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Mena E, Reboledo G, Stewart S, Montesano M, Ponce de León I. Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora. Sci Rep 2023; 13:13061. [PMID: 37567886 PMCID: PMC10421924 DOI: 10.1038/s41598-023-39695-1] [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: 09/30/2022] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Soybean stem canker (SSC) caused by the fungal pathogen Diaporthe caulivora is an important disease affecting soybean production worldwide. However, limited information related to the molecular mechanisms underlying soybean resistance to Diaporthe species is available. In the present work, we analyzed the defense responses to D. caulivora in the soybean genotypes Williams and Génesis 5601. The results showed that compared to Williams, Génesis 5601 is more resistant to fungal infection evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and in D. caulivora-inoculated and control-treated tissues at 8 and 48 h post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Génesis 5601 and Williams, respectively. Interestingly, Génesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance to D. caulivora was associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormone signaling, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense mechanisms leading to host resistance against D. caulivora, and generate a foundation for the development of resistant SSC varieties within soybean breeding programs.
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Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvina Stewart
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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Cabre L, Peyrard S, Sirven C, Gilles L, Pelissier B, Ducerf S, Poussereau N. Identification and characterization of a new soybean promoter induced by Phakopsora pachyrhizi, the causal agent of Asian soybean rust. BMC Biotechnol 2021; 21:27. [PMID: 33765998 PMCID: PMC7995590 DOI: 10.1186/s12896-021-00684-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phakopsora pachyrhizi is a biotrophic fungal pathogen responsible for the Asian soybean rust disease causing important yield losses in tropical and subtropical soybean-producing countries. P. pachyrhizi triggers important transcriptional changes in soybean plants during infection, with several hundreds of genes being either up- or downregulated. RESULTS Based on published transcriptomic data, we identified a predicted chitinase gene, referred to as GmCHIT1, that was upregulated in the first hours of infection. We first confirmed this early induction and showed that this gene was expressed as early as 8 h after P. pachyrhizi inoculation. To investigate the promoter of GmCHIT1, transgenic soybean plants expressing the green fluorescence protein (GFP) under the control of the GmCHIT1 promoter were generated. Following inoculation of these transgenic plants with P. pachyrhizi, GFP fluorescence was detected in a limited area located around appressoria, the fungal penetration structures. Fluorescence was also observed after mechanical wounding whereas no variation in fluorescence of pGmCHIT1:GFP transgenic plants was detected after a treatment with an ethylene precursor or a methyl jasmonate analogue. CONCLUSION We identified a soybean chitinase promoter exhibiting an early induction by P. pachyrhizi located in the first infected soybean leaf cells. Our results on the induction of GmCHIT1 promoter by P. pachyrhizi contribute to the identification of a new pathogen inducible promoter in soybean and beyond to the development of a strategy for the Asian soybean rust disease control using biotechnological approaches.
