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de la Rosa S, Schol CR, Ramos Peregrina Á, Winter DJ, Hilgers AM, Maeda K, Iida Y, Tarallo M, Jia R, Beenen HG, Rocafort M, de Wit PJGM, Bowen JK, Bradshaw RE, Joosten MHAJ, Bai Y, Mesarich CH. Sequential breakdown of the Cf-9 leaf mould resistance locus in tomato by Fulvia fulva. THE NEW PHYTOLOGIST 2024; 243:1522-1538. [PMID: 38922927 DOI: 10.1111/nph.19925] [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: 04/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Leaf mould, caused by Fulvia fulva, is a devastating disease of tomato plants. In many commercial tomato cultivars, resistance to this disease is governed by the Cf-9 locus, which encodes five paralogous receptor-like proteins. Two of these proteins confer resistance: Cf-9C recognises the previously identified F. fulva effector Avr9 and provides resistance during all plant growth stages, while Cf-9B recognises the yet-unidentified F. fulva effector Avr9B and provides mature plant resistance only. In recent years, F. fulva strains have emerged that can overcome the Cf-9 locus, with Cf-9C circumvented through Avr9 deletion. To understand how Cf-9B is circumvented, we set out to identify Avr9B. Comparative genomics, transient expression assays and gene complementation experiments were used to identify Avr9B, while gene sequencing was used to assess Avr9B allelic variation across a world-wide strain collection. A strict correlation between Avr9 deletion and resistance-breaking mutations in Avr9B was observed in strains recently collected from Cf-9 cultivars, whereas Avr9 deletion but no mutations in Avr9B were observed in older strains. This research showcases how F. fulva has evolved to sequentially break down the Cf-9 locus and stresses the urgent need for commercial tomato cultivars that carry novel, stacked resistance genes active against this pathogen.
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Affiliation(s)
- Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
| | - Christiaan R Schol
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Ángeles Ramos Peregrina
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - David J Winter
- Bioinformatics Group, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Anne M Hilgers
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Kazuya Maeda
- Laboratory of Plant Pathology, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Yuichiro Iida
- Laboratory of Plant Pathology, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
| | - Ruifang Jia
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Henriek G Beenen
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Mercedes Rocafort
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Ltd, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Rosie E Bradshaw
- Laboratory of Molecular Plant Pathology, School of Food Technology and Natural Sciences, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, 6708 PB, the Netherlands
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, 4410, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, 4410, New Zealand
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Tominello-Ramirez CS, Muñoz Hoyos L, Oubounyt M, Stam R. Network analyses predict major regulators of resistance to early blight disease complex in tomato. BMC PLANT BIOLOGY 2024; 24:641. [PMID: 38971719 PMCID: PMC11227178 DOI: 10.1186/s12870-024-05366-0] [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: 05/13/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Early blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility. RESULTS The induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling. CONCLUSIONS Our findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.
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Affiliation(s)
- Christopher S Tominello-Ramirez
- Department of Phytopathology and Crop Protection, Institute for Phytopathology, Christian Albrechts University, Kiel, Germany
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Lina Muñoz Hoyos
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute for Phytopathology, Christian Albrechts University, Kiel, Germany.
