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Goh FJ, Huang CY, Derevnina L, Wu CH. NRC Immune receptor networks show diversified hierarchical genetic architecture across plant lineages. THE PLANT CELL 2024; 36:3399-3418. [PMID: 38922300 PMCID: PMC11371147 DOI: 10.1093/plcell/koae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/28/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Plants' complex immune systems include nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins, which help recognize invading pathogens. In solanaceous plants, the NRC (NLR required for cell death) family includes helper NLRs that form a complex genetic network with multiple sensor NLRs to provide resistance against pathogens. However, the evolution and function of NRC networks outside solanaceous plants are currently unclear. Here, we conducted phylogenomic and macroevolutionary analyses comparing NLRs identified from different asterid lineages and found that NRC networks expanded significantly in most lamiids but not in Ericales and campanulids. Using transient expression assays in Nicotiana benthamiana, we showed that NRC networks are simple in Ericales and campanulids, but have high complexity in lamiids. Phylogenetic analyses grouped the NRC helper NLRs into three NRC0 subclades that are conserved, and several family-specific NRC subclades of lamiids that show signatures of diversifying selection. Functional analyses revealed that members of the NRC0 subclades are partially interchangeable, whereas family-specific NRC members in lamiids lack interchangeability. Our findings highlight the distinctive evolutionary patterns of the NRC networks in asterids and provide potential insights into transferring disease resistance across plant lineages.
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Affiliation(s)
- Foong-Jing Goh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 115201, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 402202, Taiwan
| | - Ching-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Lida Derevnina
- Crop Science Centre, Department of Plant Science, University of Cambridge, Cambridge CB3 0LE, UK
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei 115201, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 402202, Taiwan
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2
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Einspanier S, Tominello-Ramirez C, Hasler M, Barbacci A, Raffaele S, Stam R. High-Resolution Disease Phenotyping Reveals Distinct Resistance Mechanisms of Tomato Crop Wild Relatives against Sclerotinia sclerotiorum. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0214. [PMID: 39105186 PMCID: PMC11298253 DOI: 10.34133/plantphenomics.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 08/07/2024]
Abstract
Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR's genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host's genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.
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Affiliation(s)
- Severin Einspanier
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
| | - Christopher Tominello-Ramirez
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
| | - Mario Hasler
- Lehrfach Variationsstatistik, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, Kiel, 24118 Kiel, Germany
| | - Adelin Barbacci
- Laboratoire des Interactions Plantes Microorganismes Environnement (LIPME), INRAE, CNRS, Castanet Tolosan Cedex, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Microorganismes Environnement (LIPME), INRAE, CNRS, Castanet Tolosan Cedex, France
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences,
Christian-Albrechts-University, 24118 Kiel, Germany
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3
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Amaral DT, Bonatelli IAS, Romeiro-Brito M, Telhe MC, Moraes EM, Zappi DC, Taylor NP, Franco FF. Comparative transcriptome analysis reveals lineage- and environment-specific adaptations in cacti from the Brazilian Atlantic Forest. PLANTA 2024; 260:4. [PMID: 38775846 DOI: 10.1007/s00425-024-04442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/14/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Natural selection influenced adaptive divergence between Cereus fernambucensis and Cereus insularis, revealing key genes governing abiotic stress responses and supporting neoteny in C. insularis. Uncovering the molecular mechanisms driving adaptive divergence in traits related to habitat adaptation remains a central challenge. In this study, we focused on the cactus clade, which includes Cereus sericifer F.Ritter, Cereus fernambucensis Lem., and Cereus insularis Hemsley. These allopatric species inhabit distinct relatively drier regions within the Brazilian Atlantic Forest, each facing unique abiotic conditions. We leveraged whole transcriptome data and abiotic variables datasets to explore lineage-specific and environment-specific adaptations in these species. Employing comparative phylogenetic methods, we identified genes under positive selection (PSG) and examined their association with non-synonymous genetic variants and abiotic attributes through a PhyloGWAS approach. Our analysis unveiled signatures of selection in all studied lineages, with C. fernambucensis northern populations and C. insularis showing the most PSGs. These PSGs predominantly govern abiotic stress regulation, encompassing heat tolerance, UV stress response, and soil salinity adaptation. Our exclusive observation of gene expression tied to early developmental stages in C. insularis supports the hypothesis of neoteny in this species. We also identified genes associated with abiotic variables in independent lineages, suggesting their role as environmental filters on genetic diversity. Overall, our findings suggest that natural selection played a pivotal role in the geographic range of these species in response to environmental and biogeographic transitions.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Monique Romeiro-Brito
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Daniela Cristina Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), Brasília, Brazil
| | - Nigel Paul Taylor
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, SP 264, Sorocaba, 18052-780, Brazil.
