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Wöhner TW, Emeriewen OF. A landscape of resistance gene analogs in sour cherry (Prunus cerasus L.). BMC Res Notes 2024; 17:292. [PMID: 39370523 PMCID: PMC11457318 DOI: 10.1186/s13104-024-06952-z] [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: 03/27/2024] [Accepted: 09/19/2024] [Indexed: 10/08/2024] Open
Abstract
OBJECTIVE This research aims to analyze the presence and distribution of resistance genes in the avium and fruticosa subgenomes of Prunus cerasus through computational methods and bioinformatics tools. RESULTS Analysis of genome and transcriptome sequencing data revealed a total of 19,570 transcripts with at least one resistance gene domain in Prunus cerasus subgenome avium and 19,142 in Prunus cerasus subgenome fruticosa. Key findings include the identification of 804 "complete" resistance gene transcripts in Prunus cerasus subgenome avium and 817 in Prunus cerasus subgenome fruticosa, with distinct distributions of resistance gene classes observed between the subgenomes. Phylogenetic analysis showed clustering of resistance genes, and unique resistance proteins were identified in each subgenome. Functional annotation comparisons with Arabidopsis thaliana highlighted shared and unique resistance genes, emphasizing the complexity of disease resistance in cherry species. Additionally, a higher diversity of RLKs and RLPs was observed, with 504 transcripts identified and 18 showing similarity to known reference genes.
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Affiliation(s)
- Thomas Wolfgang Wöhner
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Dresden, 01326, Saxony, Germany.
| | - Ofere Francis Emeriewen
- Institute for Breeding Research on Fruit Crops, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Dresden, 01326, Saxony, Germany
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Ghimire B, Gogoi A, Poudel M, Stensvand A, Brurberg MB. Transcriptome analysis of Phytophthora cactorum infecting strawberry identified RXLR effectors that induce cell death when transiently expressed in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2024; 15:1379970. [PMID: 38855473 PMCID: PMC11157022 DOI: 10.3389/fpls.2024.1379970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024]
Abstract
Phytophthora cactorum is a plant pathogenic oomycete that causes crown rot in strawberry leading to significant economic losses every year. To invade the host, P. cactorum secretes an arsenal of effectors that can manipulate host physiology and impair its defense system promoting infection. A transcriptome analysis was conducted on a susceptible wild strawberry genotype (Fragaria vesca) 48 hours post inoculation with P. cactorum to identify effectors expressed during the early infection stage. The analysis revealed 4,668 P. cactorum genes expressed during infection of F. vesca. A total of 539 secreted proteins encoded by transcripts were identified, including 120 carbohydrate-active enzymes, 40 RXLRs, 23 proteolytic enzymes, nine elicitins, seven cysteine rich proteins, seven necrosis inducing proteins and 216 hypothetical proteins with unknown function. Twenty of the 40 RXLR effector candidates were transiently expressed in Nicotiana benthamiana using agroinfiltration and five previously unreported RXLR effector genes (Pc741, Pc8318, Pc10890, Pc20813, and Pc22290) triggered cell death when transiently expressed. The identified cell death inducing RXLR effectors showed 31-66% identity to known RXLR effectors in different Phytophthora species having roles in pathogenicity including both activation and suppression of defense response in the host. Furthermore, homology analysis revealed that these cell death inducing RXLR effectors were highly conserved (82 - 100% identity) across 23 different strains of P. cactorum originating from apple or strawberry.