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
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Zhang J, Dong KL, Ren MZ, Wang ZW, Li JH, Sun WJ, Zhao X, Fu XX, Ye JF, Liu B, Zhang DM, Wang MZ, Zeng G, Niu YT, Lu LM, Su JX, Liu ZJ, Soltis PS, Soltis DE, Chen ZD. Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae). HORTICULTURE RESEARCH 2024; 11:uhae077. [PMID: 38779140 PMCID: PMC11109519 DOI: 10.1093/hr/uhae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/08/2024] [Indexed: 05/25/2024]
Abstract
How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kai-Lin Dong
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Zhen Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Jian-Hua Li
- Biology Department, Hope College, Holland, MI 49423, USA
| | - Wen-Jing Sun
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Xin-Xing Fu
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China
| | - Jian-Fei Ye
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Da-Ming Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Mo-Zhu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Gang Zeng
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Yan-Ting Niu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Li-Min Lu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jun-Xia Su
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611-7800, USA
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Cao Y, Zhang C, Liu F, Li D, Zhang A, Li L, Zhang X. Genome-Wide Identification and Expression Analysis of Kiwifruit Leucine-Rich Repeat Receptor-Like Proteins Reveal Their Roles in Biotic and Abiotic Stress Responses. Int J Mol Sci 2024; 25:4497. [PMID: 38674082 PMCID: PMC11050117 DOI: 10.3390/ijms25084497] [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: 03/12/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Leucine-rich repeat receptor-like proteins (LRR-RLPs), a major group of receptor-like proteins in plants, have diverse functions in plant physiology, including growth, development, signal transduction, and stress responses. Despite their importance, the specific roles of kiwifruit LRR-RLPs in response to biotic and abiotic stresses remain poorly understood. In this study, we performed family identification, characterization, transcriptome data analysis, and differential gene expression analysis of kiwifruit LRR-RLPs. We identified totals of 101, 164, and 105 LRR-RLPs in Actinidia chinensis 'Hongyang', Actinidia eriantha 'Huate', and Actinidia chinensis 'Red5', respectively. Synteny analysis revealed that the expansion of kiwifruit LRR-RLPs was primarily attributed to segmental duplication events. Based on RNA-seq data from pathogen-infected kiwifruits, we identified specific LRR-RLP genes potentially involved in different stages of pathogen infection. Additionally, we observed the potential involvement of kiwifruit LRR-RLPs in abiotic stress responses, with upstream transcription factors possibly regulating their expression. Furthermore, protein interaction network analysis unveiled the participation of kiwifruit LRR-RLP in the regulatory network of abiotic stress responses. These findings highlight the crucial roles of LRR-RLPs in mediating both biotic and abiotic stress responses in kiwifruit, offering valuable insights for the breeding of stress-resistant kiwifruit varieties.
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Affiliation(s)
- Yingying Cao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congxiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Aidi Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiujun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (Y.C.); (C.Z.); (F.L.); (D.L.); (A.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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Zhang JH, Wei HB, Hong YH, Yang RR, Meng J, Luan YS. The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans. PLANT CELL REPORTS 2024; 43:57. [PMID: 38319523 DOI: 10.1007/s00299-024-03161-7] [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: 11/25/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans. Tomato (Solanum lycopersicum) is an important horticultural and cash crop whose yield and quality can be severely affected by Phytophthora infestans (P. infestans). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are widely involved in plant defense responses against pathogens. The involvement of Sl-lncRNA20718 and Sl-miR6022 in tomato resistance to P. infestans as well as the targeting of Sl-miR6022 to receptor-like protein genes (RLPs) were predicted in our previous study. However, uncertainty exists regarding their potential interaction as well as the molecular processes regulating tomato resistance. Here, we found that Sl-lncRNA20718 and Sl-miR6022 are positive and negative regulators of tomato resistance to P. infestans by gain- and loss-of-function experiments, respectively. Overexpression of Sl-lncRNA20718 decreased the expression of Sl-miR6022, induced the expression of PRs, reduced the diameter of lesions (DOLs), thereby enhanced disease resistance. A six-point mutation in the binding region of Sl-lncRNA20718 to Sl-miR6022 disabled the interaction, indicating that Sl-lncRNA20718 acts as an endogenous target mimic (eTM) of Sl-miR6022. We demonstrated that Sl-miR6022 cleaves SlRLP6/10. Overexpression of Sl-miR6022 decreases the expression levels of SlRLP6/10, induces the accumulation of reactive oxygen species (ROS) and reduces the content of JA and ET, thus inhibiting tomato resistance to P. infestans. In conclusion, our study provides detailed information on the lncRNA20718-miR6022-RLPs module regulating tomato resistance to P. infestans by affecting the expression of disease resistance-related genes, the accumulation of ROS and the phytohormone levels, providing a new reference for tomato disease resistance breeding.
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Affiliation(s)
- Jia-Hui Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Hong-Bo Wei
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Hui Hong
- Key Laboratory of Biotechnology and Bioresources Utilization-Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Rui-Rui Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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Oh Y, Ingram T, Shekasteband R, Adhikari T, Louws FJ, Dean RA. Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4685-4706. [PMID: 37184211 PMCID: PMC10433936 DOI: 10.1093/jxb/erad182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/12/2023] [Indexed: 05/16/2023]
Abstract
Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared with resistant tissues, including pathogen receptor, signaling pathway, pathogenesis-related protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato-V. dahliae interaction.
