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Purohit A, Ghosh S, Ganguly S, Negi MS, Tripathi SB, Chaudhuri RK, Chakraborti D. Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection. Sci Rep 2021; 11:22319. [PMID: 34785701 PMCID: PMC8595609 DOI: 10.1038/s41598-021-01587-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Vascular wilt caused by Fusarium udum Butler is the most important disease of pigeonpea throughout the world. F. udum isolate MTCC 2204 (M1) inoculated pigeonpea plants of susceptible (ICP 2376) and resistant (ICP 8863) cultivars were taken at invasion stage of pathogenesis process for transcriptomic profiling to understand defense signaling reactions that interplay at early stage of this plant-pathogen encounter. Differential transcriptomic profiles were generated through cDNA-AFLP from M1 inoculated resistant and susceptible pigeonpea root tissues. Twenty five percent of transcript derived fragments (TDFs) were found to be pathogen induced. Among them 73 TDFs were re-amplified and sequenced. Homology search of the TDFs in available databases and thorough study of scientific literature identified several pathways, which could play crucial role in defense responses of the F. udum inoculated resistant plants. Some of the defense responsive pathways identified to be active during this interaction are, jasmonic acid and salicylic acid mediated defense responses, cell wall remodeling, vascular development and pattering, abscisic acid mediated responses, effector triggered immunity, and reactive oxygen species mediated signaling. This study identified important wilt responsive regulatory pathways in pigeonpea which will be helpful for further exploration of these resistant components for pigeonpea improvement.
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Affiliation(s)
- Arnab Purohit
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sanatan Ghosh
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Shreeparna Ganguly
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
| | - Madan Singh Negi
- Sustainable Agriculture Division, TERI, India Habitat Center Complex, Lodhi Road, New Delhi, 110003, India
| | - Shashi Bhushan Tripathi
- TERI-School of Advanced Studies, 10, Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | | | - Dipankar Chakraborti
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Soil pathogen, Fusarium oxysporum induced wilt disease in chickpea: a review on its dynamicity and possible control strategies. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00030-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this "kingdom." The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The "1000 Fungal Genomes Project" represents one of the largest sequencing initiative regarding fungal organisms trying to fill some gaps on fungal genomics. Presently, there are 329 fungal families with at least one representative genome sequenced, but there is still a large number of fungal families without a single sequenced genome. In addition, additional sequencing projects helped to understand the genetic diversity within some fungal species. The availability of multiple genomes per species allows to support taxonomic organization, brings new insights for fungal evolution in short-time scales, clarifies geographical and dispersion patterns, elucidates outbreaks and transmission routes, among other objectives. Genotyping methodologies analyze only a small fraction of an individual's genome but facilitate the comparison of hundreds or thousands of isolates in a small fraction of the time and at low cost. The integration of whole genome strategies and improved genotyping panels targeting specific and relevant SNPs and/or repeated regions can represent fast and practical strategies for studying local, regional, and global epidemiology of fungi.
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Affiliation(s)
- Ricardo Araujo
- University of Porto, Porto, Portugal; School of Medicine and Health Sciences, Flinders University, Adelaide, SA, Australia.