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Affiliation(s)
- Bikal Ghimire
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Anupam Gogoi
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Mandeep Poudel
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Arne Stensvand
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - May Bente Brurberg
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
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Chen X, Wen K, Zhou X, Zhu M, Liu Y, Jin J, Nellist CF. The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features. MOLECULAR PLANT PATHOLOGY 2023; 24:1017-1032. [PMID: 37144631 PMCID: PMC10423333 DOI: 10.1111/mpp.13345] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
Phytophthora cactorum is one of the most economically important soilborne oomycete pathogens in the world. It infects more than 200 plant species spanning 54 families, most of which are herbaceous and woody species. Although traditionally considered to be a generalist, marked differences of P. cactorum isolates occur in degree of pathogenicity to different hosts. As the impact of crop loss caused by this species has increased recently, there has been a tremendous increase in the development of new tools, resources, and management strategies to study and combat this devastating pathogen. This review aims to integrate recent molecular biology analyses of P. cactorum with the current knowledge of the cellular and genetic basis of its growth, development, and host infection. The goal is to provide a framework for further studies of P. cactorum by highlighting important biological and molecular features, shedding light on the functions of pathogenicity factors, and developing effective control measures. TAXONOMY P. cactorum (Leb. & Cohn) Schröeter: kingdom Chromista; phylum Oomycota; class Oomycetes; order Peronosporales; family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 200 plant species in 154 genera representing 54 families. Economically important host plants include strawberry, apple, pear, Panax spp., and walnut. DISEASE SYMPTOMS The soilborne pathogen often causes root, stem, collar, crown, and fruit rots, as well as foliar infection, stem canker, and seedling damping off.
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Affiliation(s)
- Xiao‐Ren Chen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ke Wen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Xue Zhou
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ming‐Yue Zhu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Yang Liu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Jing‐Hao Jin
- College of Plant ProtectionYangzhou UniversityYangzhouChina
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Gogoi A, Lysøe E, Eikemo H, Stensvand A, Davik J, Brurberg MB. Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry. Int J Mol Sci 2023; 24:10851. [PMID: 37446029 DOI: 10.3390/ijms241310851] [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: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Crown rot, caused by Phytophthora cactorum, is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars (Fragaria × ananassa Duch) are generally susceptible, the diploid species Fragaria vesca is a potential source of resistance genes to P. cactorum. We previously reported several F. vesca genotypes with varying degrees of resistance to P. cactorum. To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) of F. vesca were analysed by RNA-Seq after wounding and subsequent inoculation with P. cactorum. Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response to P. cactorum after wounding. These included putative disease resistance (R) genes encoding receptor-like proteins, receptor-like kinases, nucleotide-binding sites, leucine-rich repeat proteins, RPW8-type disease resistance proteins, and 'pathogenesis-related protein 1'. Seven of these R-genes were expressed only in the resistant genotypes and not in the susceptible genotype, and these appeared to be present only in the genomes of the resistant genotypes, as confirmed by PCR analysis. We previously reported a single major gene locus RPc-1 (Resistance to Phytophthora cactorum 1) in F. vesca that contributed resistance to P. cactorum. Here, we report that 4-5% of the genes (35-38 of ca 800 genes) in the RPc-1 locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation with P. cactorum. In particular, we identified three defence-related genes encoding wall-associated receptor-like kinase 3, receptor-like protein 12, and non-specific lipid-transfer protein 1-like that were highly expressed in the resistant genotypes compared to the susceptible one. The present study reports several novel candidate disease resistance genes that warrant further investigation for their role in plant defence against P. cactorum.
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Affiliation(s)
- Anupam Gogoi
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - Håvard Eikemo
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - Arne Stensvand
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - Jahn Davik
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
| | - May Bente Brurberg
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), 1433 Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), 1433 Ås, Norway
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Tao M, Zhao Y, Hu T, Zhang Q, Feng H, Lu Y, Guo Z, Yang B. Screening of Alfalfa Varieties Resistant to Phytophthora cactorum and Related Resistance Mechanism. PLANTS (BASEL, SWITZERLAND) 2023; 12:702. [PMID: 36840050 PMCID: PMC9966651 DOI: 10.3390/plants12040702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/23/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Alfalfa is one of the most important legume forages in the world. Root rot caused by soil-borne pathogens severely restricts the production of alfalfa. The knowledge of the interaction between alfalfa and root rot-pathogens is still lacking in China. Phytophthora cactorum was isolated from symptomatic seedlings of an alfalfa field in Nanjing with high levels of damping-off. We observed the different infection stages of P. cactorum on alfalfa, and found that the purified P. cactorum strain was aggressive in causing alfalfa seed and root rot. The infecting hyphae penetrated the epidermal cells and wrapped around the alfalfa roots within 48 h. By evaluating the resistance of 37 alfalfa cultivars from different countries to P. cactorum, we found Weston is a resistant variety, while Longdong is a susceptible variety. We further compared the activities of various enzymes in the plant antioxidant enzyme system between Weston and Longdong during P. cactorum infection, as well as gene expression associated with plant hormone biosynthesis and response pathways. The results showed that the disease-resistant variety Weston has stronger antioxidant enzyme activity and high levels of SA-responsive PR genes, when compared to the susceptible variety Longdong. These findings highlighted the process of interaction between P. cactorum and alfalfa, as well as the mechanism of alfalfa resistance to P. cactorum, which provides an important foundation for breeding resistant alfalfa varieties, as well as managing Phytophthora-caused alfalfa root rot.