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Affiliation(s)
- Yeonyee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza Shekasteband
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Tika Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Ralph A Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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Chidambara B, Muthaiah G, Sadashiva AT, Reddy MK, Ravishankar KV. Transcriptome analysis during ToLCBaV disease development in contrasting tomato genotypes. 3 Biotech 2023; 13:226. [PMID: 37304404 PMCID: PMC10247599 DOI: 10.1007/s13205-023-03629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Tomato leaf curl Bangalore virus (ToLCBaV) is one of the most important plant viruses. The infection causes substantial yield losses in tomato crop. The current viral disease management is based mainly on introgression of Ty locus into new tomato cultivars. Unfortunately, strains of the leaf curl virus have been evolving and are breaking Ty based tolerance in tomato. In this study, the defence response to ToLCBaV infection has been compared between contrasting tomato genotypes, resistant line (IIHR 2611; without any known Ty markers) and the susceptible line (IIHR 2843). We carried out comparative transcriptome profiling, and gene expression analysis in an effort to identify gene networks that are associated with a novel ToLCBaV resistance. A total of 22,320 genes were examined to identify differentially expressed genes (DEGs). We found that 329 genes of them were expressed significantly and differentially between ToLBaV-infected samples of both IIHR 2611 and IIHR 2843. A good number of DEGs were related to defence response, photosynthesis, response to wounding, toxin catabolic process, glutathione metabolic process, regulation of transcription DNA-template, transcription factor activity, and sequence-specific DNA binding. A few selected genes such as, nudix hydrolase 8, MIK 2-like, RING-H2 finger protein ATL2-like, MAPKKK 18-like, EDR-2, SAG 21 wound-induced basic protein, GRXC6 and P4 were validated using qPCR. The pattern of gene expression was significantly different in resistant and susceptible plants during disease progression. Both positive and negative regulators of virus resistance were found in the present study. These findings will facilitate breeding and genetic engineering efforts to incorporate novel sources of ToLCBaV resistance in tomatoes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03629-5.
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Affiliation(s)
- Bhavya Chidambara
- Department of Plant Biotechnology, UAS, GKVK, Bengaluru, 560065 India
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089 India
| | - Gayathri Muthaiah
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089 India
| | | | - M. Krishna Reddy
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089 India
| | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089 India
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Leibman-Markus M, Gupta R, Pizarro L, Bar M. The LeEIX Locus Determines Pathogen Resistance in Tomato. PHYTOPATHOLOGY 2023; 113:277-285. [PMID: 36044638 DOI: 10.1094/phyto-01-22-0035-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The mechanisms underlying the ability of plants to differentiate between pathogens and commensals in their environment are currently unresolved. It has been suggested that spatiotemporal regulation of pattern-recognition receptor (PRR) content could be one of the components providing plants with the ability to distinguish between pathogens and nonpathogenic microbes. The LeEIX PRRs recognize xylanases derived from beneficial or commensal plant colonizers of Trichoderma species, including the xylanase known as EIX. Here, we investigated possible general roles of PRRs from the LeEIX locus in immunity and pathogen resistance in tomato. Mutating the inhibitory PRR LeEIX1, or overexpressing the activating PRR LeEIX2, resulted in resistance to a wide range of pathogens and increased basal and elicited immunity. LeEIX1 knockout caused increases in the expression level of several tested PRRs, including FLS2, as well as bacterial pathogen resistance coupled with an increase in flg22-mediated immunity. The wild tomato relative Solanum pennellii contains inactive LeEIX PRR variants. S. pennellii does not respond to elicitation with the LeEIX PRR ligand EIX. Given that EIX is derived from a mostly nonpathogenic microbe, the connection of its PRRs to disease resistance has not previously been investigated directly. Here, we observed that compared with S. lycopersicum cultivar M82, S. pennellii was more sensitive to several fungal and bacterial pathogens. Our results suggest that the LeEIX locus might determine resistance to fungal necrotrophs, whereas the resistance to biotrophs is effected in combination with a gene/quantitative trait locus not within the LeEIX locus.
