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Snoeck S, Guayazán-Palacios N, Steinbrenner AD. Molecular tug-of-war: Plant immune recognition of herbivory. THE PLANT CELL 2022; 34:1497-1513. [PMID: 35026025 PMCID: PMC9048929 DOI: 10.1093/plcell/koac009] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/07/2022] [Indexed: 05/22/2023]
Abstract
Plant defense responses against insect herbivores are induced through wound-induced signaling and the specific perception of herbivore-associated molecular patterns (HAMPs). In addition, herbivores can deliver effectors that suppress plant immunity. Here we review plant immune recognition of HAMPs and effectors, and argue that these initial molecular interactions upon a plant-herbivore encounter mediate and structure effective resistance. While the number of distinct HAMPs and effectors from both chewing and piercing-sucking herbivores has expanded rapidly with omics-enabled approaches, paired receptors and targets in the host are still not well characterized. Herbivore-derived effectors may also be recognized as HAMPs depending on the host plant species, potentially through the evolution of novel immune receptor functions. We compile examples of HAMPs and effectors where natural variation between species may inform evolutionary patterns and mechanisms of plant-herbivore interactions. Finally, we discuss the combined effects of wounding and HAMP recognition, and review potential signaling hubs, which may integrate both sensing functions. Understanding the precise mechanisms for plant sensing of herbivores will be critical for engineering resistance in agriculture.
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Affiliation(s)
- Simon Snoeck
- Department of Biology, University of Washington, Seattle, Washington, USA
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102
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Wu Z, Tian L, Liu X, Huang W, Zhang Y, Li X. The N-terminally truncated helper NLR NRG1C antagonizes immunity mediated by its full-length neighbors NRG1A and NRG1B. THE PLANT CELL 2022; 34:1621-1640. [PMID: 34871452 PMCID: PMC9048947 DOI: 10.1093/plcell/koab285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/11/2021] [Indexed: 05/19/2023]
Abstract
Both plants and animals utilize nucleotide-binding leucine-rich repeat immune receptors (NLRs) to perceive the presence of pathogen-derived molecules and induce immune responses. NLR genes are far more abundant and diverse in vascular plants than in animals. Truncated NLRs, which lack one or more of the canonical domains, are also commonly encoded in plant genomes. However, little is known about their functions, especially the N-terminally truncated ones. Here, we show that the Arabidopsis thaliana N-terminally truncated helper NLR (hNLR) gene N REQUIREMENT GENE1 (NRG1C) is highly induced upon pathogen infection and in autoimmune mutants. The immune response and cell death conferred by some Toll/interleukin-1 receptor-type NLRs (TNLs) were compromised in Arabidopsis NRG1C overexpression lines. Detailed genetic analysis revealed that NRG1C antagonizes the immunity mediated by its full-length neighbors NRG1A and NRG1B. Biochemical tests suggested that NRG1C might interfere with the EDS1-SAG101 complex, which functions in immunity signaling together with NRG1A/1B. Interestingly, Brassicaceae NRG1Cs are functionally exchangeable and that the Nicotiana benthamiana N-terminally truncated hNLR NRG2 also antagonizes NRG1 activity. Together, our study uncovers an unexpected negative role of N-terminally truncated hNLRs in immunity in different plant species.
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Affiliation(s)
- Zhongshou Wu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lei Tian
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xueru Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Weijie Huang
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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103
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. THE PLANT CELL 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
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104
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Xu G, Moeder W, Yoshioka K, Shan L. A tale of many families: calcium channels in plant immunity. THE PLANT CELL 2022; 34:1551-1567. [PMID: 35134212 PMCID: PMC9048905 DOI: 10.1093/plcell/koac033] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/26/2022] [Indexed: 05/24/2023]
Abstract
Plants launch a concerted immune response to dampen potential infections upon sensing microbial pathogen and insect invasions. The transient and rapid elevation of the cytosolic calcium concentration [Ca2+]cyt is among the essential early cellular responses in plant immunity. The free Ca2+ concentration in the apoplast is far higher than that in the resting cytoplasm. Thus, the precise regulation of calcium channel activities upon infection is the key for an immediate and dynamic Ca2+ influx to trigger downstream signaling. Specific Ca2+ signatures in different branches of the plant immune system vary in timing, amplitude, duration, kinetics, and sources of Ca2+. Recent breakthroughs in the studies of diverse groups of classical calcium channels highlight the instrumental role of Ca2+ homeostasis in plant immunity and cell survival. Additionally, the identification of some immune receptors as noncanonical Ca2+-permeable channels opens a new view of how immune receptors initiate cell death and signaling. This review aims to provide an overview of different Ca2+-conducting channels in plant immunity and highlight their molecular and genetic mode-of-actions in facilitating immune signaling. We also discuss the regulatory mechanisms that control the stability and activity of these channels.
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Affiliation(s)
- Guangyuan Xu
- MOA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wolfgang Moeder
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
| | - Keiko Yoshioka
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
- Center for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
| | - Libo Shan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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105
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Otto M, Zheng Y, Wiehe T. Recombination, selection and the evolution of tandem gene arrays. Genetics 2022; 221:6572811. [PMID: 35460227 PMCID: PMC9252282 DOI: 10.1093/genetics/iyac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Multigene families—immunity genes or sensory receptors, for instance—are often subject to diversifying selection. Allelic diversity may be favored not only through balancing or frequency-dependent selection at individual loci but also by associating different alleles in multicopy gene families. Using a combination of analytical calculations and simulations, we explored a population genetic model of epistatic selection and unequal recombination, where a trade-off exists between the benefit of allelic diversity and the cost of copy abundance. Starting from the neutral case, where we showed that gene copy number is Gamma distributed at equilibrium, we derived also the mean and shape of the limiting distribution under selection. Considering a more general model, which includes variable population size and population substructure, we explored by simulations mean fitness and some summary statistics of the copy number distribution. We determined the relative effects of selection, recombination, and demographic parameters in maintaining allelic diversity and shaping the mean fitness of a population. One way to control the variance of copy number is by lowering the rate of unequal recombination. Indeed, when encoding recombination by a rate modifier locus, we observe exactly this prediction. Finally, we analyzed the empirical copy number distribution of 3 genes in human and estimated recombination and selection parameters of our model.