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Silvia Sebastiani M, Bagnaresi P, Sestili S, Biselli C, Zechini A, Orrù L, Cattivelli L, Ficcadenti N. Transcriptome Analysis of the Melon- Fusarium oxysporum f. sp. melonis Race 1.2 Pathosystem in Susceptible and Resistant Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:362. [PMID: 28367157 PMCID: PMC5356040 DOI: 10.3389/fpls.2017.00362] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/01/2017] [Indexed: 05/20/2023]
Abstract
Fusarium oxysporum f. sp. melonis Snyd. & Hans race 1.2 (FOM1.2) is the most virulent and yield-limiting pathogen of melon (Cucumis melo L.) worldwide. Current information suggest that the resistance to race 1.2 is controlled by multiple recessive genes and strongly affected by the environment. RNA-Seq analysis was used to identify candidate resistance genes and to dissect the early molecular processes deployed during melon-FOM1.2 interaction in the resistant doubled haploid line NAD and in the susceptible genotype Charentais-T (CHT) at 24 and 48 h post-inoculation (hpi). The transcriptome analysis of the NAD-FOM1.2 interaction identified 2,461 and 821 differentially expressed genes (DEGs) at 24 hpi and at 48 hpi, respectively, while in susceptible combination CHT-FOM1.2, 882 and 2,237 DEGs were recovered at 24 hpi and at 48 hpi, respectively. The overall expression profile suggests a prompt activation of the defense responses in NAD due to its basal defense-related machinery that allows an early pathogen recognition. Gene Ontology (GO) enrichment analyses revealed a total of 57 GO terms shared by both genotypes and consistent with response to fungal infection. GO classes named "chitinase activity," "cellulase activity," "defense response, incompatible interaction," "auxin polar transport" emerged as major factors of resistance to FOM1.2. The data indicated that NAD reacts to FOM1.2 with a fine regulation of Ca2+-mediated signaling pathways, cell wall reorganization, and hormone crosstalk (jasmonate and ethylene, auxin and abscissic acid). Several unannotated transcripts were recovered providing a basis for a further exploration of the melon resistance genes. DEGs belonging to the FOM1.2 genome were also detected in planta as a resource for the identification of potential pathogenicity factors. This work provides a broader view of the dynamic changes of the melon transcriptome triggered by FOM1.2 and highlights that the resistance response of NAD is mainly signaled by jasmonic acid and ethylene pathways mediated by ABA and auxin. The role of candidate plant and fungal responsive genes involved in the resistance is discussed.
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Affiliation(s)
- M. Silvia Sebastiani
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Paolo Bagnaresi
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Sara Sestili
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Chiara Biselli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Antonella Zechini
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Orrù
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Cattivelli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Nadia Ficcadenti
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
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Thatcher LF, Williams AH, Garg G, Buck SAG, Singh KB. Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors. BMC Genomics 2016; 17:860. [PMID: 27809762 PMCID: PMC5094085 DOI: 10.1186/s12864-016-3192-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume Medicago truncatula and a pathogenic F. oxysporum forma specialis (f. sp.) medicaginis (Fom). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession. RESULTS High coverage RNA-Seq of Fom infected root samples harvested from susceptible (DZA315) or resistant (A17) M. truncatula seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of in planta differentially expressed genes. This included enrichment, particularly in DZA315 in planta up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high in-planta induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other F. oxysporum ff. spp. as well as other Fusaria (F. solani, F. fujikori, F. verticilloides, F. graminearum and F. pseudograminearum), and from another wilt pathogen of the same class, a Verticillium species. Overall, this suggests these novel effector candidates may play important roles in Fusaria and wilt pathogen virulence. CONCLUSION Combining high coverage in planta RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible M. truncatula host. The knowledge from this first in depth in planta transcriptome sequencing of any F. oxysporum ff. spp. pathogenic on legumes will facilitate the dissection of Fusarium wilt pathogenicity mechanisms on many important legume crops.