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Affiliation(s)
- Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Lorena Pizarro
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
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9
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Yu H, Sun E, Mao X, Chen Z, Xu T, Zuo L, Jiang D, Cao Y, Zuo C. Evolutionary and functional analysis reveals the crucial roles of receptor-like proteins in resistance to Valsa canker in Rosaceae. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:162-177. [PMID: 36255986 DOI: 10.1093/jxb/erac417] [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: 07/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Rosaceae is an economically important plant family that can be affected by a multitude of pathogenic microbes, some of which can cause dramatic losses in production. As a type of pattern-recognition receptor, receptor-like proteins (RLPs) are considered vital regulators of plant immunity. Based on genome-wide identification, bioinformatic analysis, and functional determination, we investigated the evolutionary characteristics of RLPs, and specifically those that regulate Valsa canker, a devastating fungal disease affecting apple and pear production. A total of 3028 RLPs from the genomes of 19 species, including nine Rosaceae, were divided into 24 subfamilies. Five subfamilies and seven co-expression modules were found to be involved in the responses to Valsa canker signals of the resistant pear rootstock Pyrus betulifolia 'Duli-G03'. Fourteen RLPs were subsequently screened as candidate genes for regulation of resistance. Among these, PbeRP23 (Chr13.g24394) and PbeRP27 (Chr16.g31400) were identified as key resistance genes that rapidly enhance the resistance of 'Duli-G03' and strongly initiate immune responses, and hence they have potential for further functional exploration and breeding applications for resistance to Valsa canker. In addition, as a consequence of this work we have established optimal methods for the classification and screening of disease-resistant RLPs.
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Affiliation(s)
- Hongqiang Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - E Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Xia Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Zhongjian Chen
- Agro-Biological Gene Research Center, Guangdong Academy of Agriculture, Guangzhou, 510640, China
| | - Tong Xu
- Chengdu Life Baseline Technology Co, Ltd, Chengdu, 610041, China
| | - Longgang Zuo
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Daji Jiang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yanan Cao
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Cunwu Zuo
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
- State Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
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10
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Li W, Lu J, Yang C, Xia S. Identification of receptor-like proteins induced by Sclerotinia sclerotiorum in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:944763. [PMID: 36061811 PMCID: PMC9429810 DOI: 10.3389/fpls.2022.944763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Heightening the resistance of plants to microbial infection is a widely concerned issue, especially for economical crops. Receptor-like proteins (RLPs), typically with tandem leucine-rich repeats (LRRs) domain, play a crucial role in mediating immune activation, being an indispensable constituent in the first layer of defense. Based on an analysis of orthologs among Brassica rapa, Brassica oleracea, and Brassica napus using Arabidopsis thaliana RLPs as a reference framework, we found that compared to A. thaliana, there were some obvious evolutionary diversities of RLPs among the three Brassicaceae species. BnRLP encoding genes were unevenly distributed on chromosomes, mainly on chrA01, chrA04, chrC03, chrC04, and chrC06. The orthologs of five AtRLPs (AtRLP3, AtRLP10, AtRLP17, AtRLP44, and AtRLP51) were highly conserved, but retrenchment and functional centralization occurred in Brassicaceae RLPs during evolution. The RLP proteins were clustered into 13 subgroups. Ten BnRLPs presented expression specificity between R and S when elicited by Sclerotinia sclerotiorum, which might be fabulous candidates for S. sclerotiorum resistance research.