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Affiliation(s)
- Menghuan Tao
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxue Hu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Quan Zhang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Feng
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yiwen Lu
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Yang
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Xiao K, Zhu H, Zhu X, Liu Z, Wang Y, Pu W, Guan P, Hu J. Overexpression of PsoRPM3, an NBS-LRR gene isolated from myrobalan plum, confers resistance to Meloidogyne incognita in tobacco. PLANT MOLECULAR BIOLOGY 2021; 107:129-146. [PMID: 34596818 DOI: 10.1007/s11103-021-01185-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGES We reported an NBS-LRR gene, PsoRPM3, is highly expressed following RKN infection, initiating an HR response that promotes plant resistance. Meloidogyne spp. are root-knot nematodes (RKNs) that cause substantial economic losses worldwide. Screening for resistant tree resources and identifying plant resistance genes is currently the most effective way to prevent RKN infestations. Here, we cloned a novel TIR-NB-LRR-type resistance gene, PsoRPM3, from Xinjiang wild myrobalan plum (Prunus sogdiana Vassilcz.) and demonstrated that its protein product localized to the nucleus. In response to Meloidogyne incognita infection, PsoRPM3 gene expression levels were significantly higher in resistant myrobalan plum plants compared to susceptible plants. We investigated this difference, discovering that the - 309 to - 19 bp region of the susceptible PsoRPM3 promoter was highly methylated. Indeed, heterologous expression of PsoRPM3 significantly enhanced the resistance of susceptible tobacco plants to M. incognita. Moreover, transient expression of PsoRPM3 induced a hypersensitive response in tobacco, whereas RNAi-mediated silencing of PsoRPM3 in transgenic tobacco reduced this hypersensitive response. Several hypersensitive response marker genes were considerably up-regulated in resistant myrobalan plum plants when compared with susceptible counterparts inoculated with M. incognita. PsoPR1a (a SA marker gene), PsoPR2 (a JA marker gene), and PsoACS6 (an ET signaling marker gene) were all more highly expressed in resistant than in susceptible plants. Together, these results support a model in which PsoRPM3 is highly expressed following RKN infection, initiating an HR response that promotes plant resistance through activated salicylic acid, jasmonic acid, and ethylene signaling pathways.
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Affiliation(s)
- Kun Xiao
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Haifeng Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Xiang Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
- Institute of Laboratory Animal Science, Guizhou University of Traditional Chinese, Guiyang, China
| | - Zhenhua Liu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Yan Wang
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Wenjiang Pu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Pingyin Guan
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Jianfang Hu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China.