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4
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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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5
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Locci F, Parker JE. Plant NLR immunity activation and execution: a biochemical perspective. Open Biol 2024; 14:230387. [PMID: 38262605 PMCID: PMC10805603 DOI: 10.1098/rsob.230387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.
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Affiliation(s)
- Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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6
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Schmey T, Small C, Einspanier S, Hoyoz LM, Ali T, Gamboa S, Mamani B, Sepulveda GC, Thines M, Stam R. Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species. Environ Microbiol 2023; 25:1830-1846. [PMID: 37171093 DOI: 10.1111/1462-2920.16394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.
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Affiliation(s)
- Tamara Schmey
- Chair of Phytopathology, TUM School of Life Science, Technische Universität München, Freising-Weihenstephan, Germany
| | - Corinn Small
- Chair of Phytopathology, TUM School of Life Science, Technische Universität München, Freising-Weihenstephan, Germany
| | - Severin Einspanier
- Department for Phytopathology and Crop Protection, Institute for Phytopathology, Faculty of Agricultural and Nutritional Sciences, Christian Albrechts University, Kiel, Germany
| | - Lina Muñoz Hoyoz
- Chair of Phytopathology, TUM School of Life Science, Technische Universität München, Freising-Weihenstephan, Germany
| | - Tahir Ali
- Translational Biodiversity Genomics Centre, Senckenberg Institute, Frankfurt am Main, Germany
- Institute of Plant Sciences, University of Cologne, Cologne, Germany
| | - Soledad Gamboa
- Plant Pathology and Bacteriology, International Potato Centre, Lima, Peru
| | - Betty Mamani
- Instituto Basadre de Investigación en Agrobiotecnología y Recursos Genéticos, Escuela de Agronomía, Facultad Ciencias Agropecuarias, Universidad Nacional Jorge Basadre Grohmann, Tacna, Peru
| | - German C Sepulveda
- Departmento de recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Arapacá, Arica, Chile
| | - Marco Thines
- Translational Biodiversity Genomics Centre, Senckenberg Institute, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Department of Biology, Institute of Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Remco Stam
- Department for Phytopathology and Crop Protection, Institute for Phytopathology, Faculty of Agricultural and Nutritional Sciences, Christian Albrechts University, Kiel, Germany
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7
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Adachi H, Sakai T, Kourelis J, Pai H, Gonzalez Hernandez JL, Utsumi Y, Seki M, Maqbool A, Kamoun S. Jurassic NLR: Conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. THE PLANT CELL 2023; 35:3662-3685. [PMID: 37467141 PMCID: PMC10533333 DOI: 10.1093/plcell/koad175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/21/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors generally exhibit hallmarks of rapid evolution, even at the intraspecific level. We used iterative sequence similarity searches coupled with phylogenetic analyses to reconstruct the evolutionary history of HOPZ-ACTIVATED RESISTANCE1 (ZAR1), an atypically conserved NLR that traces its origin to early flowering plant lineages ∼220 to 150 million yrs ago (Jurassic period). We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colocasia esculenta, the magnoliid Cinnamomum micranthum, and most eudicots, notably the Ranunculales species Aquilegia coerulea, which is outside the core eudicots. Ortholog sequence analyses revealed highly conserved features of ZAR1, including regions for pathogen effector recognition and cell death activation. We functionally reconstructed the cell death activity of ZAR1 and its partner receptor-like cytoplasmic kinase (RLCK) from distantly related plant species, experimentally validating the hypothesis that ZAR1 evolved to partner with RLCKs early in its evolution. In addition, ZAR1 acquired novel molecular features. In cassava (Manihot esculenta) and cotton (Gossypium spp.), ZAR1 carries a C-terminal thioredoxin-like domain, and in several taxa, ZAR1 duplicated into 2 paralog families, which underwent distinct evolutionary paths. ZAR1 stands out among angiosperm NLR genes for having experienced relatively limited duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 also gave rise to noncanonical NLRs with integrated domains and degenerated molecular features.