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Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- College of Life Science, Chongqing Normal University, Chongqing, China
| | - Junxing Lu
- College of Life Science, Chongqing Normal University, Chongqing, China
| | - Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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11
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Paul S, Duhan JS, Jaiswal S, Angadi UB, Sharma R, Raghav N, Gupta OP, Sheoran S, Sharma P, Singh R, Rai A, Singh GP, Kumar D, Iquebal MA, Tiwari R. RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:904392. [PMID: 35720556 PMCID: PMC9201344 DOI: 10.3389/fpls.2022.904392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Heat stress is one of the significant constraints affecting wheat production worldwide. To ensure food security for ever-increasing world population, improving wheat for heat stress tolerance is needed in the presently drifting climatic conditions. At the molecular level, heat stress tolerance in wheat is governed by a complex interplay of various heat stress-associated genes. We used a comparative transcriptome sequencing approach to study the effect of heat stress (5°C above ambient threshold temperature of 20°C) during grain filling stages in wheat genotype K7903 (Halna). At 7 DPA (days post-anthesis), heat stress treatment was given at four stages: 0, 24, 48, and 120 h. In total, 115,656 wheat genes were identified, including 309 differentially expressed genes (DEGs) involved in many critical processes, such as signal transduction, starch synthetic pathway, antioxidant pathway, and heat stress-responsive conserved and uncharacterized putative genes that play an essential role in maintaining the grain filling rate at the high temperature. A total of 98,412 Simple Sequences Repeats (SSR) were identified from de novo transcriptome assembly of wheat and validated. The miRNA target prediction from differential expressed genes was performed by psRNATarget server against 119 mature miRNA. Further, 107,107 variants including 80,936 Single nucleotide polymorphism (SNPs) and 26,171 insertion/deletion (Indels) were also identified in de novo transcriptome assembly of wheat and wheat genome Ensembl version 31. The present study enriches our understanding of known heat response mechanisms during the grain filling stage supported by discovery of novel transcripts, microsatellite markers, putative miRNA targets, and genetic variant. This enhances gene functions and regulators, paving the way for improved heat tolerance in wheat varieties, making them more suitable for production in the current climate change scenario.
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Affiliation(s)
- Surinder Paul
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, India
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR, National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, India
| | | | - Sarika Jaiswal
- Indian Council of Agricultural Research, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- Indian Council of Agricultural Research, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ruchika Sharma
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Nishu Raghav
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Om Prakash Gupta
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- Indian Council of Agricultural Research, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- Indian Council of Agricultural Research, Indian Agricultural Statistics Research Institute, New Delhi, India
- Department of Biotechnology, Central University of Haryana, Gurgaon, India
| | - Mir Asif Iquebal
- Indian Council of Agricultural Research, Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- Indian Council of Agricultural Research, Indian Institute of Wheat and Barley Research, Karnal, India
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Genome-Wide Analysis of the LRR-RLP Gene Family in a Wild Banana (Musa acuminata ssp. malaccensis) Uncovers Multiple Fusarium Wilt Resistance Gene Candidates. Genes (Basel) 2022; 13:genes13040638. [PMID: 35456444 PMCID: PMC9025879 DOI: 10.3390/genes13040638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (LRR-RLP) disease resistance gene family in a wild banana. We identified 78 LRR-RLP genes in the banana genome. Remarkably, seven MaLRR-RLPs formed a gene cluster in the distal part of chromosome 10, where resistance to Fusarium wilt caused by Foc race 1 has been previously mapped. Hence, we proposed these seven MaLRR-RLPs as resistance gene candidates (RGCs) for Fusarium wilt. We also identified seven other banana RGCs based on their close phylogenetic relationships with known LRR-RLP proteins. Moreover, phylogenetic analysis of the banana, rice, and Arabidopsis LRR-RLP families revealed five major phylogenetic clades shared by these plant species. Finally, transcriptomic analysis of the MaLRR-RLP gene family in plants treated with Foc race 1 or Foc TR4 showed the expression of several members of this family, and some of them were upregulated in response to these Foc races. Our study provides novel insights into the structure, distribution, evolution, and expression of the LRR-RLP gene family in bananas as well as valuable RGCs that will facilitate the identification of disease resistance genes for the genetic improvement of this crop.