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Bhattarai K, Conesa A, Xiao S, Peres NA, Clark DG, Parajuli S, Deng Z. Sequencing and analysis of gerbera daisy leaf transcriptomes reveal disease resistance and susceptibility genes differentially expressed and associated with powdery mildew resistance. BMC PLANT BIOLOGY 2020; 20:539. [PMID: 33256589 PMCID: PMC7706040 DOI: 10.1186/s12870-020-02742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/16/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND RNA sequencing has been widely used to profile genome-wide gene expression and identify candidate genes controlling disease resistance and other important traits in plants. Gerbera daisy is one of the most important flowers in the global floricultural trade, and powdery mildew (PM) is the most important disease of gerbera. Genetic improvement of gerbera PM resistance has become a crucial goal in gerbera breeding. A better understanding of the genetic control of gerbera resistance to PM can expedite the development of PM-resistant cultivars. RESULTS The objectives of this study were to identify gerbera genotypes with contrasting phenotypes in PM resistance and sequence and analyze their leaf transcriptomes to identify disease resistance and susceptibility genes differentially expressed and associated with PM resistance. An additional objective was to identify SNPs and SSRs for use in future genetic studies. We identified two gerbera genotypes, UFGE 4033 and 06-245-03, that were resistant and susceptible to PM, respectively. De novo assembly of their leaf transcriptomes using four complementary pipelines resulted in 145,348 transcripts with a N50 of 1124 bp, of which 67,312 transcripts contained open reading frames and 48,268 were expressed in both genotypes. A total of 494 transcripts were likely involved in disease resistance, and 17 and 24 transcripts were up- and down-regulated, respectively, in UFGE 4033 compared to 06-245-03. These gerbera disease resistance transcripts were most similar to the NBS-LRR class of plant resistance genes conferring resistance to various pathogens in plants. Four disease susceptibility transcripts (MLO-like) were expressed only or highly expressed in 06-245-03, offering excellent candidate targets for gene editing for PM resistance in gerbera. A total of 449,897 SNPs and 19,393 SSRs were revealed in the gerbera transcriptomes, which can be a valuable resource for developing new molecular markers. CONCLUSION This study represents the first transcriptomic analysis of gerbera PM resistance, a highly important yet complex trait in a globally important floral crop. The differentially expressed disease resistance and susceptibility transcripts identified provide excellent targets for development of molecular markers and genetic maps, cloning of disease resistance genes, or targeted mutagenesis of disease susceptibility genes for PM resistance in gerbera.
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Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, IFAS, Gainesville, FL, 32611, USA
- University of Florida, Genetics Institute, Gainesville, FL, 32611, USA
| | - Shunyuan Xiao
- University of Maryland, College of Agriculture and Natural Resources, 4291 Fieldhouse Drive, Rockville, MD, 20850, USA
| | - Natalia A Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, 32611, USA
| | - Saroj Parajuli
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL, 33598, USA.
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Marimon N, Luque J, Arús P, Eduardo I. Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3. HORTICULTURE RESEARCH 2020; 7:175. [PMID: 33328431 PMCID: PMC7603514 DOI: 10.1038/s41438-020-00396-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 06/12/2023]
Abstract
Powdery mildew is one of the major diseases of peach (Prunus persica), caused by the ascomycete Podosphaera pannosa. Currently, it is controlled through calendar-based fungicide treatments starting at petal fall, but an alternative is to develop resistant peach varieties. Previous studies mapped a resistance gene (Vr3) in interspecific populations between almond ('Texas') and peach ('Earlygold'). To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes, we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated genes. To find evidence supporting one of these positional candidate genes as being responsible of Vr3, we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines (NILs) for expression analysis of the positional candidate genes in symptomatic or asymptomatic leaves. Genes differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2 (Prupe2G111700) or an Eceriferum 1 protein involved in epicuticular wax biosynthesis (Prupe2G112800). Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein, and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele, compared with susceptible individuals. This information was also useful to identify and validate molecular markers tightly linked and flanking Vr3. In addition, the NILs used in this work will facilitate the introgression of this gene into peach elite materials, alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.
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Grants
- RTA2015-00050-00-00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2013-00004-C03-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2013-00004-C03-01 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- RTA2015-00050-00-00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)
- COTPA-FRUIT3CAT Generalitat de Catalunya (Government of Catalonia)
- SEV-2015-0533 Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)
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Affiliation(s)
- Neus Marimon
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Plant Pathology, IRTA Cabrils, Carretera de Cabrils km 2, 08348, Cabrils, Spain
| | - Jordi Luque
- Plant Pathology, IRTA Cabrils, Carretera de Cabrils km 2, 08348, Cabrils, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain.