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Affiliation(s)
- Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jose L Gonzalez Hernandez
- Agronomy, Horticulture and Plant Sciences Department, South Dakota State University, Brookings, SD 57007, USA
| | - Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
| | - Abbas Maqbool
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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8
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Kahlon PS, Förner A, Muser M, Oubounyt M, Gigl M, Hammerl R, Baumbach J, Hückelhoven R, Dawid C, Stam R. Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3240-3254. [PMID: 36880316 DOI: 10.1093/jxb/erad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/06/2023] [Indexed: 05/21/2023]
Abstract
Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.
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Affiliation(s)
- Parvinderdeep S Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Andrea Förner
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Michael Muser
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Mhaned Oubounyt
- Research Group of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Richard Hammerl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Jan Baumbach
- Research Group of Computational Systems Biology, University of Hamburg, Notkestrasse 9, 22607, Hamburg, Germany
- Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute for Phytopathology, Kiel University, Hermann Rodewald Str 9, 24118 Kiel, Germany
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9
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Wei K, Silva-Arias GA, Tellier A. Selective sweeps linked to the colonization of novel habitats and climatic changes in a wild tomato species. THE NEW PHYTOLOGIST 2023; 237:1908-1921. [PMID: 36419182 DOI: 10.1111/nph.18634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Positive selection is the driving force underpinning local adaptation and leaves footprints of selective sweeps on the underlying major genes. Quantifying the timing of selection and revealing the genetic bases of adaptation in plant species occurring in steep and varying environmental gradients are crucial to predict a species' ability to colonize new niches. We use whole-genome sequence data from six populations across three different habitats of the wild tomato species Solanum chilense to infer the past demographic history and search for genes under strong positive selection. We then correlate current and past climatic projections with the demographic history, allele frequencies, the age of selection events and distribution shifts. Several selective sweeps occur at regulatory networks involved in root-hair development in low altitude and response to photoperiod and vernalization in high-altitude populations. These sweeps appear to occur in a concerted fashion in a given regulatory gene network at particular periods of substantial climatic change. Using a unique combination of genome scans and modelling of past climatic data, we quantify the timing of selection at genes likely underpinning local adaptation to semiarid habitats.
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Affiliation(s)
- Kai Wei
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
| | - Gustavo A Silva-Arias
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Liesel-Beckmann Strasse 2, 85354, Freising, Germany
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10
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Rogozina EV, Gurina AA, Chalaya NA, Zoteyeva NM, Kuznetsova MA, Beketova MP, Muratova OA, Sokolova EA, Drobyazina PE, Khavkin EE. Diversity of Late Blight Resistance Genes in the VIR Potato Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:273. [PMID: 36678985 PMCID: PMC9862067 DOI: 10.3390/plants12020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Late blight (LB) caused by the oomycete Phytophthora infestans (Mont.) de Bary is the greatest threat to potato production worldwide. Current potato breeding for LB resistance heavily depends on the introduction of new genes for resistance to P. infestans (Rpi genes). Such genes have been discovered in highly diverse wild, primitive, and cultivated species of tuber-bearing potatoes (Solanum L. section Petota Dumort.) and introgressed into the elite potato cultivars by hybridization and transgenic complementation. Unfortunately, even the most resistant potato varieties have been overcome by LB due to the arrival of new pathogen strains and their rapid evolution. Therefore, novel sources for germplasm enhancement comprising the broad-spectrum Rpi genes are in high demand with breeders who aim to provide durable LB resistance. The Genbank of the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg harbors one of the world's largest collections of potato and potato relatives. In this study, LB resistance was evaluated in a core selection representing 20 species of seven Petota series according to the Hawkes (1990) classification: Bulbocastana (Rydb.) Hawkes, Demissa Buk., Longipedicellata Buk., Maglia Bitt., Pinnatisecta (Rydb.) Hawkes, Tuberosa (Rydb.) Hawkes (wild and cultivated species), and Yungasensa Corr. LB resistance was assessed in 96 accessions representing 18 species in the