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Kang WH, Lee J, Koo N, Kwon JS, Park B, Kim YM, Yeom SI. Universal gene co-expression network reveals receptor-like protein genes involved in broad-spectrum resistance in pepper (Capsicum annuum L.). HORTICULTURE RESEARCH 2022; 9:uhab003. [PMID: 35043174 PMCID: PMC8968494 DOI: 10.1093/hr/uhab003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 09/08/2021] [Indexed: 05/21/2023]
Abstract
Receptor-like proteins (RLPs) on plant cells have been implicated in immune responses and developmental processes. Although hundreds of RLP genes have been identified in plants, only a few RLPs have been functionally characterized in a limited number of plant species. Here, we identified RLPs in the pepper (Capsicum annuum) genome and performed comparative transcriptomics coupled with the analysis of conserved gene co-expression networks (GCNs) to reveal the role of core RLP regulators in pepper-pathogen interactions. A total of 102 RNA-seq datasets of pepper plants infected with four pathogens were used to construct CaRLP-targeted GCNs (CaRLP-GCNs). Resistance-responsive CaRLP-GCNs were merged to construct a universal GCN. Fourteen hub CaRLPs, tightly connected with defense-related gene clusters, were identified in eight modules. Based on the CaRLP-GCNs, we evaluated whether hub CaRLPs in the universal GCN are involved in the biotic stress response. Of the nine hub CaRLPs tested by virus-induced gene silencing, three genes (CaRLP264, CaRLP277, and CaRLP351) showed defense suppression with less hypersensitive response-like cell death in race-specific and non-host resistance response to viruses and bacteria, respectively, and consistently enhanced susceptibility to Ralstonia solanacearum and/or Phytophthora capsici. These data suggest that key CaRLPs are involved in the defense response to multiple biotic stresses and can be used to engineer a plant with broad-spectrum resistance. Together, our data show that generating a universal GCN using comprehensive transcriptome datasets can provide important clues to uncover genes involved in various biological processes.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828,
Republic of Korea
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ji-Su Kwon
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Boseul Park
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Genome Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828,
Republic of Korea
- Department of Horticulture, Division of Applied Life Science (BK21 four), Gyeongsang National University, 501, Jinju-daero, Gajwa-dong, Jinju, 52828, Republic of Korea
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Klymiuk V, Coaker G, Fahima T, Pozniak CJ. Tandem Protein Kinases Emerge as New Regulators of Plant Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1094-1102. [PMID: 34096764 PMCID: PMC8761531 DOI: 10.1094/mpmi-03-21-0073-cr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plant-pathogen interactions result in disease development in a susceptible host. Plants actively resist pathogens via a complex immune system comprising both surface-localized receptors that sense the extracellular space as well as intracellular receptors recognizing pathogen effectors. To date, the majority of cloned resistance genes encode intracellular nucleotide-binding leucine-rich repeat receptor proteins. Recent discoveries have revealed tandem kinase proteins (TKPs) as another important family of intracellular proteins involved in plant immune responses. Five TKP genes-barley Rpg1 and wheat WTK1 (Yr15), WTK2 (Sr60), WTK3 (Pm24), and WTK4-protect against devastating fungal diseases. Moreover, a large diversity and numerous putative TKPs exist across the plant kingdom. This review explores our current knowledge of TKPs and serves as a basis for future studies that aim to develop and exploit a deeper understanding of innate plant immunity receptor proteins.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences,
University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California,
Davis, CA, U.S.A
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi
Avenue, Mt. Carmel, 3498838 Haifa, Israel
- Department of Evolutionary and Environmental Biology,
University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838 Haifa, Israel
| | - Curtis J. Pozniak
- Crop Development Centre and Department of Plant Sciences,
University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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15
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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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16
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Jocković M, Jocić S, Cvejić S, Marjanović-Jeromela A, Jocković J, Radanović A, Miladinović D. Genetic Improvement in Sunflower Breeding—Integrated Omics Approach. PLANTS 2021; 10:plants10061150. [PMID: 34200113 PMCID: PMC8228292 DOI: 10.3390/plants10061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/23/2023]
Abstract
Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.