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Affiliation(s)
- Moritz Otto
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
| | - Yichen Zheng
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
| | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, Zülpicher Straße 47a, 50674 Köln, Germany
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106
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Simón D, Borsani O, Filippi CV. RFPDR: a random forest approach for plant disease resistance protein prediction. PeerJ 2022; 10:e11683. [PMID: 35480565 PMCID: PMC9037127 DOI: 10.7717/peerj.11683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 01/06/2023] Open
Abstract
Background Plant innate immunity relies on a broad repertoire of receptor proteins that can detect pathogens and trigger an effective defense response. Bioinformatic tools based on conserved domain and sequence similarity are within the most popular strategies for protein identification and characterization. However, the multi-domain nature, high sequence diversity and complex evolutionary history of disease resistance (DR) proteins make their prediction a real challenge. Here we present RFPDR, which pioneers the application of Random Forest (RF) for Plant DR protein prediction. Methods A recently published collection of experimentally validated DR proteins was used as a positive dataset, while 10x10 nested datasets, ranging from 400-4,000 non-DR proteins, were used as negative datasets. A total of 9,631 features were extracted from each protein sequence, and included in a full dimension (FD) RFPDR model. Sequence selection was performed, to generate a reduced-dimension (RD) RFPDR model. Model performances were evaluated using an 80/20 (training/testing) partition, with 10-cross fold validation, and compared to baseline, sequence-based and state-of-the-art strategies. To gain some insights into the underlying biology, the most discriminatory sequence-based features in the RF classifier were identified. Results and Discussion RD-RFPDR showed to be sensitive (86.4 ± 4.0%) and specific (96.9 ± 1.5%) for identifying DR proteins, while robust to data imbalance. Its high performance and robustness, added to the fact that RD-RFPDR provides valuable information related to DR proteins underlying properties, make RD-RFPDR an interesting approach for DR protein prediction, complementing the state-of-the-art strategies.
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Affiliation(s)
- Diego Simón
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay,Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay,Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Omar Borsani
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Carla Valeria Filippi
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
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107
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Discovery of Resistance Genes in Rye by Targeted Long-Read Sequencing and Association Genetics. Cells 2022; 11:cells11081273. [PMID: 35455953 PMCID: PMC9032263 DOI: 10.3390/cells11081273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 02/06/2023] Open
Abstract
The majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust resistance, we phenotyped a diverse panel of inbred lines from the less prevalent Gülzow germplasm using six distinct isolates of Puccinia recondita f. sp. secalis and found that 55 out of 92 lines were resistant to all isolates. By performing a genome-wide association study using 261,406 informative SNP markers, we identified five resistance-associated QTLs on chromosome arms 1RS, 1RL, 2RL, 5RL and 7RS. To identify candidate Puccinia recondita (Pr) resistance genes in these QTLs, we sequenced the rye nucleotide-binding leucine-rich repeat (NLR) intracellular immune receptor complement using a Triticeae NLR bait-library and PacBio® long-read single-molecule high-fidelity (HiFi) sequencing. Trait-genotype correlations across 10 resistant and 10 susceptible lines identified four candidate NLR-encoding Pr genes. One of these physically co-localized with molecular markers delimiting Pr3 on chromosome arm 1RS and the top-most resistance-associated QTL in the panel.
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108
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Avni R, Lux T, Minz‐Dub A, Millet E, Sela H, Distelfeld A, Deek J, Yu G, Steuernagel B, Pozniak C, Ens J, Gundlach H, Mayer KFX, Himmelbach A, Stein N, Mascher M, Spannagl M, Wulff BBH, Sharon A. Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:179-192. [PMID: 34997796 PMCID: PMC10138734 DOI: 10.1111/tpj.15664] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 05/20/2023]
Abstract
Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.
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Affiliation(s)
- Raz Avni
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Anna Minz‐Dub
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Eitan Millet
- Wise Faculty of Life Sciences, Institute for Cereal Crops ImprovementTel Aviv UniversityTel Aviv6997801Israel
| | - Hanan Sela
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Assaf Distelfeld
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
- Present address: Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of EvolutionUniversity of Haifa199 Aba Khoushy Ave., Mount CarmelHaifa3498838Israel
| | - Jasline Deek
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
| | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | | | - Curtis Pozniak
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Jennifer Ens
- Department of Plant Sciences and Crop Development Centre, College of Agriculture and BioresourcesUniversity of SaskatchewanCampus Drive 51SaskatoonS7N 5A8Canada
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
- Faculty of Life SciencesTechnical University MunichWeihenstephanMunichD‐80333Germany
| | - Axel Himmelbach
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Nils Stein
- Center of Integrated Breeding Research (CiBreed), Department of Crop SciencesGeorg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
| | - Martin Mascher
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 3Seeland06466Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigPuschstrasse 4LeipzigD‐04103Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB)Helmholtz‐Center MunichIngolstädter Landstraße 1NeuherbergD‐85764Germany
| | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Saudi Arabia
| | - Amir Sharon
- Wise Faculty of Life Sciences, Institute for Cereal Crops Improvement and School of Plant Sciences and Food SecurityTel Aviv UniversityTel Aviv6997801Israel
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109
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Cesari S, Xi Y, Declerck N, Chalvon V, Mammri L, Pugnière M, Henriquet C, de Guillen K, Chochois V, Padilla A, Kroj T. New recognition specificity in a plant immune receptor by molecular engineering of its integrated domain. Nat Commun 2022; 13:1524. [PMID: 35314704 PMCID: PMC8938504 DOI: 10.1038/s41467-022-29196-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPlant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that recognize pathogen effectors. Here, we show that molecular engineering of the integrated decoy domain (ID) of an NLR can extend its recognition spectrum to a new effector. We relied for this on detailed knowledge on the recognition of the Magnaporthe oryzae effectors AVR-PikD, AVR-Pia, and AVR1-CO39 by, respectively, the rice NLRs Pikp-1 and RGA5. Both receptors detect their effectors through physical binding to their HMA (Heavy Metal-Associated) IDs. By introducing into RGA5_HMA the AVR-PikD binding residues of Pikp-1_HMA, we create a high-affinity binding surface for this effector. RGA5 variants carrying this engineered binding surface perceive the new ligand, AVR-PikD, and still recognize AVR-Pia and AVR1-CO39 in the model plant N. benthamiana. However, they do not confer extended disease resistance specificity against M. oryzae in transgenic rice plants. Altogether, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs.