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Affiliation(s)
- Louise F. Thatcher
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Angela H. Williams
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Sally-Anne G. Buck
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
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Sonah H, Zhang X, Deshmukh RK, Borhan MH, Fernando WGD, Bélanger RR. Comparative Transcriptomic Analysis of Virulence Factors in Leptosphaeria maculans during Compatible and Incompatible Interactions with Canola. FRONTIERS IN PLANT SCIENCE 2016; 7:1784. [PMID: 27990146 PMCID: PMC5131014 DOI: 10.3389/fpls.2016.01784] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 11/11/2016] [Indexed: 05/08/2023]
Abstract
Leptosphaeria maculans is a hemibiotrophic fungus that causes blackleg of canola (Brassica napus), one of the most devastating diseases of this crop. In the present study, transcriptome profiling of L. maculans was performed in an effort to understand and define the pathogenicity genes that govern both the biotrophic and the necrotrophic phase of the fungus, as well as those that separate a compatible from an incompatible interaction. For this purpose, comparative RNA-seq analyses were performed on L. maculans isolate D5 at four different time points following inoculation on susceptible cultivar Topas-DH16516 or resistant introgression line Topas-Rlm2. Analysis of 1.6 billion Illumina reads readily identified differentially expressed genes that were over represented by candidate secretory effector proteins, CAZymes, and other pathogenicity genes. Comparisons between the compatible and incompatible interactions led to the identification of 28 effector proteins whose chronology and level of expression suggested a role in the establishment and maintenance of biotrophy with the plant. These included all known Avr genes of isolate D5 along with eight newly characterized effectors. In addition, another 15 effector proteins were found to be exclusively expressed during the necrotrophic phase of the fungus, which supports the concept that L. maculans has a separate and distinct arsenal contributing to each phase. As for CAZymes, they were often highly expressed at 3 dpi but with no difference in expression between the compatible and incompatible interactions, indicating that other factors were necessary to determine the outcome of the interaction. However, their significantly higher expression at 11 dpi in the compatible interaction confirmed that they contributed to the necrotrophic phase of the fungus. A notable exception was LysM genes whose high expression was singularly observed on the susceptible host at 7 dpi. In the case of TFs, their higher expression at 7 and 11 dpi on susceptible Topas support an important role in regulating the genes involved in the different pathogenic phases of L. maculans. In conclusion, comparison of the transcriptome of L. maculans during compatible and incompatible interactions has led to the identification of key pathogenicity genes that regulate not only the fate of the interaction but also lifestyle transitions of the fungus.
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Affiliation(s)
- Humira Sonah
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université LavalQuébec QC, Canada
| | - Xuehua Zhang
- Department of Plant Science, University of Manitoba WinnipegWinnipeg, MB, Canada
| | - Rupesh K. Deshmukh
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université LavalQuébec QC, Canada
| | | | | | - Richard R. Bélanger
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université LavalQuébec QC, Canada
- *Correspondence: Richard R. Bélanger
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Lanubile A, Muppirala UK, Severin AJ, Marocco A, Munkvold GP. Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum. BMC Genomics 2015; 16:1089. [PMID: 26689712 PMCID: PMC4687377 DOI: 10.1186/s12864-015-2318-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/15/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Fusarium oxysporum is one of the most common fungal pathogens causing soybean root rot and seedling blight in U.S.A. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. RESULTS We used RNA-seq analysis to investigate the molecular aspects of the interactions of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 h post inoculation (hpi). Markedly different gene expression profiles were observed in response to the two isolates. A peak of highly differentially expressed genes (HDEGs) was triggered at 72 hpi in soybean roots and the number of HDEGs was about eight times higher in response to the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 HDEGs, respectively). Furthermore, the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of defense-related genes, transcription factors, and genes involved in ethylene biosynthesis, secondary and sugar metabolism. CONCLUSIONS The obtained data provide an important insight into the transcriptional responses of soybean-F. oxysporum interactions and illustrate the more drastic changes in the host transcriptome in response to the pathogenic isolate. These results may be useful in the developing new methods of broadening resistance of soybean to F. oxysporum, including the over-expression of key soybean genes.
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Affiliation(s)
- Alessandra Lanubile
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy.
- Department of Plant Pathology and Microbiology, Iowa State University, 50011, Ames, IA, USA.
| | - Usha K Muppirala
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, 50011, Ames, IA, USA.
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, 50011, Ames, IA, USA.
| | - Adriano Marocco
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy.
| | - Gary P Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, 50011, Ames, IA, USA.