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Affiliation(s)
- Milan Jocković
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
- Correspondence:
| | - Siniša Jocić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Sandra Cvejić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Ana Marjanović-Jeromela
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Jelena Jocković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Dositeja Obradovića 3, 21000 Novi Sad, Serbia;
| | - Aleksandra Radanović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
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Kang WH, Park B, Lee J, Yeom SI. Tissue-Specific RNA-Seq Analysis and Identification of Receptor-Like Proteins Related to Plant Growth in Capsicum annuum. PLANTS (BASEL, SWITZERLAND) 2021; 10:972. [PMID: 34068172 PMCID: PMC8152994 DOI: 10.3390/plants10050972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/03/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
Receptor-like proteins (RLPs) are a gene family of cell surface receptors that are involved in plant growth, development, and disease resistance. In a recent study, 438 pepper RLP genes were identified in the Capsicum annuum genome (CaRLPs) and determined to be present in response to multiple biotic stresses. To further understand the role of CaRLPs in plant growth and development, we analyzed expression patterns of all CaRLPs from various pepper tissues and developmental stages using RNA-seq. Ten CaRLP genes were selected for further analysis according to transcript levels with hierarchical clustering. The selected CaRLP genes displayed similarity of motifs within the same groups and structures typical of RLPs. To examine RLP function in growth and development, we performed loss-of-function analysis using a virus-induced gene silencing system. Three of the ten tested CaRLPs (CaRLP238, 253, and 360) in silenced plants exhibited phenotypic alteration with growth retardation compared to controls. All three gene-silenced peppers showed significant differences in root dry weight. Only CaRLP238 had significant differences in both root and shoot dry weight. Our results suggest that CaRLPs may play important roles in regulation of plant growth and development as well as function in defense responses to biotic stresses in the RLP gene family.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Boseul Park
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
| | - Junesung Lee
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea;
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Korea; (B.P.); (J.L.)
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18
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O’Rourke JA, Graham MA. Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean. Int J Mol Sci 2021; 22:1252. [PMID: 33513952 PMCID: PMC7866191 DOI: 10.3390/ijms22031252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.
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Affiliation(s)
- Jamie A. O’Rourke
- Corn Insects and Crop Genetics Research Unit, USDA—Agricultural Research Service, Ames, IA 50010, USA;
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19
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Lee J, Nam JY, Jang H, Kim N, Kim YM, Kang WH, Yeom SI. Comprehensive transcriptome resource for response to phytohormone-induced signaling in Capsicum annuum L. BMC Res Notes 2020; 13:440. [PMID: 32943083 PMCID: PMC7499990 DOI: 10.1186/s13104-020-05281-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in major crops. Here, we aimed to provide transcriptome dataset using RNA sequencing for phytohormone-induced signaling in plant. DATA DESCRIPTION We used high-throughput RNA sequencing profiling to investigate the pepper plant response to treatment with four major phytohormones (salicylic acid, jasmonic acid, ethylene, and abscisic acid). This dataset yielded 78 samples containing three biological replicates per six different time points for each treatment and the control, constituting 187.8 Gb of transcriptome data (2.4 Gb of each sample). This comprehensive parallel transcriptome data provides valuable information for understanding the relationships and molecular networks that regulate the expression of phytohormone-related genes involved in plant developments and environmental stress adaptation.
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Affiliation(s)
- Junesung Lee
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Jae-Young Nam
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Hakgi Jang
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Nayoung Kim
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Yong-Min Kim
- Genome Engineering Research Center, Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141 Republic of Korea
| | - Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21), Gyeongsang National University, Jinju, 52828 Republic of Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea
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20
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Iakovidis M, Soumpourou E, Anderson E, Etherington G, Yourstone S, Thomas C. Genes Encoding Recognition of the Cladosporium fulvum Effector Protein Ecp5 Are Encoded at Several Loci in the Tomato Genome. G3 (BETHESDA, MD.) 2020; 10:1753-1763. [PMID: 32209596 PMCID: PMC7202015 DOI: 10.1534/g3.120.401119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022]
Abstract
The molecular interactions between tomato and Cladosporium fulvum have been an important model for molecular plant pathology. Complex genetic loci on tomato chromosomes 1 and 6 harbor genes for resistance to Cladosporium fulvum, encoding receptor like-proteins that perceive distinct Cladosporium fulvum effectors and trigger plant defenses. Here, we report classical mapping strategies for loci in tomato accessions that respond to Cladosporium fulvum effector Ecp5, which is very sequence-monomorphic. We screened 139 wild tomato accessions for an Ecp5-induced hypersensitive response, and in five accessions, the Ecp5-induced hypersensitive response segregated as a monogenic trait, mapping to distinct loci in the tomato genome. We identified at least three loci on chromosomes 1, 7 and 12 that harbor distinct Cf-Ecp5 genes in four different accessions. Our mapping showed that the Cf-Ecp5 in Solanum pimpinellifolium G1.1161 is located at the Milky Way locus. The Cf-Ecp5 in Solanum pimpinellifolium LA0722 was mapped to the bottom arm of chromosome 7, while the Cf-Ecp5 genes in Solanum lycopersicum Ontario 7522 and Solanum pimpinellifolium LA2852 were mapped to the same locus on the top arm of chromosome 12. Bi-parental crosses between accessions carrying distinct Cf-Ecp5 genes revealed putative genetically unlinked suppressors of the Ecp5-induced hypersensitive response. Our mapping also showed that Cf-11 is located on chromosome 11, close to the Cf-3 locus. The Ecp5-induced hypersensitive response is widely distributed within tomato species and is variable in strength. This novel example of convergent evolution could be used for choosing different functional Cf-Ecp5 genes according to individual plant breeding needs.