laboratory test with detached leaves using a highly virulent and aggressive isolate of P. infestans. The Petota species notably differed in their LB resistance: S. bulbocastanum Dun., S. demissum Lindl., S. cardiophyllum Lindl., and S. berthaultii Hawkes stood out at a high frequency of resistant accessions (7-9 points on a 9-point scale). Well-established specific SCAR markers of ten Rpi genes-Rpi-R1, Rpi-R2/Rpi-blb3, Rpi-R3a, Rpi-R3b, Rpi-R8, Rpi-blb1/Rpi-sto1, Rpi-blb2, and Rpi-vnt1-were used to mine 117 accessions representing 20 species from seven Petota series. In particular, our evidence confirmed the diverse Rpi gene location in two American continents. The structural homologs of the Rpi-R2, Rpi-R3a, Rpi-R3b, and Rpi-R8 genes were found in the North American species other than S. demissum, the species that was the original source of these genes for early potato breeding, and in some cases, in the South American Tuberosa species. The Rpi-blb1/Rpi-sto1 orthologs from S. bulbocastanum and S. stoloniferum Schlechtd et Bché were restricted to genome B in the Mesoamerican series Bulbocastana, Pinnatisecta, and Longipedicellata. The structural homologs of the Rpi-vnt1 gene that were initially identified in the South American species S. venturii Hawkes and Hjert. were reported, for the first time, in the North American series of Petota species.
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Affiliation(s)
- Elena V. Rogozina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Alyona A. Gurina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda A. Chalaya
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda M. Zoteyeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | | | | | | | | | | | - Emil E. Khavkin
- Institute of Agricultural Biotechnology, Moscow 127550, Russia
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11
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Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
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Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
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12
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Adachi H, Kamoun S. NLR receptor networks in plants. Essays Biochem 2022; 66:541-549. [PMID: 35593644 DOI: 10.1042/ebc20210075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/17/2022]
Abstract
To fight off diverse pathogens and pests, the plant immune system must recognize these invaders; however, as plant immune receptors evolve to recognize a pathogen, the pathogen often evolves to escape this recognition. Plant-pathogen co-evolution has led to the vast expansion of a family of intracellular immune receptors-nucleotide-binding domain and leucine-rich repeat proteins (NLRs). When an NLR receptor recognizes a pathogen ligand, it activates immune signaling and thus initiates defense responses. However, in contrast with the model of NLRs acting individually to activate resistance, an emerging paradigm holds that plants have complex receptor networks where the large repertoire of functionally specialized NLRs function together to act against the large repertoire of rapidly evolving pathogen effectors. In this article, we highlight key aspects of immune receptor networks in plant NLR biology and discuss NLR network architecture, the advantages of this receptor network system, and the evolution of the NLR network in asterid plants.
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Affiliation(s)
- Hiroaki Adachi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Mozume, Muko, Kyoto 617-0001, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK
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13
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Evolution of resistance (R) gene specificity. Essays Biochem 2022; 66:551-560. [PMID: 35612398 DOI: 10.1042/ebc20210077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
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14
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Särkinen T, Gagnon E, Knapp S. Out of the wild: the wild (and often weedy) roots of our crops. THE NEW PHYTOLOGIST 2022; 234:1107-1108. [PMID: 35383934 DOI: 10.1111/nph.18107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Edeline Gagnon
- Chair of Phytopathology, TUM School of Life Sciences, Technische Universität München, Freising 85354, Germany
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
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15
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Ke L, Yan WY, Zhang LZ, Zeng ZJ, Evans JD, Huang Q. Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae. MICROBIAL ECOLOGY 2022; 83:1105-1111. [PMID: 34342699 DOI: 10.1007/s00248-021-01827-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.
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Affiliation(s)
- Li Ke
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Wei Yu Yan
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Li Zhen Zhang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Zhi Jiang Zeng
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China
| | - Jay D Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, 20705, USA
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Zhimin Ave. 1101, Nanchang, 330045, China.