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110
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Qi X, Chen L, Zhang Y, Gao W, Chen L, Wang D, Tang L, Wang Z, Wang NN, Fan Z. Methoxyacrylate Fungicide Candidate CL-15C Also Functions as a Plant Elicitor in Arabidopsis thaliana and Oryza sativa L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3142-3150. [PMID: 35254068 DOI: 10.1021/acs.jafc.1c07757] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Unlike traditional fungicides targeting fungi, plant elicitors usually lack direct fungicidal activity but improve the plant immune system to resist fungi infection, which has gained increasing attention for better fungi resistance management and environment protection. (E)-methyl-2-(2-((((Z)-(amino-(3,4-dichloroisothiazol-5-yl)methylene)amino)oxy)methyl)phenyl)-2-(methoxyimino)acetate (CL-15C) was found to be a fungicide candidate with a broad spectrum. Here, we studied its immune-inducing ability and mechanism to strengthen the resistance of Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) and Oryza sativa L. against Magnaporthe oryzae. CL-15C promoted a 2.20- and 1.47-fold increase in phenylalanine ammonia-lyase (PAL) activity in A. thaliana and O. sativa, respectively. It also facilitated a 1.89- and 1.32-fold increase in accumulation of salicylic acid (SA) in A. thaliana and O. sativa, respectively. Differential genes were clustered in the SA signaling pathway at 24 h after a CL-15C treatment in A. thaliana. Because PAL is a rate-limiting enzyme in the phenylalanine metabolic pathway, after a CL-15C treatment, a pal1(PAL 1) mutant was more susceptible to Pst DC3000 when compared with the wild type. Bacterial counts in leaves after a CL-15C treatment showed a 1.11-fold reduction in the pal1 mutant and a 1.54-fold reduction in the wild type. The effect of CL-15C on the PAL enzyme activity and SA content was attenuated in the pal1 mutant. Present experimental data implied that the immune-inducing activity of CL-15C was dependent on PAL gene-mediated synthesis of SA.
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Affiliation(s)
- Xin Qi
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lei Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yue Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Wei Gao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lai Chen
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, P. R. China
| | - Dan Wang
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhihong Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Ning Ning Wang
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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111
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Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat Genet 2022; 54:342-348. [PMID: 35241824 PMCID: PMC8920897 DOI: 10.1038/s41588-022-01015-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
Abstract
Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding. Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding.
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Huang Z, Qiao F, Yang B, Liu J, Liu Y, Wulff BBH, Hu P, Lv Z, Zhang R, Chen P, Xing L, Cao A. Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq. BMC Genomics 2022; 23:118. [PMID: 35144544 PMCID: PMC8832786 DOI: 10.1186/s12864-022-08334-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/24/2022] [Indexed: 01/19/2023] Open
Abstract
Background Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. Results In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. Conclusion SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08334-w.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Fangyuan Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Boming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Zengshuai Lv
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Peidu Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
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Ence D, Smith KE, Fan S, Gomide Neves L, Paul R, Wegrzyn J, Peter GF, Kirst M, Brawner J, Nelson CD, Davis JM. NLR diversity and candidate fusiform rust resistance genes in loblolly pine. G3 GENES|GENOMES|GENETICS 2022; 12:6460333. [PMID: 34897455 PMCID: PMC9210285 DOI: 10.1093/g3journal/jkab421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently, single nucleotide polymorphism (SNP) markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for a nucleotide-binding site leucine-rich repeat (NLR) protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified 10 SNPs and 2 quantitative trait loci associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.
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Affiliation(s)
- Daniel Ence
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Katherine E Smith
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- USDA Forest Service, Southern Research, Southern Institute of Forest Genetics, Saucier, MS 39574, USA
| | - Shenghua Fan
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546, USA
- Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
| | | | - Robin Paul
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Gary F Peter
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - C Dana Nelson
- USDA Forest Service, Southern Research, Southern Institute of Forest Genetics, Saucier, MS 39574, USA
- USDA Forest Service, Southern Research Station, Forest Health Research and Education Center, Lexington, KY 40546, USA
| | - John M Davis
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
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Functional characterization of powdery mildew resistance gene MlIW172, a new Pm60 allele and its allelic variation in wild emmer wheat. J Genet Genomics 2022; 49:787-795. [DOI: 10.1016/j.jgg.2022.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022]
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115
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Maruta N, Burdett H, Lim BYJ, Hu X, Desa S, Manik MK, Kobe B. Structural basis of NLR activation and innate immune signalling in plants. Immunogenetics 2022; 74:5-26. [PMID: 34981187 PMCID: PMC8813719 DOI: 10.1007/s00251-021-01242-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
Animals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens and initiate innate immune responses. In plants, there are three types of NLRs distinguished by their N-terminal domain: the CC (coiled-coil) domain NLRs, the TIR (Toll/interleukin-1 receptor) domain NLRs and the RPW8 (resistance to powdery mildew 8)-like coiled-coil domain NLRs. CC-NLRs (CNLs) and TIR-NLRs (TNLs) generally act as sensors of effectors secreted by pathogens, while RPW8-NLRs (RNLs) signal downstream of many sensor NLRs and are called helper NLRs. Recent studies have revealed three dimensional structures of a CNL (ZAR1) including its inactive, intermediate and active oligomeric state, as well as TNLs (RPP1 and ROQ1) in their active oligomeric states. Furthermore, accumulating evidence suggests that members of the family of lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which are uniquely found in seed plants, play a key role in providing a link between sensor NLRs and helper NLRs during innate immune responses. Here, we summarize the implications of the plant NLR structures that provide insights into distinct mechanisms of action by the different sensor NLRs and discuss plant NLR-mediated innate immune signalling pathways involving the EDS1 family proteins and RNLs.