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Affiliation(s)
- Michail Iakovidis
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Eleni Soumpourou
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Elisabeth Anderson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Scott Yourstone
- Department of Biological Sciences, University of North Carolina at Chapel Hill, NC, 27510
| | - Colwyn Thomas
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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21
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Kang WH, Sim YM, Koo N, Nam JY, Lee J, Kim N, Jang H, Kim YM, Yeom SI. Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L. Sci Data 2020; 7:17. [PMID: 31932587 PMCID: PMC6957515 DOI: 10.1038/s41597-020-0352-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/17/2019] [Indexed: 01/17/2023] Open
Abstract
Peppers (Capsicum annuum L.), belonging to the Solanaceae family, are one of the most economically important crops globally. Like other crops, peppers are threatened by diverse environmental conditions due to different pathogens and abiotic stresses. High-quality reference genomes with massive datasets of transcriptomes from various conditions can provide clues to preferred agronomic traits for breeding. However, few global gene expression profiling datasets have been published to examine the environmental stress-resistant mechanisms in peppers. In this study, we report the RNA-seq analyses of peppers treated with heat, cold, salinity, and osmotic stress at six different time points. RNA-seq libraries from 78 RNA samples containing three biological replicates per time point for each of the abiotic stresses and a mock control were constructed. A total of 204.68 Gb of transcriptome data were verified by differentially expressed genes and gene ontology enrichment analysis. Analyses of the transcriptome data in this study will provide useful information for basic studies of various stimuli to facilitate the development of stress-resistant pepper cultivars.
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Affiliation(s)
- Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jae-Young Nam
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Junesung Lee
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Nayoung Kim
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hakgi Jang
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seon-In Yeom
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828, Republic of Korea.
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22
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Wu CH, Adachi H, De la Concepcion JC, Castells-Graells R, Nekrasov V, Kamoun S. NRC4 Gene Cluster Is Not Essential for Bacterial Flagellin-Triggered Immunity. PLANT PHYSIOLOGY 2020; 182:455-459. [PMID: 31712307 PMCID: PMC6945836 DOI: 10.1104/pp.19.00859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/29/2019] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas9-mediated mutation of NRC2, NRC3, and NRC4 genes did not affect bacterial flagellin-triggered immunity.
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Affiliation(s)
- Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | | | - Roger Castells-Graells
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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23
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Kim N, Kang WH, Lee J, Yeom SI. Development of Clustered Resistance Gene Analogs-Based Markers of Resistance to Phytophthora capsici in Chili Pepper. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1093186. [PMID: 30719438 PMCID: PMC6335758 DOI: 10.1155/2019/1093186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/24/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022]
Abstract
The soil-borne pathogen Phytophthora capsici causes severe destruction of Capsicum spp. Resistance in Capsicum against P. capsici is controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers on Capsicum chromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between two Capsicum germplasms that are resistant and susceptible, respectively, to P. capsici. 11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL for P. capsici resistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61 Capsicum accessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes against P. capsici in pepper.
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Affiliation(s)
- Nayoung Kim
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Won-Hee Kang
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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24
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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 DOI: 10.1007/s13580-019-00157-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/19/2019] [Accepted: 10/06/2017] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. CONCLUSIONS Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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