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16
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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Kahlon PS, Verin M, Hückelhoven R, Stam R. Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans. Ecol Evol 2021; 11:7768-7778. [PMID: 34188850 PMCID: PMC8216925 DOI: 10.1002/ece3.7610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 01/01/2023] Open
Abstract
The wild tomato species Solanum chilense is divided into geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype versus pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance can be observed between but also within populations at the level of individual plants. Our data also did not reveal complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggests that the observed quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is the result of basal defense responses that depend on the host genotype and are pathogen isolate-unspecific.
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Affiliation(s)
| | - Melissa Verin
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Ralph Hückelhoven
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Remco Stam
- TUM School of Life SciencesTechnical University of MunichFreisingGermany
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24
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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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25
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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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26
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O'Hara NB, Franks SJ, Kane NC, Tittes S, Rest JS. Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. BMC Ecol Evol 2021; 21:61. [PMID: 33882815 PMCID: PMC8060997 DOI: 10.1186/s12862-021-01789-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
Background Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the underlying genetic basis of this evolution. To address this, we took advantage of a historical seed collection of a Brassica rapa population, which we previously demonstrated evolved an increase in disease susceptibility to a necrotrophic fungal pathogen following a drought. Results Previously, we combined a resurrection experiment with genome-wide sequencing of 124 pooled ancestral and descendant plants. Here, using these previously generated sequence data (Franks et al. in Mol Ecol 25(15):3622–3631, 2016), we show that well-characterized necrotrophic fungal pathogen response (NFPR) genes have evolved, as indicated by changes in allele frequency, between ancestors and descendants, with several of them identified as extreme FST outliers. The jasmonic acid (JA) signaling pathway in particular seems to underlie the evolution of disease susceptibility, in addition to its well characterized role in plastic disease response. We identify a list of 260 genes that are both NFPR genes and are differentially expressed in response to drought, based on publicly available data. We present evidence that five of these genes evolved between ancestors and descendants, suggesting that the drought acted as the evolutionary driver, and that the accompanying increase in disease susceptibility may have been a consequence of genetic pleiotropy. Conclusions Our study provides evidence that for this population, standing variation in NFPR genes is affected by natural selection related to climate change. Our results reveal potentially important candidates that may underlie trait evolution in both crops and natural systems. Additionally, this trade-off between adaptation to biotic and abiotic stresses is an example of how climate change can have diverse and unexpected consequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01789-7.
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Affiliation(s)
- Niamh B O'Hara
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY, 10011, USA. .,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA. .,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Steven J Franks
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Nolan C Kane
- Department of Ecology and Evolution, The University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Silas Tittes
- Department of Ecology and Evolution, The University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
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27
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Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, Stam R, van Oosterhout C, Fairhead S, Heal R, Cocker JM, Bhanvadia S, Barrett W, Wu CH, Adachi H, Song T, Kamoun S, Vleeshouwers VGAA, Tomlinson L, Wulff BBH, Jones JDG. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. NATURE PLANTS 2021; 7:198-208. [PMID: 33574576 PMCID: PMC7116783 DOI: 10.1038/s41477-021-00854-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Affiliation(s)
- Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- US Department of Agriculture-Agricultural Research Service, Madison, WI, USA
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Bayer Crop Science, Chesterfield, MO, USA
| | - Agnieszka I Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Remco Stam
- Phytopathology, Technical University Munich, Freising, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan M Cocker
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- University of Hull, Hull, UK
| | - Shivani Bhanvadia
- Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
| | - William Barrett
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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28
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Andolfo G, D’Agostino N, Frusciante L, Ercolano MR. The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies. Genes (Basel) 2021; 12:genes12020184. [PMID: 33514027 PMCID: PMC7911644 DOI: 10.3390/genes12020184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.
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29
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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Kahlon PS, Seta SM, Zander G, Scheikl D, Hückelhoven R, Joosten MHAJ, Stam R. Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance. Proc Biol Sci 2020; 287:20202723. [PMID: 33352079 DOI: 10.1098/rspb.2020.2723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Natural plant populations encounter strong pathogen pressure and defence-associated genes are known to be under selection dependent on the pressure by the pathogens. Here, we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene-mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene-mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.