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Affiliation(s)
- Natsumi Maruta
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Bryan Y J Lim
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiahao Hu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sneha Desa
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammad Kawsar Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
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116
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Delplace F, Huard-Chauveau C, Berthomé R, Roby D. Network organization of the plant immune system: from pathogen perception to robust defense induction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:447-470. [PMID: 34399442 DOI: 10.1111/tpj.15462] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The plant immune system has been explored essentially through the study of qualitative resistance, a simple form of immunity, and from a reductionist point of view. The recent identification of genes conferring quantitative disease resistance revealed a large array of functions, suggesting more complex mechanisms. In addition, thanks to the advent of high-throughput analyses and system approaches, our view of the immune system has become more integrative, revealing that plant immunity should rather be seen as a distributed and highly connected molecular network including diverse functions to optimize expression of plant defenses to pathogens. Here, we review the recent progress made to understand the network complexity of regulatory pathways leading to plant immunity, from pathogen perception, through signaling pathways and finally to immune responses. We also analyze the topological organization of these networks and their emergent properties, crucial to predict novel immune functions and test them experimentally. Finally, we report how these networks might be regulated by environmental clues. Although system approaches remain extremely scarce in this area of research, a growing body of evidence indicates that the plant response to combined biotic and abiotic stresses cannot be inferred from responses to individual stresses. A view of possible research avenues in this nascent biology domain is finally proposed.
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Affiliation(s)
- Florent Delplace
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Carine Huard-Chauveau
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Richard Berthomé
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, 31326, France
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Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG. An Improved Assembly of the Albugo candida Ac2V Genome Reveals the Expansion of the "CCG" Class of Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:39-48. [PMID: 34546764 DOI: 10.1094/mpmi-04-21-0075-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Kate Bailey
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Department of Genetics, University of Córdoba, Córdoba 14071, Spain
| | - Christian Schudoma
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Eric B Holub
- University of Warwick, School of Life Sciences, Warwick Crop Centre, Wellesbourne, CV35 9EF, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
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118
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Pasin F, Daròs JA, Tzanetakis IE. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6534904. [PMID: 35195244 PMCID: PMC9249622 DOI: 10.1093/femsre/fuac011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.
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Affiliation(s)
- Fabio Pasin
- Corresponding author: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), UPV Building 8E, Ingeniero Fausto Elio, 46011 Valencia, Spain. E-mail:
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, AR, USA
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Cantó-Pastor A, Mason GA, Brady SM, Provart NJ. Arabidopsis bioinformatics: tools and strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1585-1596. [PMID: 34695270 DOI: 10.1111/tpj.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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121
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Recurrent expansions of B30.2-associated immune receptor families in fish. Immunogenetics 2021; 74:129-147. [PMID: 34850255 DOI: 10.1007/s00251-021-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.
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122
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Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.). Sci Rep 2021; 11:23057. [PMID: 34845285 PMCID: PMC8630102 DOI: 10.1038/s41598-021-02488-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
Powdery mildew is one of the most destructive diseases in the world, causing substantial grain yield losses and quality reduction in cereal crops. At present 23 powdery mildew resistance genes have been identified in rye, of which the majority are in wheat-rye translocation lines developed for wheat improvement. Here, we investigated the genetics underlying powdery mildew resistance in the Gülzow-type elite hybrid rye (Secale cereale L.) breeding germplasm. In total, 180 inbred breeding lines were genotyped using the state-of-the-art 600 K SNP array and phenotyped for infection type against three distinct field populations of B. graminis f. sp. secalis from Northern Germany (2013 and 2018) and Denmark (2020). We observed a moderate level of powdery mildew resistance in the non-restorer germplasm population, and by performing a genome-wide association study using 261,406 informative SNP markers, we identified a powdery mildew resistance locus, provisionally denoted PmNOS1, on the distal tip of chromosome arm 7RL. Using recent advances in rye genomic resources, we investigated whether nucleotide-binding leucine-rich repeat genes residing in the identified 17 Mbp block associated with PmNOS1 on recent reference genomes resembled known Pm genes.
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De la Concepcion JC, Vega Benjumea J, Bialas A, Terauchi R, Kamoun S, Banfield MJ. Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair. eLife 2021; 10:e71662. [PMID: 34783652 PMCID: PMC8631799 DOI: 10.7554/elife.71662] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Cooperation between receptors from the nucleotide-binding, leucine-rich repeats (NLR) superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses, whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.
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Affiliation(s)
- Juan Carlos De la Concepcion
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of SciencesViennaAustria
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
| | - Javier Vega Benjumea
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
- Servicio de Bioquímica-Análisis clínicos, Hospital Universitario Puerta de HierroMadridSpain
| | - Aleksandra Bialas
- The Sainsbury Laboratory, University of East AngliaNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CenterIwateJapan
- Laboratory of Crop Evolution, Graduate School of AgricultureKyotoJapan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East AngliaNorwichUnited Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
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Wang W, Chen L, Fengler K, Bolar J, Llaca V, Wang X, Clark CB, Fleury TJ, Myrvold J, Oneal D, van Dyk MM, Hudson A, Munkvold J, Baumgarten A, Thompson J, Cai G, Crasta O, Aggarwal R, Ma J. A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean. Nat Commun 2021; 12:6263. [PMID: 34741017 PMCID: PMC8571336 DOI: 10.1038/s41467-021-26554-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Phytophthora root and stem rot caused by P. sojae is a destructive soybean soil-borne disease found worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is a need to prevent the outbreak of the disease. Here, we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of large NLR genes of a single origin in soybean, and is derived from rounds of unequal recombination. Such events result in promoter fusion and LRR expansion that may contribute to the broad resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 in any of the non-Rps11-donor varieties examined, exemplifying innovative evolution of NLR genes and NLR gene clusters.
