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Arora S, Steed A, Goddard R, Gaurav K, O'Hara T, Schoen A, Rawat N, Elkot AF, Korolev AV, Chinoy C, Nicholson MH, Asuke S, Antoniou-Kourounioti R, Steuernagel B, Yu G, Awal R, Forner-Martínez M, Wingen L, Baggs E, Clarke J, Saunders DGO, Krasileva KV, Tosa Y, Jones JDG, Tiwari VK, Wulff BBH, Nicholson P. A wheat kinase and immune receptor form host-specificity barriers against the blast fungus. Nat Plants 2023; 9:385-392. [PMID: 36797350 PMCID: PMC10027608 DOI: 10.1038/s41477-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/20/2023] [Indexed: 05/18/2023]
Abstract
Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.
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Affiliation(s)
- Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Andrew Steed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Goddard
- John Innes Centre, Norwich Research Park, Norwich, UK
- Limagrain UK Ltd, Lincolnshire, UK
| | - Kumar Gaurav
- John Innes Centre, Norwich Research Park, Norwich, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | - Tom O'Hara
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ahmed F Elkot
- Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | | | | | | | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Rea Antoniou-Kourounioti
- John Innes Centre, Norwich Research Park, Norwich, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, UK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rajani Awal
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Luzie Wingen
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | | | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, UK.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021; 373:655-662. [PMID: 34353948 PMCID: PMC8733867 DOI: 10.1126/science.abg5289] [Citation(s) in RCA: 195] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | | | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Silas Tittes
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Asher I Hudson
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | | | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Qiuhan Jiang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael L Syring
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Doreen Ware
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - R Kelly Dawe
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, Yu G, Baggs E, Witek AI, Yadav I, Krasileva KV, Jones JDG, Uauy C, Keller B, Ridout CJ, Wulff BBH. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire. Plant Physiol 2020; 183:468-482. [PMID: 32184345 PMCID: PMC7271791 DOI: 10.1104/pp.19.01273] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.
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Affiliation(s)
| | - Kamil Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Agnieszka I Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Dr. G.S. Khush Laboratories, Punjab Agricultural University, Ludhiana-141 004, Punjab, India
| | - Ksenia V Krasileva
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jonathan D G Jones
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | | | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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4
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Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol 2018; 19:23. [PMID: 29458393 PMCID: PMC5819176 DOI: 10.1186/s13059-018-1392-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/16/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. RESULTS We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. CONCLUSIONS The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."
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Affiliation(s)
- Paul C Bailey
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | | | - William Jackson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Gulay Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ksenia V Krasileva
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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