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Affiliation(s)
- L. Cabre
- Univ Lyon, Université Lyon 1, CNRS, INSA-Lyon, Bayer SAS Crop Science Division, UMR 5240 MAP, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet BP 99163, 69263 Lyon Cedex 09, France
| | - S. Peyrard
- Bayer SAS, Crop Science Division, 14 Impasse Pierre Baizet, BP 99163, 69263 Lyon Cedex 09, France
| | - C. Sirven
- Bayer SAS, Crop Science Division, 14 Impasse Pierre Baizet, BP 99163, 69263 Lyon Cedex 09, France
| | - L. Gilles
- Bayer SAS, Crop Science Division, 14 Impasse Pierre Baizet, BP 99163, 69263 Lyon Cedex 09, France
- Present address: Limagrain, Biopôle Clermont-Limagne, Rue Henri Mondor, 63360 Saint Beauzire, France
| | - B. Pelissier
- Bayer SAS, Crop Science Division, 14 Impasse Pierre Baizet, BP 99163, 69263 Lyon Cedex 09, France
| | - S. Ducerf
- Bayer SAS, Crop Science Division, 14 Impasse Pierre Baizet, BP 99163, 69263 Lyon Cedex 09, France
| | - N. Poussereau
- Univ Lyon, Université Lyon 1, CNRS, INSA-Lyon, Bayer SAS Crop Science Division, UMR 5240 MAP, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet BP 99163, 69263 Lyon Cedex 09, France
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Parmezan TR, Brito Júnior SL, Carvalho KD, Aquino MD, Birkett M, Pickett J, Nunes EDO, Abdelnor RV, Campo CBH, Marcelino-Guimarães FC. Transcriptional profile of genes involved in the production of terpenes and glyceollins in response to biotic stresses in soybean. Genet Mol Biol 2020; 43:e20190388. [PMID: 33174975 PMCID: PMC7644969 DOI: 10.1590/1678-4685-gmb-2019-0388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/08/2020] [Indexed: 11/21/2022] Open
Abstract
Terpenes produced by plants comprise a diverse range of secondary metabolites, including volatile organic compounds (VOCs). Terpene VOC production may be altered after damage or by biological stimuli such as bacterial, fungal and insects, and subsequent triggering of plant defense responses. These VOCs originate in plants from two independent pathways: the mevalonate and the methylerythritol phosphate pathways, which utilize dimethylallyl and isopentenyl diphosphates to form the terpenoidal precursors. Phakopsora pachyrhizi fungi causes Asian soybean rust, limiting soybean production and resulting in losses of up to 80% if no control strategies are applied. By using a transcriptome datasets, we investigated the regulation of genes of the mevalonate pathway under different biotic stresses. We studied the impact of P. pachyrhizi infection in vivo expression profile of genes involved in terpenoid and glyceollin biosynthesis in genotypes harboring different resistance genes (Rpp), and across the infection cycle. In addition, we used UPLC and UPGC analysis to evaluate glyceollin and VOC production, respectively, to identify metabolites associated with soybean responses to pathogen infection. The regulation of soybean genes involved in terpene production was influenced by genotypes, depending on the Rpp gene, while glyceollin was induced in all genotypes. Furthermore, a sesquiterpene was identified as a potential marker associated with rust symptoms on soybean.
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Affiliation(s)
- Talitta Regina Parmezan
- Universidade Estadual de Londrina, Departamento de Bioquímica e Biotecnologia, Londrina, PR, Brazil
| | | | - Kenia de Carvalho
- Universidade Estadual de Londrina, Departamento de Genética e Biologia Molecular, Londrina, PR, Brazil
| | - Moisés de Aquino
- Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA Soja, Londrina, PR, Brazil
| | - Michael Birkett
- Rothamsted Research, Biointeractions and Crop Protection Department, Harpenden, UK
| | - John Pickett
- Cardiff University, School of Chemistry, Wales, UK
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de Carvalho MCDCG, Costa Nascimento L, Darben LM, Polizel‐Podanosqui AM, Lopes‐Caitar VS, Qi M, Rocha CS, Carazzolle MF, Kuwahara MK, Pereira GAG, Abdelnoor RV, Whitham SA, Marcelino‐Guimarães FC. Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families. MOLECULAR PLANT PATHOLOGY 2017; 18:363-377. [PMID: 27010366 PMCID: PMC6638266 DOI: 10.1111/mpp.12405] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, can cause losses greater than 80%. Despite its economic importance, there is no soybean cultivar with durable ASR resistance. In addition, the P. pachyrhizi genome is not yet available. However, the availability of other rust genomes, as well as the development of sample enrichment strategies and bioinformatics tools, has improved our knowledge of the ASR secretome and its potential effectors. In this context, we used a combination of laser capture microdissection (LCM), RNAseq and a bioinformatics pipeline to identify a total of 36 350 P. pachyrhizi contigs expressed in planta and a predicted secretome of 851 proteins. Some of the predicted secreted proteins had characteristics of candidate effectors: small size, cysteine rich, do not contain PFAM domains (except those associated with pathogenicity) and strongly expressed in planta. A comparative analysis of the predicted secreted proteins present in Pucciniales species identified new members of soybean rust and new Pucciniales- or P. pachyrhizi-specific families (tribes). Members of some families were strongly up-regulated during early infection, starting with initial infection through haustorium formation. Effector candidates selected from two of these families were able to suppress immunity in transient assays, and were localized in the plant cytoplasm and nuclei. These experiments support our bioinformatics predictions and show that these families contain members that have functions consistent with P. pachyrhizi effectors.