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Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Kevin Fengler
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Joy Bolar
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Victor Llaca
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Tomara J Fleury
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Crop Production and Pest Control Research Unit, USDA, ARS, West Lafayette, IN, 47907, USA
| | - Jon Myrvold
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - David Oneal
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | | | - Ashley Hudson
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Jesse Munkvold
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Andy Baumgarten
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Jeff Thompson
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Guohong Cai
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Crop Production and Pest Control Research Unit, USDA, ARS, West Lafayette, IN, 47907, USA
| | - Oswald Crasta
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
- R&D, Equinom, Inc., Indianapolis, IN, 46268, USA
| | - Rajat Aggarwal
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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125
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Bellucci E, Mario Aguilar O, Alseekh S, Bett K, Brezeanu C, Cook D, De la Rosa L, Delledonne M, Dostatny DF, Ferreira JJ, Geffroy V, Ghitarrini S, Kroc M, Kumar Agrawal S, Logozzo G, Marino M, Mary‐Huard T, McClean P, Meglič V, Messer T, Muel F, Nanni L, Neumann K, Servalli F, Străjeru S, Varshney RK, Vasconcelos MW, Zaccardelli M, Zavarzin A, Bitocchi E, Frontoni E, Fernie AR, Gioia T, Graner A, Guasch L, Prochnow L, Oppermann M, Susek K, Tenaillon M, Papa R. The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:646-660. [PMID: 34427014 PMCID: PMC9293105 DOI: 10.1111/tpj.15472] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 05/14/2023]
Abstract
Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Orlando Mario Aguilar
- Instituto de Biotecnología y Biología MolecularUNLP‐CONICETCCT La PlataLa PlataArgentina
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Kirstin Bett
- Department of Plant SciencesUniversity of Saskatchewan51 Campus DriveSaskatoonSKS7N 5A8Canada
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru LegumiculturăBacău600388Romania
| | - Douglas Cook
- Department of Plant PathologyUniversity of California DavisDavisCA95616‐8680USA
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Massimo Delledonne
- Department of BiotechnologyUniversity of VeronaStrada Le Grazie 15Verona37134Italy
| | - Denise F. Dostatny
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute‐NRIRadzikówBłonie05‐870Poland
| | - Juan J. Ferreira
- Regional Service for Agrofood Research and Development (SERIDA)Ctra AS‐267, PK 19VillaviciosaAsturias33300Spain
| | - Valérie Geffroy
- CNRSINRAEInstitute of Plant Sciences Paris‐Saclay (IPS2)Univ EvryUniversité Paris‐SaclayOrsay91405France
- CNRSINRAEInstitute of Plant Sciences Paris Saclay (IPS2)Université de ParisOrsay91405France
| | | | - Magdalena Kroc
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Shiv Kumar Agrawal
- Genetic Resources SectionInternational Center for Agricultural Research in the Dry AreasICARDAAgdal RabatMorocco
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Mario Marino
- International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA)Food and Agriculture Organization of the United Nations (FAO)Viale delle Terme di CaracallaRome00153Italy
| | - Tristan Mary‐Huard
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Phil McClean
- Department of Plant Sciences, Genomics and Bioinformatics ProgramNorth Dakota State UniversityFargoND58108USA
| | - Vladimir Meglič
- Crop Science DepartmentAgricultural Institute of SloveniaHacquetova ulica 17Ljubljana1000Slovenia
| | - Tamara Messer
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Frédéric Muel
- Terres InoviaInstitut Technique des oléagineux, des protéagineux eu du chanvren1 Av L. BrétignièresThiverval-Grignon78850France
| | - Laura Nanni
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Filippo Servalli
- Comunità del Mais Spinato di Gandino (MASP)Via XX Settembre, 5GandinoBergamo24024Italy
| | - Silvia Străjeru
- Suceava Genebank (BRGV)Bdul 1 Mai, nr. 17Suceava720224Romania
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi- Arid Tropics (ICRISAT)PatancheruIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Marta W. Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina – Laboratório AssociadoEscola Superior de BiotecnologiaUniversidade Católica PortuguesaRua Diogo Botelho 1327Porto4169-005Portugal
| | - Massimo Zaccardelli
- Council for Agricultural Research and EconomicsResearch Centre for Vegetable and Ornamental CropsVia Cavalleggeri 25Pontecagnano‐FaianoSA84098Italy
| | - Aleksei Zavarzin
- Federal Research CenterThe N.I. Vavilov All‐Russian Institute of Plant Genetic ResourcesSt. Petersburg190031Russia
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Emanuele Frontoni
- Department of Information EngineeringPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Luis Guasch
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Lena Prochnow
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Karolina Susek
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Maud Tenaillon
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
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126
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Song JM, Xie WZ, Wang S, Guo YX, Koo DH, Kudrna D, Gong C, Huang Y, Feng JW, Zhang W, Zhou Y, Zuccolo A, Long E, Lee S, Talag J, Zhou R, Zhu XT, Yuan D, Udall J, Xie W, Wing RA, Zhang Q, Poland J, Zhang J, Chen LL. Two gap-free reference genomes and a global view of the centromere architecture in rice. MOLECULAR PLANT 2021; 14:1757-1767. [PMID: 34171480 DOI: 10.1016/j.molp.2021.06.018] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xiong Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Chenbo Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Evan Long
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Joshua Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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127
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Gottin C, Dievart A, Summo M, Droc G, Périn C, Ranwez V, Chantret N. A new comprehensive annotation of leucine-rich repeat-containing receptors in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:492-508. [PMID: 34382706 PMCID: PMC9292849 DOI: 10.1111/tpj.15456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties.