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Gétaz M, Puławska J, Smits TH, Pothier JF. Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis. Microorganisms 2020; 8:E1253. [PMID: 32824783 PMCID: PMC7465820 DOI: 10.3390/microorganisms8081253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/31/2022] Open
Abstract
Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100 Skierniewice, Poland;
| | - Theo H.M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
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Loarce Y, Dongil P, Fominaya A, González JM, Ferrer E. PK-profiling method for identifying the expression of resistance-associated genes in partially resistant oats to crown rust. BMC PLANT BIOLOGY 2018; 18:376. [PMID: 30594125 PMCID: PMC6311036 DOI: 10.1186/s12870-018-1604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Protein kinases play a key role in plant cell homeostasis and the activation of defense mechanisms. Partial resistance to fungi in plants is interesting because of its durability. However, the variable number of minor loci associated with this type of resistance hampers the reliable identification of the full range of genes involved. The present work reports the technique of protein kinase (PK)-profiling for the identification of the PK genes induced in the partially resistant oats line MN841801-1 following exposure to the fungus Puccinia coronata. This is the first time this technique has been used with cDNA (complementary DNA) from a suppression subtractive hybridization library obtained after the hybridization of cDNAs from inoculated and mock-inoculated plants. RESULTS Six degenerate primers based on the conserved domains of protein kinases were used in a PK-profiling assay including cDNA from mock-inoculated leaves and subtracted cDNA. Of the 75.7% of sequences cloned and sequenced that showed significant similarity to resistance genes, 76% were found to code for PKs. Translation and ClustalW2 alignment of each sequence cloned with the complete sequences of the most similar B. distachyon PKs allowed those of the partially resistant oat line to be deduced and characterized. Further, a phylogenetic study carried out after alignment of these B. distachyon PK sequences with the most similar protein sequences of related species also allowed to deduce different functions for the PK cloned. RT-qPCR (Reverse Transcription-quantitative PCR) was analyzed on nine representative sequences to validate the reliability of the employed PK-profiling method as a tool for identifying the expression of resistance-associated genes. CONCLUSIONS PK-profiling would appear to be a useful tool for the identification of the PKs expressed in oats after challenge by P. coronata, and perhaps other pathogens. Most of the PKs studied are related to receptor-like protein kinases expressed shortly after infection. This is in agreement with previous studies indicating a close relationship between partial resistance and the first layer of defense against pathogen used by plants.
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Affiliation(s)
- Yolanda Loarce
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Pilar Dongil
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Araceli Fominaya
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Juan M. González
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, University of Alcalá, Campus Universitario, 28805 Alcalá de Henares, Madrid Spain
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11
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Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 2018; 7:1-7. [PMID: 29253147 PMCID: PMC5801600 DOI: 10.1093/gigascience/gix124] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 12/18/2022] Open
Abstract
Background Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Conclusions Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Robert VanBuren
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Marivi Colle
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Thomas J Poorten
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
| | - Ching Man Wai
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Chad E Niederhuth
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Elizabeth I Alger
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Shujun Ou
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Charlotte B Acharya
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
| | - Jie Wang
- Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Pete Callow
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Michael R McKain
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132
| | - Jinghua Shi
- Bionano Genomics, San Diego, California, 92121
| | | | - Zhiyong Xiong
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, 010021, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, 68588
| | - Janet P Slovin
- USDA/ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, Maryland, 20705
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Ning Jiang
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Kevin L Childs
- Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Steven J Knapp
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
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12
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Zhang Q, Ma C, Zhang Y, Gu Z, Li W, Duan X, Wang S, Hao L, Wang Y, Wang S, Li T. A Single-Nucleotide Polymorphism in the Promoter of a Hairpin RNA Contributes to Alternaria alternata Leaf Spot Resistance in Apple ( Malus × domestica). THE PLANT CELL 2018; 30:1924-1942. [PMID: 30065047 PMCID: PMC6139694 DOI: 10.1105/tpc.18.00042] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/11/2018] [Accepted: 07/26/2018] [Indexed: 05/04/2023]
Abstract
Apple leaf spot caused by the Alternaria alternata f. sp mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA) named MdhpRNA277 that produces small RNAs and is induced by ALT1 infection in 'Golden Delicious' apple. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five resistance (R) genes that are expressed at high levels in resistant apple variety 'Hanfu' and at low levels in susceptible variety 'Golden Delicious' following ALT1 infection. MdhpRNA277 was strongly induced in 'Golden Delicious' but not 'Hanfu' following ALT1 inoculation. MdhpRNA277 promoter activity was much stronger in inoculated 'Golden Delicious' versus 'Hanfu'. We identified a single-nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between 'Golden Delicious' (pMdhpRNA277-GD) and 'Hanfu' (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF Transgenic 'GL-3' apple expressing pMdhpRNA277-GD:MdhpRNA277 was more susceptible to ALT1 infection than plants expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and reduced expression of the five target R genes. We confirmed that the SNP in pMdhpRNA277 is associated with A. alternata leaf spot resistance by crossing. This SNP could be used as a marker to distinguish between apple varieties that are resistant or susceptible to A. alternata leaf spot.