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Affiliation(s)
- Parvinderdeep S Kahlon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Shallet Mindih Seta
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Gesche Zander
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Daniela Scheikl
- Section of Population Genetics, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann Str. 2, 85354 Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354 Freising, Germany
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Seong K, Seo E, Witek K, Li M, Staskawicz B. Evolution of NLR resistance genes with noncanonical N-terminal domains in wild tomato species. THE NEW PHYTOLOGIST 2020; 227:1530-1543. [PMID: 32344448 DOI: 10.1111/nph.16628] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
Nucleotide-binding and leucine-rich repeat immune receptors (NLRs) provide resistance against diverse pathogens. To create comparative NLR resources, we conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real-time sequencing of PacBio for 18 accessions in Solanaceae, including 15 accessions of five wild tomato species. We investigated the evolution of a class of NLRs, CNLs with extended N-terminal sequences previously named Solanaceae Domain. Through comparative genomic analysis, we revealed that the extended CNLs (exCNLs) anciently emerged in the most recent common ancestor between Asterids and Amaranthaceae, far predating the Solanaceae family. In tomatoes, the exCNLs display exceptional modes of evolution in a clade-specific manner. In the clade G3, exCNLs have substantially elongated their N-termini through tandem duplications of exon segments. In the clade G1, exCNLs have evolved through recent proliferation and sequence diversification. In the clade G6, an ancestral exCNL has lost its N-terminal domains in the course of evolution. Our study provides high-quality NLR gene models for close relatives of domesticated tomatoes that can serve as a useful resource for breeding and molecular engineering for disease resistance. Our findings regarding the exCNLs offer unique backgrounds and insights for future functional studies of the NLRs.
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Affiliation(s)
- Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Eunyoung Seo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Meng Li
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
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32
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Lee RR, Chae E. Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes. PLANT COMMUNICATIONS 2020; 1:100089. [PMID: 33367252 PMCID: PMC7747988 DOI: 10.1016/j.xplc.2020.100089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 05/04/2023]
Abstract
The nucleotide-binding domain and leucine-rich repeat (NLR) gene family is highly expanded in the plant lineage with extensive sequence and structure polymorphisms. To survey the landscape of NLR expansion, we mined the published long-read data generated by the resistance gene enrichment sequencing of 64 diverse Arabidopsis thaliana accessions. We found that the hot spots of massive multi-gene NLR cluster expansion did not typically span the whole cluster; instead, they were restricted to a handful of, or only one, dominant radiation(s). All sequences in such a radiation were distinct from other genes in the cluster but not from each other in the clade, making it difficult to assign trustworthy reference-based orthologies when multiple reference genes were present in the radiation. Consequently, NLR genes can be broadly divided into two types: radiating or high-fidelity, where high-fidelity genes are well conserved and well separated from other clades. A similar distinction could be made for NLR clusters, depending on whether cluster size was determined primarily by extensive radiation or the presence of numerous high-fidelity genes. We also identified groups of well-conserved NLR clades that were missing from the Columbia-0 reference genome. This suggests that the classification of NLRs using gene IDs from a single reference accession can rarely capture all major paralogs in a cluster accurately and representatively and that a reference-agnostic perspective is required to properly characterize these additional variations. Finally, we present a quantitative visualization method for differentiating these situations in a given clade of interest.
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Affiliation(s)
- Rachelle R.Q. Lee
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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33
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Baggs EL, Monroe JG, Thanki AS, O'Grady R, Schudoma C, Haerty W, Krasileva KV. Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Coevolved Components of Plant Immunity and Drought Response. THE PLANT CELL 2020; 32:2158-2177. [PMID: 32409319 PMCID: PMC7346574 DOI: 10.1105/tpc.19.00903] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 05/19/2023]
Abstract
Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived molecules and activate downstream signaling pathways. We analyzed the variation in NLR gene copy number and identified plants with a low number of NLR genes relative to sister species. We specifically focused on four plants from two distinct lineages, one monocot lineage (Alismatales) and one eudicot lineage (Lentibulariaceae). In these lineages, the loss of NLR genes coincides with loss of the well-known downstream immune signaling complex ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)/PHYTOALEXIN DEFICIENT 4 (PAD4). We expanded our analysis across whole proteomes and found that other characterized immune genes were absent only in Lentibulariaceae and Alismatales. Additionally, we identified genes of unknown function that were convergently lost together with EDS1/PAD4 in five plant species. Gene expression analyses in Arabidopsis (Arabidopsis thaliana) and Oryza sativa revealed that several homologs of the candidates are differentially expressed during pathogen infection, drought, and abscisic acid treatment. Our analysis provides evolutionary evidence for the rewiring of plant immunity in some plant lineages, as well as the coevolution of the EDS1/PAD4 pathway and drought responses.