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Castillejo MÁ, Bani M, Rubiales D. Understanding pea resistance mechanisms in response to Fusarium oxysporum through proteomic analysis. PHYTOCHEMISTRY 2015; 115:44-58. [PMID: 25672548 DOI: 10.1016/j.phytochem.2015.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/05/2015] [Accepted: 01/15/2015] [Indexed: 05/06/2023]
Abstract
Fusarium oxysporum f. sp. pisi (Fop) is an important and destructive pathogen affecting pea crop (Pisum sativum) throughout the world. Control of this disease is achieved mainly by integration of different disease management procedures. However, the constant evolution of the pathogen drives the necessity to broaden the molecular basis of resistance to Fop. Our proteomic study was performed on pea with the aim of identifying proteins involved in different resistance mechanisms operating during F. oxysporum infection. For such purpose, we used a two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MALDI-TOF/TOF) analysis to study the root proteome of three pea genotypes showing different resistance response to Fop race 2. Multivariate statistical analysis identified 132 differential protein spots under the experimental conditions (genotypes/treatments). All of these protein spots were subjected to mass spectrometry analysis to deduce their possible functions. A total of 53 proteins were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. The following main functional categories were assigned to the identified proteins: carbohydrate and energy metabolism, nucleotides and aminoacid metabolism, signal transduction and cellular process, folding and degradation, redox and homeostasis, defense, biosynthetic process and transcription/translation. Results obtained in this work suggest that the most susceptible genotypes have increased levels of enzymes involved in the production of reducing power which could then be used as cofactor for enzymes of the redox reactions. This is in concordance with the fact that a ROS burst occurred in the same genotypes, as well as an increase of PR proteins. Conversely, in the resistant genotype proteins responsible to induce changes in the membrane and cell wall composition related to reinforcement were identified. Results are discussed in terms of the differential response to Fop.
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Affiliation(s)
| | - Moustafa Bani
- Institute for Sustainable Agriculture, CSIC, 4084, 14080 Córdoba, Spain; Biotechnology Department, University of Blida, 09000 Blida, Algeria
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 4084, 14080 Córdoba, Spain
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Soresi D, Carrera AD, Echenique V, Garbus I. Identification of genes induced by Fusarium graminearum inoculation in the resistant durum wheat line Langdon(Dic-3A)10 and the susceptible parental line Langdon. Microbiol Res 2015. [PMID: 26211966 DOI: 10.1016/j.micres.2015.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The wheat recombinant chromosome inbred line LDN(Dic-3A)10, obtained through introgression of a Triticum dicoccoides disomic chromosome 3A fragment into Triticum turgidum spp. durum var. Langdon, is resistant to fusarium head blight (FHB) caused by Fusarium graminearum. To identify genes involved in FHB resistance, we used a cDNA-AFLP approach to compare gene expression between LDN(Dic-3A)10 and the susceptible parental line LDN at different time points post-inoculation. In total, 85 out of the ∼ 500 transcript-derived fragments (TDFs) were found to be differentially expressed: 36 and 19% were upregulated in LDN(Dic-3A)10 and LDN, respectively, whereas 45% were induced in both genotypes. Several of the cloned TDFs showed similarity to proteins involved in specific recognition of plant pathogens or associated with early responses to infection. Some TDFs specific to the inoculation response did not show similarity to characterized proteins. The availability of T. aestivum genome sequences allowed the in silico mapping of 28 TDFs and the acquirement of the corresponding gene sequences and, in some cases, their regulatory regions. Analysis of promoter regions revealed the potential existence of shared transcription regulation mechanisms. For instance, three TDF-associated genes contained binding sites for WRKY transcription factors, which have been implicated in the regulation of genes associated with pathogen defense, and three for abscisic acid-responsive element (ABRE). Collectively, our results revealed specific pathogen recognition in the interactions of LDN and LDN(Dic-3A)10 with F. graminearum. Such recognition leads to changes in the expression of several transcripts, attributable to the presence of the wheat QTL Qfhs.ndsu-3AS.