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Affiliation(s)
- Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chao Ma
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuwei Duan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yuanhua Wang
- Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
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13
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Jiang N, Cui J, Meng J, Luan Y. A Tomato Nucleotide Binding Sites-Leucine-Rich Repeat Gene Is Positively Involved in Plant Resistance to Phytophthora infestans. PHYTOPATHOLOGY 2018; 108:980-987. [PMID: 29595084 DOI: 10.1094/phyto-12-17-0389-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The nucleotide binding sites-leucine-rich repeat (NBS-LRR) genes are key regulatory components of plant to pathogens. Phytophthora infestans-inducible coding sequence encoding an NBS-LRR (SpNBS-LRR) protein in tomato (Solanum pimpinellifolium L3708) was cloned and characterized based on our RNA-Seq data and tomato genome. After sequence analysis, SpNBS-LRR was identified as a hydrophilic protein with no transmembrane topological structure and no signal peptide. SpNBS-LRR had a close genetic relationship to RPS2 of Arabidopsis thaliana by phylogenetic analysis. In addition, SpNBS-LRR gene was mainly expressed in root, with low expression observed in leaf and stem. To further investigate the role of SpNBS-LRR in tomato-P. infestans interaction, SpNBS-LRR was introduced in susceptible tomatoes and three transgenic lines with higher expression level of SpNBS-LRR were selected. These transgenic tomato plants that overexpressed SpNBS-LRR displayed greater resistance than wild-type tomato plants after infection with P. infestans, as shown by decreased disease index, lesion diameters, number of necrotic cells, P. infestans abundance, and higher expression levels of the defense-related genes. This information provides insight into SpNBS-LRR involved in the resistance of tomato to P. infestans infection and candidate for breeding to enhance biotic stress-resistance in tomato.
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Affiliation(s)
- Ning Jiang
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jun Cui
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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14
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Ye W, Zhang W, Liu T, Huang Z, Zhu M, Chen Y, Li H, Li S. De Novo Transcriptome Sequencing of the Deep-Sea-Derived Fungus Dichotomomyces cejpii and Analysis of Gliotoxin Biosynthesis Genes. Int J Mol Sci 2018; 19:E1910. [PMID: 29966253 PMCID: PMC6073683 DOI: 10.3390/ijms19071910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/17/2018] [Accepted: 06/26/2018] [Indexed: 12/03/2022] Open
Abstract
Gliotoxin, produced by fungi, is an epipolythiodioxopiperazine (ETP) toxin with bioactivities such as anti-liver fibrosis, antitumor, antifungus, antivirus, antioxidation, and immunoregulation. Recently, cytotoxic gliotoxins were isolated from a deep-sea-derived fungus, Dichotomomyces cejpii. However, the biosynthetic pathway for gliotoxins in D. cejpii remains unclear. In this study, the transcriptome of D. cejpii was sequenced using an Illumina Hiseq 2000. A total of 19,125 unigenes for D. cejpii were obtained from 9.73 GB of clean reads. Ten genes related to gliotoxin biosynthesis were annotated. The expression levels of gliotoxin-related genes were detected through quantitative real-time polymerase chain reaction (qRT-PCR). The GliG gene, encoding a glutathione S-transferase (DC-GST); GliI, encoding an aminotransferase (DC-AI); and GliO, encoding an aldehyde reductase (DC-AR), were cloned and expressed, purified, and characterized. The results suggested the important roles of DC-GST, DC-AT, and DC-AR in the biosynthesis of gliotoxins. Our study on the genes related to gliotoxin biosynthesis establishes a molecular foundation for the wider application of gliotoxins from D. cejpii in the biomedical industry in the future.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
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15
