INRA/Université de Lorraine, Centre INRA Nancy Lorraine, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes Université de Lorraine/INRA, Faculté des Sciences et Technologies, Vandoeuvre-lès-Nancy, France
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21
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Ramos AP, Tavares S, Tavares D, Silva MDC, Loureiro J, Talhinhas P. Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported--2489 Mbp. MOLECULAR PLANT PATHOLOGY 2015; 16:1006-1010. [PMID: 25784533 PMCID: PMC6638392 DOI: 10.1111/mpp.12255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Among the Eukaryotes, Fungi have relatively small genomes (average of 44.2 Mbp across 1850 species). The order Pucciniales (Basidiomycota) has the largest average genome size among fungi (305 Mbp), and includes the two largest fungal genomes reported so far (Puccinia chrysanthemi and Gymnosporangium confusum, with 806.5 and 893.2 Mbp, respectively). In this work, flow cytometry was employed to determine the genome size of the Bidens pilosa rust pathogen, Uromyces bidentis. The results obtained revealed that U. bidentis presents a surprisingly large haploid genome size of 2489 Mbp. This value is almost three times larger than the previous largest fungal genome reported and over 50 times larger than the average fungal genome size. Microscopic examination of U. bidentis nuclei also showed that they are not as different in size from the B. pilosa nuclei when compared with the differences between other rusts and their host plants. This result further reinforces the position of the Pucciniales as the fungal group with the largest genomes, prompting studies addressing the role of repetitive elements and polyploidy in the evolution, pathological specialization and diversity of fungal species.
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Affiliation(s)
- Ana Paula Ramos
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
| | - Sílvia Tavares
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
| | - Daniela Tavares
- CFE, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Maria Do Céu Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
| | - João Loureiro
- CFE, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Pedro Talhinhas
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, 1349-017, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical, 2780-505, Oeiras, Portugal
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22
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Dong S, Raffaele S, Kamoun S. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev 2015; 35:57-65. [PMID: 26451981 DOI: 10.1016/j.gde.2015.09.001] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/04/2015] [Accepted: 09/04/2015] [Indexed: 02/02/2023]
Abstract
Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the 'two-speed genome' model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.
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Affiliation(s)
- Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Sylvain Raffaele
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan 31326, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan 31326, France
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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Liu JJ, Sturrock RN, Sniezko RA, Williams H, Benton R, Zamany A. Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors. BMC Genomics 2015; 16:678. [PMID: 26338692 PMCID: PMC4559923 DOI: 10.1186/s12864-015-1861-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Background The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq. Results cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses. Conclusion This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1861-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Rona N Sturrock
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA.
| | - Holly Williams
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Ross Benton
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Arezoo Zamany
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
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