1
|
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; 23:9629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
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
| | - 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
| |
Collapse
|
2
|
Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
Collapse
Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | |
Collapse
|
3
|
Bai Q, Wang M, Xia C, See DR, Chen X. Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen. Int J Mol Sci 2022; 23:ijms23084114. [PMID: 35456934 PMCID: PMC9033109 DOI: 10.3390/ijms23084114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 01/14/2023] Open
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.
Collapse
Affiliation(s)
- Qing Bai
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
| | - Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA; (Q.B.); (M.W.); (C.X.); (D.R.S.)
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
- Correspondence: ; Tel.: +1-509-335-8086
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Zheng W, Peng Z, Peng S, Yu Z, Cao Z. Multinuclei Occurred Under Cryopreservation and Enhanced the Pathogenicity of Melampsora larici-populina. Front Microbiol 2021; 12:650902. [PMID: 34248868 PMCID: PMC8270653 DOI: 10.3389/fmicb.2021.650902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Melampsora larici-populina is a macrocyclic rust, and the haploid stage with two nuclei and the diploid of mononuclear sequentially occur annually. During the preservation of dry urediniospores at −80°C, we found that one isolate, ΔTs06, was different from the usual wild-type isolate Ts06 at −20°C because it has mixed polykaryotic urediniospores. However, the other spores, including the 0, I, III, and IV stages of a life cycle, were the same as Ts06. After five generations of successive inoculation and harvest of urediniospores from the compatible host Populus purdomii, the isolate ΔTs06 steadily maintained more than 20% multiple nucleus spores. To test the pathogenesis variation of ΔTs06, an assay of host poplars was applied to evaluate the differences between ΔTs06 and Ts06. After ΔTs06 and Ts06 inoculation, leaves of P. purdomii were used to detect the expression of small secreted proteins (SSPs) and fungal biomasses using quantitative real-time PCR (qRT-PCR) and trypan blue staining. ΔTs06 displayed stronger expression of five SSPs and had a shorter latent period, a higher density of uredinia, and higher DNA mass. A transcriptomic comparison between ΔTs06 and Ts06 revealed that 3,224 were differentially expressed genes (DEGs), 55 of which were related to reactive oxygen species metabolism, the Mitogen-activated protein kinase (MAPK) signaling pathway, and the meiosis pathway. Ten genes in the mitotic and meiotic pathways and another two genes associated with the “response to DNA damage stimulus” all had an upward expression, which were detected by qRT-PCR in ΔTs06 during cryopreservation. Gas chromatography–mass spectrometry (GC-MS) confirmed that the amounts of hexadecanoic acid and octadecadienoic acid were much more in ΔTs06 than in Ts06. In addition, using spectrophotometry, hydrogen peroxide (H2O2) was also present in greater quantities in ΔTs06 compared with those found in Ts06. Increased fatty acids metabolism could prevent damage to urediniospores in super-low temperatures, but oxidant species that involved H2O2 may destroy tube proteins of mitosis and meiosis, which could cause abnormal nuclear division and lead to multinucleation, which has a different genotype. Therefore, the multinuclear isolate is different from the wild-type isolate in terms of phenotype and genotype; this multinucleation phenomenon in urediniospores improves the pathogenesis and environmental fitness of M. larici-populina.
Collapse
Affiliation(s)
- Wei Zheng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zijia Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Shaobing Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhongdong Yu
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, China
| |
Collapse
|
6
|
Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
Collapse
Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
| |
Collapse
|
7
|
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: 75] [Impact Index Per Article: 15.0] [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.
Collapse
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
| |
Collapse
|
8
|
Lorrain C, Marchal C, Hacquard S, Delaruelle C, Pétrowski J, Petre B, Hecker A, Frey P, Duplessis S. The Rust Fungus Melampsora larici-populina Expresses a Conserved Genetic Program and Distinct Sets of Secreted Protein Genes During Infection of Its Two Host Plants, Larch and Poplar. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:695-706. [PMID: 29336199 DOI: 10.1094/mpmi-12-17-0319-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mechanisms required for broad-spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycles. Melampsora larici-populina infects two taxonomically unrelated plants, larch, on which sexual reproduction is achieved, and poplar, on which clonal multiplication occurs, leading to severe epidemics in plantations. We applied deep RNA sequencing to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia, and aecia, and we performed comparative transcriptomics of infection on poplar and larch hosts, using available expression data. Secreted protein was the only significantly overrepresented category among differentially expressed M. larici-populina genes between the basidial, the pycnial, and the aecial stages, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes were commonly expressed on the two hosts and a fraction exhibited host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.
Collapse
Affiliation(s)
- Cécile Lorrain
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Clémence Marchal
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Stéphane Hacquard
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Christine Delaruelle
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Jérémy Pétrowski
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Benjamin Petre
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
- 2 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH, Norwich, U.K
| | - Arnaud Hecker
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Pascal Frey
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| | - Sébastien Duplessis
- 1 INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, F-54280 Champenoux, France; and
| |
Collapse
|
9
|
Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data. Genetics 2018; 209:389-400. [PMID: 29588288 PMCID: PMC5972415 DOI: 10.1534/genetics.118.300831] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022] Open
Abstract
High-throughput sequencing methods provide a cost-effective approach for genotyping and are commonly used in population genetics studies. A drawback of these methods, however, is that sequencing and genotyping errors can arise... High-throughput sequencing methods that multiplex a large number of individuals have provided a cost-effective approach for discovering genome-wide genetic variation in large populations. These sequencing methods are increasingly being utilized in population genetic studies across a diverse range of species. Two side-effects of these methods, however, are (1) sequencing errors and (2) heterozygous genotypes called as homozygous due to only one allele at a particular locus being sequenced, which occurs when the sequencing depth is insufficient. Both of these errors have a profound effect on the estimation of linkage disequilibrium (LD) and, if not taken into account, lead to inaccurate estimates. We developed a new likelihood method, GUS-LD, to estimate pairwise linkage disequilibrium using low coverage sequencing data that accounts for undercalled heterozygous genotypes and sequencing errors. Our findings show that accurate estimates were obtained using GUS-LD, whereas underestimation of LD results if no adjustment is made for the errors.
Collapse
|
10
|
Lorrain C, Petre B, Duplessis S. Show me the way: rust effector targets in heterologous plant systems. Curr Opin Microbiol 2018; 46:19-25. [PMID: 29454191 DOI: 10.1016/j.mib.2018.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 11/27/2022]
Abstract
For years, the study of rust fungal effectors has been impeded by the lack of molecular genetic tools in rust pathosystems. The recent use of heterologous plants to perform effector screens (effectoromics)-including effector localisation (cellular targets) and protein interactors (molecular targets) in plant cells-has changed the game. These screens revealed that many candidate effectors from various rust fungi target specific plant cell compartments, including chloroplasts, and associate with specific plant protein complexes. Such information represents unparalleled opportunities to understand how effectors sustain extreme parasitic interactions and obligate biotrophy. Despite their limitations, we here portray how the use of heterologous expression systems has been essential for gaining new insight into rust effectors.
Collapse
Affiliation(s)
- Cécile Lorrain
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Benjamin Petre
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Sébastien Duplessis
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France.
| |
Collapse
|
11
|
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]
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Hamelin FM, Castella F, Doli V, Marçais B, Ravigné V, Lewis MA. Mate Finding, Sexual Spore Production, and the Spread of Fungal Plant Parasites. Bull Math Biol 2016; 78:695-712. [DOI: 10.1007/s11538-016-0157-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/14/2016] [Indexed: 12/25/2022]
|
14
|
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.
Collapse
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
| |
Collapse
|