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Affiliation(s)
- Daniela Soresi
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) - CONICET, Camino de La Carrindanga Km 7, 8000 Bahía Blanca, Argentina
| | - Alicia D Carrera
- Departamento de Agronomía, Universidad Nacional del Sur, San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) - CONICET, Camino de La Carrindanga Km 7, 8000 Bahía Blanca, Argentina; Departamento de Agronomía, Universidad Nacional del Sur, San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Ingrid Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) - CONICET, Camino de La Carrindanga Km 7, 8000 Bahía Blanca, Argentina; Departamento de Ciencias de la Salud, Universidad Nacional del Sur, Florida 1450, 8000 Bahía Blanca, Argentina.
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10
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Kumar D, Kirti PB. Transcriptomic and proteomic analyses of resistant host responses in Arachis diogoi challenged with late leaf spot pathogen, Phaeoisariopsis personata. PLoS One 2015; 10:e0117559. [PMID: 25646800 PMCID: PMC4315434 DOI: 10.1371/journal.pone.0117559] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 12/27/2014] [Indexed: 11/19/2022] Open
Abstract
Late leaf spot is a serious disease of peanut caused by the imperfect fungus, Phaeoisariopsis personata. Wild diploid species, Arachis diogoi. is reported to be highly resistant to this disease and asymptomatic. The objective of this study is to investigate the molecular responses of the wild peanut challenged with the late leaf spot pathogen using cDNA-AFLP and 2D proteomic study. A total of 233 reliable, differentially expressed genes were identified in Arachis diogoi. About one third of the TDFs exhibit no significant similarity with the known sequences in the data bases. Expressed sequence tag data showed that the characterized genes are involved in conferring resistance in the wild peanut to the pathogen challenge. Several genes for proteins involved in cell wall strengthening, hypersensitive cell death and resistance related proteins have been identified. Genes identified for other proteins appear to function in metabolism, signal transduction and defence. Nineteen TDFs based on the homology analysis of genes associated with defence, signal transduction and metabolism were further validated by quantitative real time PCR (qRT-PCR) analyses in resistant wild species in comparison with a susceptible peanut genotype in time course experiments. The proteins corresponding to six TDFs were differentially expressed at protein level also. Differentially expressed TDFs and proteins in wild peanut indicate its defence mechanism upon pathogen challenge and provide initial breakthrough of genes possibly involved in recognition events and early signalling responses to combat the pathogen through subsequent development of resistivity. This is the first attempt to elucidate the molecular basis of the response of the resistant genotype to the late leaf spot pathogen, and its defence mechanism.
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Affiliation(s)
- Dilip Kumar
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
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Cregeen S, Radisek S, Mandelc S, Turk B, Stajner N, Jakse J, Javornik B. Different Gene Expressions of Resistant and Susceptible Hop Cultivars in Response to Infection with a Highly Aggressive Strain of Verticillium albo-atrum. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:689-704. [PMID: 25999664 PMCID: PMC4432018 DOI: 10.1007/s11105-014-0767-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Verticillium wilt has become a serious threat to hop production in Europe due to outbreaks of lethal wilt caused by a highly virulent strain of Verticillium albo-atrum. In order to enhance our understanding of resistance mechanisms, the fungal colonization patterns and interactions of resistant and susceptible hop cultivars infected with V. albo-atrum were analysed in time course experiments. Quantification of fungal DNA showed marked differences in spatial and temporal fungal colonization patterns in the two cultivars. Two differential display methods obtained 217 transcripts with altered expression, of which 84 showed similarity to plant proteins and 8 to fungal proteins. Gene ontology categorised them into cellular and metabolic processes, response to stimuli, biological regulation, biogenesis and localization. The expression patterns of 17 transcripts with possible implication in plant immunity were examined by real-time PCR (RT-qPCR). Our results showed strong expression of genes encoding pathogenesis-related (PR) proteins in susceptible plants and strong upregulation of genes implicated in ubiquitination and vesicle trafficking in the incompatible interaction and their downregulation in susceptible plants, suggesting the involvement of these processes in the hop resistance reaction. In the resistant cultivar, the RT-qPCR expression patterns of most genes showed their peak at 20 dpi and declined towards 30 dpi, comparable to the gene expression pattern of in planta detected fungal protein and coinciding with the highest fungal biomass in plants at 15 dpi. These expression patterns suggest that the defence response in the resistant cultivar is strong enough at 20 dpi to restrict further fungus colonization.