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Zhong Y, Zhang X, Cheng ZM. Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species. BMC Genomics 2018; 19:128. [PMID: 29422035 PMCID: PMC5806312 DOI: 10.1186/s12864-018-4521-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/31/2018] [Indexed: 12/16/2022] Open
Abstract
Background Plant disease resistance (R) genes are evolving rapidly and play a critical role in the innate immune system of plants. The nucleotide binding sites-leucine rich repeat (NBS-LRR) genes are one of the largest classes in plant R genes. Previous studies have focused on the NBS-LRR genes from one or several species of different genera, and the sequenced genomes of the genus Fragaria offer the opportunity to study the evolutionary processes of these R genes among the closely related species. Results In this study, 325, 155, 190, 187, and 133 NBS-LRRs were discovered from F. x ananassa, F. iinumae, F. nipponica, F. nubicola, and F. orientalis, respectively. Together with the 144 NBS-LRR genes from F. vesca, a total of 1134 NBS-LRRs containing 866 multi-genes comprised 184 gene families across the six Fragaria genomes. Extremely short branch lengths and shallow nodes were widely present in the phylogenetic tree constructed with all of the NBS-LRR genes of the six strawberry species. The identities of the orthologous genes were highly significantly greater than those of the paralogous genes, while the Ks ratios of the former were very significantly lower than those of the latter in all of the NBS-LRR gene families. In addition, the Ks and Ka/Ks values of the TIR-NBS-LRR genes (TNLs) were significantly greater than those of the non-TIR-NBS-LRR genes (non-TNLs). Furthermore, the expression patterns of the NBS-LRR genes revealed that the same gene expressed differently under different genetic backgrounds in response to pathogens. Conclusions These results, combined with the shared hotspot regions of the duplicated NBS-LRRs on the chromosomes, indicated that the lineage-specific duplication of the NBS-LRR genes occurred before the divergence of the six Fragaria species. The Ks and Ka/Ks ratios suggested that the TNLs are more rapidly evolving and driven by stronger diversifying selective pressures than the non-TNLs. Electronic supplementary material The online version of this article (10.1186/s12864-018-4521-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Xiaohui Zhang
- School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Zong-Ming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. .,Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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16
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Transcription profiling and identification of infection-related genes in Phytophthora cactorum. Mol Genet Genomics 2017; 293:541-555. [PMID: 29218408 DOI: 10.1007/s00438-017-1400-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/23/2017] [Indexed: 10/18/2022]
Abstract
Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively. Furthermore, the transcriptome difference among MY, ZO and GC stages was investigated. Gene ontology (GO) and KEGG pathway enrichment analyses revealed diverse biological functions and processes. Comparative analysis identified a large number of genes that are associated with specific stages and pathogenicity, including 166 effector genes. Of them, most of RXLR and NLP genes showed induction while the majority of CRN genes were down-regulated in GC, the important pre-infection stage, compared to either MY or ZO. And 14 genes encoding small cysteine-rich (SCR) secretory proteins showed differential expression during the developmental stages and in planta. Ectopic expression in the Solanaceae indicated that SCR113 and one elicitin PcINF1 can trigger cell death on Nicotiana benthamiana, tobacco (N. tabacum) and tomato (Solanum lycopersicum) leaves. Neither conserved domain nor homologues of SCR113 in other organisms can be identified. Collectively, our study provides a comprehensive examination of gene expression across three P. cactorum developmental stages and describes pathogenicity-related genes, all of which will help elucidate the pathogenicity mechanism of this destructive pathogen.