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Affiliation(s)
- Erin L Baggs
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- University of California Berkeley, Berkeley, California 94720
| | - J Grey Monroe
- University of California Davis, Davis, California 95616
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anil S Thanki
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Ruby O'Grady
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Christian Schudoma
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Ksenia V Krasileva
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- University of California Berkeley, Berkeley, California 94720
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Sucher J, Mbengue M, Dresen A, Barascud M, Didelon M, Barbacci A, Raffaele S. Phylotranscriptomics of the Pentapetalae Reveals Frequent Regulatory Variation in Plant Local Responses to the Fungal Pathogen Sclerotinia sclerotiorum. THE PLANT CELL 2020; 32:1820-1844. [PMID: 32265317 PMCID: PMC7268813 DOI: 10.1105/tpc.19.00806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Quantitative disease resistance (QDR) is a conserved form of plant immunity that limits infections caused by a broad range of pathogens. QDR has a complex genetic determinism. The extent to which molecular components of the QDR response vary across plant species remains elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold diseases on hundreds of plant species, triggers QDR in host populations. To document the diversity of local responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptomes of six species spanning the Pentapetalae (Phaseolus vulgaris, Ricinus communis, Arabidopsis [Arabidopsis thaliana], Helianthus annuus, Solanum lycopersicum, and Beta vulgaris) inoculated with the same strain of S. sclerotiorum About one-third of plant transcriptomes responded locally to S. sclerotiorum, including a high proportion of broadly conserved genes showing frequent regulatory divergence at the interspecific level. Evolutionary inferences suggested a trend toward the acquisition of gene induction relatively recently in several lineages. Focusing on a group of ABCG transporters, we propose that exaptation by regulatory divergence contributed to the evolution of QDR. This evolutionary scenario has implications for understanding the QDR spectrum and durability. Our work provides resources for functional studies of gene regulation and QDR molecular mechanisms across the Pentapetalae.
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Affiliation(s)
- Justine Sucher
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Malick Mbengue
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Axel Dresen
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Marielle Barascud
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Marie Didelon
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Adelin Barbacci
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environement (INRAE) - Centre National de la Recherche Scientifique (CNRS), F31326 Castanet Tolosan, France
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Tamborski J, Krasileva KV. Evolution of Plant NLRs: From Natural History to Precise Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:355-378. [PMID: 32092278 DOI: 10.1146/annurev-arplant-081519-035901] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) monitor the plant intracellular environment for signs of pathogen infection. Several mechanisms of NLR-mediated immunity arose independently across multiple species. These include the functional specialization of NLRs into sensors and helpers, the independent emergence of direct and indirect recognition within NLR subfamilies, the regulation of NLRs by small RNAs, and the formation of NLR networks. Understanding the evolutionary history of NLRs can shed light on both the origin of pathogen recognition and the common constraints on the plant immune system. Attempts to engineer disease resistance have been sparse and rarely informed by evolutionary knowledge. In this review, we discuss the evolution of NLRs, give an overview of previous engineering attempts, and propose how to use evolutionary knowledge to advance future research in the generation of novel disease-recognition capabilities.