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Affiliation(s)
| | - Leandro Costa Nascimento
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | - Luana M. Darben
- Embrapa sojaPlant BiotechnologyLondrinaParanáCEP 70770‐901Brazil
| | | | - Valéria S. Lopes‐Caitar
- Embrapa sojaPlant BiotechnologyLondrinaParanáCEP 70770‐901Brazil
- Universidade Estadual de LondrinaLondrinaParanáCEP 86057‐970Brazil
| | - Mingsheng Qi
- Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | | | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | | | - Goncalo A. G. Pereira
- Laboratório de Genômica e Expressão (LGE) – Instituto de Biologia ‐ Universidade Estadual de CampinasCampinasSão PauloCEP 13083‐862Brazil
| | | | - Steven A. Whitham
- Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
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Schaker PDC, Palhares AC, Taniguti LM, Peters LP, Creste S, Aitken KS, Van Sluys MA, Kitajima JP, Vieira MLC, Monteiro-Vitorello CB. RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease. PLoS One 2016; 11:e0162237. [PMID: 27583836 PMCID: PMC5008620 DOI: 10.1371/journal.pone.0162237] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/21/2016] [Indexed: 11/25/2022] Open
Abstract
Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic functions toward reproductive organ differentiation, requiring strong changes in carbon partitioning and energy production. These changes include the overexpression of genes coding for invertases and trehalose-6P synthase, as well as other enzymes from key metabolic pathways, such as from lignin biosynthesis. This is the first report describing changes in the transcriptional profiles following whip development, providing a hypothetical model and candidate genes to further study sugarcane smut disease progression.
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Affiliation(s)
- Patricia D. C. Schaker
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Alessandra C. Palhares
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Lucas M. Taniguti
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Leila P. Peters
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Instituto Agronômico de Campinas, Centro de Cana, Ribeirão Preto, São Paulo, Brazil
| | - Karen S. Aitken
- CSIRO Agriculture, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Maria L. C. Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
| | - Claudia B. Monteiro-Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura “Luiz de Queiroz”, Piracicaba, São Paulo, Brazil
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Meyer FE, Shuey LS, Naidoo S, Mamni T, Berger DK, Myburg AA, van den Berg N, Naidoo S. Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility. FRONTIERS IN PLANT SCIENCE 2016; 7:191. [PMID: 26973660 PMCID: PMC4773608 DOI: 10.3389/fpls.2016.00191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction.
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Affiliation(s)
- Febé E. Meyer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Louise S. Shuey
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sitha Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Thandekile Mamni
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Dave K. Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Noëlani van den Berg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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Laura M, Borghi C, Bobbio V, Allavena A. The effect on the transcriptome of Anemone coronaria following infection with rust (Tranzschelia discolor). PLoS One 2015; 10:e0118565. [PMID: 25768012 PMCID: PMC4359109 DOI: 10.1371/journal.pone.0118565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/20/2015] [Indexed: 12/25/2022] Open
Abstract
In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3'end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.
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Affiliation(s)
- Marina Laura
- CRA—Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy
| | - Cristina Borghi
- CRA—Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy
| | - Valentina Bobbio
- CRA—Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy
| | - Andrea Allavena
- CRA—Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy
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