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Affiliation(s)
- Céline Gottin
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Anne Dievart
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Marilyne Summo
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Gaëtan Droc
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Christophe Périn
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Vincent Ranwez
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
| | - Nathalie Chantret
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
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Castel B, Fairhead S, Furzer OJ, Redkar A, Wang S, Cevik V, Holub EB, Jones JDG. Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida race recognition specificities. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1490-1502. [PMID: 34181787 DOI: 10.1111/tpj.15396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR) genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Columbia (Col-0) provides resistance to many but not all white rust races, and encodes a nucleotide-binding, leucine-rich repeat immune receptor. Col-0 WRR4A resistance is broken by AcEx1, an isolate of A. candida. We identified an allele of WRR4A in Arabidopsis accession Øystese-0 (Oy-0) and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed in the oilseed crop Camelina sativa.
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Affiliation(s)
- Baptiste Castel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Genetics, University of Cordoba, 14071, Cordoba, Spain
| | - Shanshan Wang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, BA2 7AY, Bath, United Kingdom
| | - Eric B Holub
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
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Bi G, Zhou JM. Regulation of Cell Death and Signaling by Pore-Forming Resistosomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:239-263. [PMID: 33957051 DOI: 10.1146/annurev-phyto-020620-095952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) are the largest class of immune receptors in plants. They play a key role in the plant surveillance system by monitoring pathogen effectors that are delivered into the plant cell. Recent structural biology and biochemical analyses have uncovered how NLRs are activated to form oligomeric resistosomes upon the recognition of pathogen effectors. In the resistosome, the signaling domain of the NLR is brought to the center of a ringed structure to initiate immune signaling and regulated cell death (RCD). The N terminus of the coiled-coil (CC) domain of the NLR protein HOPZ-ACTIVATED RESISTANCE 1 likely forms a pore in the plasma membrane to trigger RCD in a way analogous to animal pore-forming proteins that trigger necroptosis or pyroptosis. NLRs that carry TOLL-INTERLEUKIN1-RECEPTOR as a signaling domain may also employ pore-forming resistosomes for RCD execution. In addition, increasing evidence supports intimate connections between NLRs and surface receptors in immune signaling. These new findings are rapidly advancing our understanding of the plant immune system.
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Affiliation(s)
- Guozhi Bi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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130
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Li L, Weigel D. One Hundred Years of Hybrid Necrosis: Hybrid Autoimmunity as a Window into the Mechanisms and Evolution of Plant-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:213-237. [PMID: 33945695 DOI: 10.1146/annurev-phyto-020620-114826] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hybrid necrosis in plants refers to a genetic autoimmunity syndrome in the progeny of interspecific or intraspecific crosses. Although the phenomenon was first documented in 1920, it has been unequivocally linked to autoimmunity only recently, with the discovery of the underlying genetic and biochemical mechanisms. The most common causal loci encode immune receptors, which are known to differ within and between species. One mechanism can be explained by the guard hypothesis, in which a guard protein, often a nucleotide-binding site-leucine-rich repeat protein, is activated by interaction with a plant protein that mimics standard guardees modified by pathogen effector proteins. Another surprising mechanism is the formation of inappropriately active immune receptor complexes. In this review, we summarize our current knowledge of hybrid necrosis and discuss how its study is not only informing the understanding of immune gene evolution but also revealing new aspects of plant immune signaling.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; ,
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; ,
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131
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Kahveci E, Devran Z, Özkaynak E, Hong Y, Studholme DJ, Tör M. Genomic-Assisted Marker Development Suitable for CsCvy-1 Selection in Cucumber Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:691576. [PMID: 34489994 PMCID: PMC8416629 DOI: 10.3389/fpls.2021.691576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 06/02/2023]
Abstract
Cucumber is a widely grown vegetable crop plant and a host to many different plant pathogens. Cucumber vein yellowing virus (CVYV) causes economic losses on cucumber crops in Mediterranean countries and in some part of India such as West Bengal and in African countries such as Sudan. CVYV is an RNA potyvirus transmitted mechanically and by whitefly (Bemisia tabaci) in a semipersistent manner. Control of this virus is heavily dependent on the management of the insect vector and breeding virus-resistant lines. DNA markers have been used widely in conventional plant breeding programs via marker-assisted selection (MAS). However, very few resistance sources against CVYV in cucumber exist, and also the lack of tightly linked molecular markers to these sources restricts the rapid generation of resistant lines. In this work, we used genomics coupled with the bulked segregant analysis method and generated the MAS-friendly Kompetitive allele specific PCR (KASP) markers suitable for CsCvy-1 selection in cucumber breeding using a segregating F2 mapping population and commercial plant lines. Variant analysis was performed to generate single-nucleotide polymorphism (SNP)-based markers for mapping the population and genotyping the commercial lines. We fine-mapped the region by generating new markers down to 101 kb with eight genes. We provided SNP data for this interval, which could be useful for breeding programs and cloning the candidate genes.
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Affiliation(s)
- Erdem Kahveci
- M.Y. Genetik Tarim Tek. Lab. Tic. Ltd. Sti., Antalya, Turkey
| | - Zübeyir Devran
- Department of Plant Protection, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - David J. Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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132
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Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance. Curr Issues Mol Biol 2021; 43:965-977. [PMID: 34449534 PMCID: PMC8929112 DOI: 10.3390/cimb43020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.
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133
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Kahlon PS, Stam R. Polymorphisms in plants to restrict losses to pathogens: From gene family expansions to complex network evolution. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102040. [PMID: 33882435 DOI: 10.1016/j.pbi.2021.102040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Genetic polymorphisms are the basis of the natural diversity seen in all life on earth, also in plant-pathogen interactions. Initially, studies on plant-pathogen interaction focused on reporting phenotypic variation in resistance properties and on the identification of underlying major genes. Nowadays, the field of plant-pathogen interactions is moving from focusing on families of single dominant genes involved in gene-for-gene interactions to an understanding of the plant immune system in the context of a much more complex signaling network and quantitative resistance. Simultaneously, studies on pathosystems from the wild and genome analyses advanced, revealing tremendous variation in natural plant populations. It is now imperative to place studies on genetic diversity and evolution of plant-pathogen interactions in the appropriate molecular biological, as well as evolutionary, context.