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Affiliation(s)
- Sara Cregeen
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radisek
- Slovenian Institute for Hop Research and Brewing, Cesta ŽalskegaTabora 2, SI-3320 Žalec, Slovenia
| | - Stanislav Mandelc
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Natasa Stajner
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Jernej Jakse
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Branka Javornik
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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12
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Kong Q, Yuan J, Niu P, Xie J, Jiang W, Huang Y, Bie Z. Screening suitable reference genes for normalization in reverse transcription quantitative real-time PCR analysis in melon. PLoS One 2014; 9:e87197. [PMID: 24475250 DOI: 10.1371/journal.pone.008719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 12/18/2013] [Indexed: 05/25/2023] Open
Abstract
Melon (Cucumis melo. L) is not only an economically important cucurbitaceous crop but also an attractive model for studying many biological characteristics. Screening appropriate reference genes is essential to reverse transcription quantitative real-time PCR (RT-qPCR), which is key to many studies involving gene expression analysis. In this study, 14 candidate reference genes were selected, and the variations in their expression in roots and leaves of plants subjected to biotic stress, abiotic stress, and plant growth regulator treatment were assessed by RT-qPCR. The stability of the expression of the selected genes was determined and ranked using geNorm and NormFinder. geNorm identified the two most stable genes for each set of conditions: CmADP and CmUBIep across all samples, CmUBIep and CmRPL in roots, CmRAN and CmACT in leaves, CmADP and CmRPL under abiotic stress conditions, CmTUA and CmACT under biotic stress conditions, and CmRAN and CmACT under plant growth regulator treatments. NormFinder determined CmRPL to be the best reference gene in roots and under biotic stress conditions and CmADP under the other experimental conditions. CmUBC2 and CmPP2A were not found to be suitable under many experimental conditions. The catalase family genes CmCAT1, CmCAT2, and CmCAT3 were identified in melon genome and used as target genes to validate the reliability of identified reference genes. The catalase family genes showed the most upregulation 3 days after inoculation with Fusarium wilt in roots, after which they were downregulated. Their levels of expression were significantly overestimated when the unsuitable reference gene was used for normalization. These results not only provide guidelines for the selection of reference genes for gene expression analyses in melons but may also provide valuable information for studying the functions of catalase family genes in stress responses.
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Affiliation(s)
- Qiusheng Kong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jingxian Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Penghui Niu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Junjun Xie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Wei Jiang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yuan Huang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
| | - Zhilong Bie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P. R. China
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Screening suitable reference genes for normalization in reverse transcription quantitative real-time PCR analysis in melon. PLoS One 2014; 9:e87197. [PMID: 24475250 PMCID: PMC3903635 DOI: 10.1371/journal.pone.0087197] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 12/18/2013] [Indexed: 12/17/2022] Open
Abstract
Melon (Cucumis melo. L) is not only an economically important cucurbitaceous crop but also an attractive model for studying many biological characteristics. Screening appropriate reference genes is essential to reverse transcription quantitative real-time PCR (RT-qPCR), which is key to many studies involving gene expression analysis. In this study, 14 candidate reference genes were selected, and the variations in their expression in roots and leaves of plants subjected to biotic stress, abiotic stress, and plant growth regulator treatment were assessed by RT-qPCR. The stability of the expression of the selected genes was determined and ranked using geNorm and NormFinder. geNorm identified the two most stable genes for each set of conditions: CmADP and CmUBIep across all samples, CmUBIep and CmRPL in roots, CmRAN and CmACT in leaves, CmADP and CmRPL under abiotic stress conditions, CmTUA and CmACT under biotic stress conditions, and CmRAN and CmACT under plant growth regulator treatments. NormFinder determined CmRPL to be the best reference gene in roots and under biotic stress conditions and CmADP under the other experimental conditions. CmUBC2 and CmPP2A were not found to be suitable under many experimental conditions. The catalase family genes CmCAT1, CmCAT2, and CmCAT3 were identified in melon genome and used as target genes to validate the reliability of identified reference genes. The catalase family genes showed the most upregulation 3 days after inoculation with Fusarium wilt in roots, after which they were downregulated. Their levels of expression were significantly overestimated when the unsuitable reference gene was used for normalization. These results not only provide guidelines for the selection of reference genes for gene expression analyses in melons but may also provide valuable information for studying the functions of catalase family genes in stress responses.