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Affiliation(s)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
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Märkle H, Tellier A. Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments. PLoS Comput Biol 2020; 16:e1007668. [PMID: 32203545 PMCID: PMC7156111 DOI: 10.1371/journal.pcbi.1007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/14/2020] [Accepted: 01/19/2020] [Indexed: 01/27/2023] Open
Abstract
There is a long-standing interest in understanding host-parasite coevolutionary dynamics and associated fitness effects. Increasing amounts of genomic data for both interacting species offer a promising source to identify candidate loci and to infer the main parameters of the past coevolutionary history. However, so far no method exists to perform the latter. By coupling a gene-for-gene model with coalescent simulations, we first show that three types of biological costs, namely, resistance, infectivity and infection, define the allele frequencies at the internal equilibrium point of the coevolution model. These in return determine the strength of selective signatures at the coevolving host and parasite loci. We apply an Approximate Bayesian Computation (ABC) approach on simulated datasets to infer these costs by jointly integrating host and parasite polymorphism data at the coevolving loci. To control for the effect of genetic drift on coevolutionary dynamics, we assume that 10 or 30 repetitions are available from controlled experiments or several natural populations. We study two scenarios: 1) the cost of infection and population sizes (host and parasite) are unknown while costs of infectivity and resistance are known, and 2) all three costs are unknown while populations sizes are known. Using the ABC model choice procedure, we show that for both scenarios, we can distinguish with high accuracy pairs of coevolving host and parasite loci from pairs of neutrally evolving loci, though the statistical power decreases with higher cost of infection. The accuracy of parameter inference is high under both scenarios especially when using both host and parasite data because parasite polymorphism data do inform on costs applying to the host and vice-versa. As the false positive rate to detect pairs of genes under coevolution is small, we suggest that our method complements recently developed methods to identify host and parasite candidate loci for functional studies.
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Affiliation(s)
- Hanna Märkle
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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Živković D, John S, Verin M, Stephan W, Tellier A. Neutral genomic signatures of host-parasite coevolution. BMC Evol Biol 2019; 19:230. [PMID: 31856710 PMCID: PMC6924072 DOI: 10.1186/s12862-019-1556-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.
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Affiliation(s)
- Daniel Živković
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| | - Sona John
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Mélissa Verin
- Section of Population Genetics, Technical University of Munich, Freising, Germany.,Department of Mathematics and Statistics, Queen's University, Kingston, Ontario, Canada
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
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The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species. G3-GENES GENOMES GENETICS 2019; 9:3933-3941. [PMID: 31604826 PMCID: PMC6893187 DOI: 10.1534/g3.119.400529] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved. We generated ∼134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to S. chilense. Synteny analysis suggests significant degree of the gene order conservation between the S. chilense, S. lycopersicum and S. pennellii genomes. We generated the first genome and transcriptome sequence assemblies for the wild tomato species Solanum chilense and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility and for tomato breeding.
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Adachi H, Contreras MP, Harant A, Wu CH, Derevnina L, Sakai T, Duggan C, Moratto E, Bozkurt TO, Maqbool A, Win J, Kamoun S. An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. eLife 2019; 8:e49956. [PMID: 31774397 PMCID: PMC6944444 DOI: 10.7554/elife.49956] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/23/2019] [Indexed: 12/19/2022] Open
Abstract
The molecular codes underpinning the functions of plant NLR immune receptors are poorly understood. We used in vitro Mu transposition to generate a random truncation library and identify the minimal functional region of NLRs. We applied this method to NRC4-a helper NLR that functions with multiple sensor NLRs within a Solanaceae receptor network. This revealed that the NRC4 N-terminal 29 amino acids are sufficient to induce hypersensitive cell death. This region is defined by the consensus MADAxVSFxVxKLxxLLxxEx (MADA motif) that is conserved at the N-termini of NRC family proteins and ~20% of coiled-coil (CC)-type plant NLRs. The MADA motif matches the N-terminal α1 helix of Arabidopsis NLR protein ZAR1, which undergoes a conformational switch during resistosome activation. Immunoassays revealed that the MADA motif is functionally conserved across NLRs from distantly related plant species. NRC-dependent sensor NLRs lack MADA sequences indicating that this motif has degenerated in sensor NLRs over evolutionary time.
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Affiliation(s)
- Hiroaki Adachi
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Chih-hang Wu
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Lida Derevnina
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Toshiyuki Sakai
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Cian Duggan
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Eleonora Moratto
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Tolga O Bozkurt
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Abbas Maqbool
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Joe Win
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel) 2019; 10:E691. [PMID: 31500388 PMCID: PMC6771003 DOI: 10.3390/genes10090691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.
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Affiliation(s)
- Alice MacQueen
- Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210008, China.
| | - Wenhan Chang
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Eric Holub
- School of Life Sciences, Wellesbourne Innovation Campus, University of Warwick, Wellesbourne CV359EF, UK.
| | - Martin Kreitman
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Joy Bergelson
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
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