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Affiliation(s)
- Parvinderdeep S Kahlon
- TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Remco Stam
- TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany.
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134
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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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135
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Schultink A, Steinbrenner AD. A playbook for developing disease-resistant crops through immune receptor identification and transfer. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102089. [PMID: 34333377 DOI: 10.1016/j.pbi.2021.102089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/08/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Plants are resistant to most pathogens because of an immune system that perceives invading microbes and activates defense. A large repertoire of innate immune receptors mediates specific direct or indirect recognition of pathogen-derived molecules. Disease is often a consequence of insufficient immune surveillance, and the transfer of immune receptor genes from resistant plants to susceptible crop varieties is an effective strategy for combating disease outbreaks. We discuss approaches for identifying intracellular and cell surface immune receptors, with particular focus on recently developed and emerging methodologies. We also review considerations for the transfer of immune receptor genes into crop species, including additional host factors that may be required for immune receptor function. Together, these concepts lay out a broadly applicable playbook for developing crop varieties with durable disease resistance.
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136
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CEM, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:e66961. [PMID: 34288868 PMCID: PMC8294853 DOI: 10.7554/elife.66961] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Clare EM Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CentreIwateJapan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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137
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CE, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:66961. [PMID: 34288868 DOI: 10.1101/2021.01.26.428286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 05/21/2023] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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138
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Steidele CE, Stam R. Multi-omics approach highlights differences between RLP classes in Arabidopsis thaliana. BMC Genomics 2021; 22:557. [PMID: 34284718 PMCID: PMC8290556 DOI: 10.1186/s12864-021-07855-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/28/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The Leucine rich-repeat (LRR) receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others are involved in defence responses. However, functional data is currently only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function. RESULTS Using publicly available datasets, we annotated RLPs of unknown function as either likely defence-related or likely fulfilling a more basal function in plants. Then, using these categories, we can identify important characteristics that differ between the RLP subclasses. We found that the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic di versity of their individual members in accessible pan-genome data. CONCLUSIONS Our work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions on which RLPs can be identified as potential immune receptors using genetics tools and thereby complement disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.
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Affiliation(s)
- C E Steidele
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann- Straße 2, 85354, Freising, Germany
| | - R Stam
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann- Straße 2, 85354, Freising, Germany.
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139
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Safdari P, Höckerstedt L, Brosche M, Salojärvi J, Laine AL. Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata. FRONTIERS IN PLANT SCIENCE 2021; 12:675760. [PMID: 34322142 PMCID: PMC8311189 DOI: 10.3389/fpls.2021.675760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.
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Affiliation(s)
- Pezhman Safdari
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Layla Höckerstedt
- Climate System Research, Finnish Meteorological Institute, Helsinki, Finland
| | - Mikael Brosche
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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140
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Hafeez AN, Arora S, Ghosh S, Gilbert D, Bowden RL, Wulff BBH. Creation and judicious application of a wheat resistance gene atlas. MOLECULAR PLANT 2021; 14:1053-1070. [PMID: 33991673 DOI: 10.1016/j.molp.2021.05.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 05/18/2023]
Abstract
Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.
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Affiliation(s)
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - David Gilbert
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert L Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
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141
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Jayakodi M, Schreiber M, Stein N, Mascher M. Building pan-genome infrastructures for crop plants and their use in association genetics. DNA Res 2021; 28:6117190. [PMID: 33484244 PMCID: PMC7934568 DOI: 10.1093/dnares/dsaa030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/20/2022] Open
Abstract
Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Mona Schreiber
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Mascher
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Saxony, Germany
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142
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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143
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Badet T, Fouché S, Hartmann FE, Zala M, Croll D. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. Nat Commun 2021; 12:3551. [PMID: 34112792 PMCID: PMC8192914 DOI: 10.1038/s41467-021-23862-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere genome assemblies of a fungal pathogen of wheat to establish a nucleotide-level map of structural variation. We show that the recent emergence of pesticide resistance has been disproportionally driven by rearrangements. We use machine learning to train a model on structural variation events based on 30 chromosomal sequence features. We show that base composition and gene density are the major determinants of structural variation. Retrotransposons explain most inversion, indel and duplication events. We apply our model to Arabidopsis thaliana and show that our approach extends to more complex genomes. Finally, we analyze complete genomes of haploid offspring in a four-generation pedigree. Meiotic crossover locations are enriched for new rearrangements consistent with crossovers being mutational hotspots. The model trained on species-wide structural variation accurately predicts the position of >74% of newly generated variants along the pedigree. The predictive power highlights causality between specific sequence features and the induction of chromosomal rearrangements. Our work demonstrates that training sequence-derived models can accurately identify regions of intrinsic DNA instability in eukaryotic genomes.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Simone Fouché
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Marcello Zala
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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144
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Kim MS, Chae GY, Oh S, Kim J, Mang H, Kim S, Choi D. Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper. BMC PLANT BIOLOGY 2021; 21:247. [PMID: 34059006 PMCID: PMC8166135 DOI: 10.1186/s12870-021-03057-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper. RESULTS Here, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers. CONCLUSIONS Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.
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Affiliation(s)
- Myung-Shin Kim
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea
| | - Geun Young Chae
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea
| | - Soohyun Oh
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jihyun Kim
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyunggon Mang
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
| | - Doil Choi
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.
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145
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Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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146
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Prigozhin DM, Krasileva KV. Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites. THE PLANT CELL 2021; 33:998-1015. [PMID: 33561286 PMCID: PMC8226289 DOI: 10.1093/plcell/koab013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/28/2020] [Indexed: 05/21/2023]
Abstract
The evolution of recognition specificities by the immune system depends on the generation of receptor diversity and on connecting the binding of new antigens with the initiation of downstream signaling. In plant immunity, the innate Nucleotide-Binding Leucine-Rich Repeat (NLR) receptor family enables antigen binding and immune signaling. In this study, we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies that show high allelic diversity. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine-Rich Repeat domains, but the locations of the clusters vary among NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for the emergence of direct and indirect pathogen-sensing receptors and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and can inform NLR engineering efforts.