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17
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Zhang S, Ding F, Peng H, Huang Y, Lu J. Molecular cloning of a CC-NBS-LRR gene from Vitis quinquangularis and its expression pattern in response to downy mildew pathogen infection. Mol Genet Genomics 2017; 293:61-68. [PMID: 28864888 DOI: 10.1007/s00438-017-1360-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Downy mildew, caused by Plasmopara viticola, can result in a substantial decrease in grapevine productivity. Vitis vinifera is a widely cultivated grapevine species, which is susceptible to this disease. Repeated pesticide applications are harmful for both the environment and human health. Thus, it is essential to develop varieties/cultivars that are resistant to downy mildew and other diseases. In our previous studies, we investigated the natural resistance of the Chinese wild grapevine V. quinquangularis accession 'PS' against P. viticola and obtained several candidate resistance (R) genes that may play important roles in plant disease resistance. In the present study, we isolated a CC-NBS-LRR-type R gene from 'PS' and designated it VqCN. Its open reading frame is 2676 bp which encodes a protein of 891 amino acids with a predicted molecular mass of 102.12 kDa and predicted isoelectric point of 6.53. Multiple alignments with other disease resistant (R) proteins revealed a conserved phosphate-binding loop (P-loop), resistance nucleotide binding site, a hydrophobic domain (GLPL) and methionine-histidine-aspartate (MHD) motifs, which are typical components of nucleotide-binding site leucine-rich repeat proteins, as well as a coiled-coil region in the N-terminus. Quantitative real-time polymerase chain reaction analysis showed that the transcript of VqCN was rapidly and highly induced after infection with P. viticola in 'PS'. Moreover, the leaves of susceptible 'Cabernet Sauvignon' transiently expressing VqCN manifested increased resistance to P. viticola. The results indicated that VqCN might play a positive role in protecting grapevine against infection with P. viticola. Cloning and functional analysis of a putative resistance gene provide a basis for disease-resistance breeding.
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Affiliation(s)
- Shuwei Zhang
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hongxiang Peng
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yu Huang
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jiang Lu
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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18
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Ye W, Liu T, Zhu M, Zhang W, Li H, Huang Z, Li S. De Novo Transcriptome Analysis of Plant Pathogenic Fungus Myrothecium roridum and Identification of Genes Associated with Trichothecene Mycotoxin Biosynthesis. Int J Mol Sci 2017; 18:E497. [PMID: 28245611 PMCID: PMC5372513 DOI: 10.3390/ijms18030497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 12/20/2022] Open
Abstract
Myrothecium roridum is a plant pathogenic fungus that infects different crops and decreases the yield of economical crops, including soybean, cotton, corn, pepper, and tomato. Until now, the pathogenic mechanism of M. roridum has remained unclear. Different types of trichothecene mycotoxins were isolated from M. roridum, and trichothecene was considered as a plant pathogenic factor of M. roridum. In this study, the transcriptome of M. roridum in different incubation durations was sequenced using an Illumina Hiseq 2000. A total of 35,485 transcripts and 25,996 unigenes for M. roridum were obtained from 8.0 Gb clean reads. The protein-protein network of the M. roridum transcriptome indicated that the mitogen-activated protein kinases signal pathway also played an important role in the pathogenicity of M. roridum. The genes related to trichothecene biosynthesis were annotated. The expression levels of these genes were also predicted and validated through quantitative real-time polymerase chain reaction. Tri5 gene encoding trichodiene synthase was cloned and expressed, and the purified trichodiene synthase was able to catalyze farnesyl pyrophosphate into different kinds of sesquiterpenoids.Tri4 and Tri11 genes were expressed in Escherichia coli, and their corresponding enzymatic properties were characterized. The phylogenetic tree of trichodiene synthase showed a great discrepancy between the trichodiene synthase from M. roridum and other species. Our study on the genes related to trichothecene biosynthesis establishes a foundation for the M. roridum hazard prevention, thus improving the yields of economical crops.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
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