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147
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Van Dingenen J. Intraspecies diversity in immune receptors: recurring patterns of evolution point to functional residues. THE PLANT CELL 2021; 33:788-789. [PMID: 35234970 PMCID: PMC8226281 DOI: 10.1093/plcell/koab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Judith Van Dingenen
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
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148
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Baduel P, Leduque B, Ignace A, Gy I, Gil J, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol 2021; 22:138. [PMID: 33957946 PMCID: PMC8101250 DOI: 10.1186/s13059-021-02348-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leverage publicly available multi-omic and bio-climatic data for more than 1000 wild Arabidopsis thaliana accessions to determine the rate of transposable element (TE) mobilization and its potential to create adaptive variation in natural settings. RESULTS We demonstrate that TE insertions arise at almost the same rate as base substitutions. Mobilization activity of individual TE families varies greatly between accessions, in association with genetic and environmental factors as well as through complex gene-environment interactions. Although the distribution of TE insertions across the genome is ultimately shaped by purifying selection, reflecting their typically strong deleterious effects when located near or within genes, numerous recent TE-containing alleles show signatures of positive selection. Moreover, high rates of transposition appear positively selected at the edge of the species' ecological niche. Based on these findings, we predict through mathematical modeling higher transposition activity in Mediterranean regions within the next decades in response to global warming, which in turn should accelerate the creation of large-effect alleles. CONCLUSIONS Our study reveals that TE mobilization is a major generator of genetic variation in A. thaliana that is finely modulated by genetic and environmental factors. These findings and modeling indicate that TEs may be essential genomic players in the demise or rescue of native populations in times of climate crises.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Basile Leduque
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Amandine Ignace
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - José Gil
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
- Present Address: Institut Curie, 26 rue d'Ulm, 75005, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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149
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Ordon J, Martin P, Erickson JL, Ferik F, Balcke G, Bonas U, Stuttmann J. Disentangling cause and consequence: genetic dissection of the DANGEROUS MIX2 risk locus, and activation of the DM2h NLR in autoimmunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1008-1023. [PMID: 33629456 DOI: 10.1111/tpj.15215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding domain-leucine-rich repeat-type immune receptors (NLRs) protect plants against pathogenic microbes through intracellular detection of effector proteins. However, this comes at a cost, as NLRs can also induce detrimental autoimmunity in genetic interactions with foreign alleles. This may occur when independently evolved genomes are combined in inter- or intraspecific crosses, or when foreign alleles are introduced by mutagenesis or transgenesis. Most autoimmunity-inducing NLRs are encoded within highly variable NLR gene clusters with no known immune functions, which were termed autoimmune risk loci. Whether risk NLRs differ from sensor NLRs operating in natural pathogen resistance and how risk NLRs are activated in autoimmunity is unknown. Here, we analyzed the DANGEROUS MIX2 risk locus, a major autoimmunity hotspot in Arabidopsis thaliana. By gene editing and heterologous expression, we show that a single gene, DM2h, is necessary and sufficient for autoimmune induction in three independent cases of autoimmunity in accession Landsberg erecta. We focus on autoimmunity provoked by an EDS1-yellow fluorescent protein (YFP)NLS fusion protein to characterize DM2h functionally and determine features of EDS1-YFPNLS activating the immune receptor. Our data suggest that risk NLRs function in a manner reminiscent of sensor NLRs, while autoimmunity-inducing properties of EDS1-YFPNLS in this context are unrelated to the protein's functions as an immune regulator. We propose that autoimmunity, at least in some cases, may be caused by spurious, stochastic interactions of foreign alleles with coincidentally matching risk NLRs.
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Affiliation(s)
- Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Patrick Martin
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jessica Lee Erickson
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Filiz Ferik
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
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150
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Liu Y, Zhang X, Han K, Li R, Xu G, Han Y, Cui F, Fan S, Seim I, Fan G, Li G, Wan S. Insights into amphicarpy from the compact genome of the legume Amphicarpaea edgeworthii. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:952-965. [PMID: 33236503 PMCID: PMC8131047 DOI: 10.1111/pbi.13520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Amphicarpy (seed heteromorphy) is a unique and fascinating reproductive strategy wherein a single plant produces both aerial and subterranean fruits. This strategy is believed to be an adaptation to life under stressful or uncertain environments. Here, we sequenced and de novo assembled a chromosome-level genome assembly of the legume Amphicarpaea edgeworthii Benth. The 299-Mb A. edgeworthii genome encodes 27 899 protein-coding genes and is the most compact sequenced legume genome reported until date. Its reduced genome size may be attributed to the reduced long-terminal repeat retrotransposon content, which stems from the unequal homologous recombination. Gene families related to immunity and stress resistance have been contracted in A. edgeworthii, which is consistent with the notion that the amphicarpic reproductive strategy may be a complementary mechanism for its weak environmental-adaptation ability. We demonstrated the 'ABCE' model for the differentiation of chasmogamous and cleistogamous flowers. In addition, the characteristics of aerial and subterranean seeds in hard-seededness were explored. Thus, we suggest that the A. edgeworthii genome, which is the first of an amphicarpic plant, offers significant insights into its unusual reproductive strategy that is a key resource towards comprehending the evolution of angiosperms.
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Affiliation(s)
- Yiyang Liu
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Xuejie Zhang
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Kai Han
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | - Rongchong Li
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Guoxin Xu
- Shandong Rice Research InstituteShandong Academy of Agricultural SciencesJi’nanChina
| | - Yan Han
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Feng Cui
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Inge Seim
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Guangyi Fan
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- BGI‐ShenzhenShenzhenChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Guowei Li
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Shubo Wan
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
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