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Albuquerque LPD, Santana GMDS, Napoleão TH, Coelho LCBB, Silva MVD, Paiva PMG. Antifungal activity of Microgramma vacciniifolia rhizome lectin on genetically distinct Fusarium oxysporum f. sp. lycopersici races. Appl Biochem Biotechnol 2013; 172:1098-105. [PMID: 24142386 DOI: 10.1007/s12010-013-0600-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
Abstract
Fusarium oxysporum f. sp. lycopersici races 1, 2, and 3 deteriorate tomato crops since they cause a vascular wilt. Lectins are carbohydrate-binding proteins with hemagglutinating and antifungal activities. This work reports that Microgramma vacciniifolia rhizome lectin (MvRL) inhibits F. oxysporum f. sp. lycopersici race 3 growth (61 %) more intensely than of races 1 (55 %) and 2 (45 %). The hemagglutinating activity of MvRL was inhibited by glycoprotein preparations from mycelia of races 1, 2, and 3, and these data indicate that lectin carbohydrate-binding sites recognized glycosylated molecules from races. Inter-simple sequence repeat (ISSR) marker system showed that race 3 is genetically distinct from races 1 and 2, and thus the highest sensitiveness of F. oxysporum f. sp. lycopersici race 3 to MvRL may be due to molecular characteristics of this race.
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Affiliation(s)
- Lidiane Pereira de Albuquerque
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, Pernambuco, 50670-420, Brazil
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15
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Haegi A, Catalano V, Luongo L, Vitale S, Scotton M, Ficcadenti N, Belisario A. A newly developed real-time PCR assay for detection and quantification of Fusarium oxysporum and its use in compatible and incompatible interactions with grafted melon genotypes. PHYTOPATHOLOGY 2013; 103:802-10. [PMID: 23464901 DOI: 10.1094/phyto-11-12-0293-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A reliable and species-specific real-time quantitative polymerase chain reaction (qPCR) assay was developed for detection of the complex soilborne anamorphic fungus Fusarium oxysporum. The new primer pair, designed on the translation elongation factor 1-α gene with an amplicon of 142 bp, was highly specific to F. oxysporum without cross reactions with other Fusarium spp. The protocol was applied to grafted melon plants for the detection and quantification of F. oxysporum f. sp. melonis, a devastating pathogen of this cucurbit. Grafting technologies are widely used in melon to confer resistance against new virulent races of F. oxysporum f. sp. melonis, while maintaining the properties of valuable commercial varieties. However, the effects on the vascular pathogen colonization have not been fully investigated. Analyses were performed on 'Charentais-T' (susceptible) and 'Nad-1' (resistant) melon cultivars, both used either as rootstock and scion, and inoculated with F. oxysporum f. sp. melonis race 1 and race 1,2. Pathogen development was compared using qPCR and isolations from stem tissues. Early asymptomatic melon infections were detected with a quantification limit of 1 pg of fungal DNA. The qPCR protocol clearly showed that fungal development was highly affected by host-pathogen interaction (compatible or incompatible) and time (days postinoculation). The principal significant effect (P ≤ 0.01) on fungal development was due to the melon genotype used as rootstock, and this effect had a significant interaction with time and F. oxysporum f. sp. melonis race. In particular, the amount of race 1,2 DNA was significantly higher compared with that estimated for race 1 in the incompatible interaction at 18 days postinoculation. The two fungal races were always present in both the rootstock and scion of grafted plants in either the compatible or incompatible interaction.
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Affiliation(s)
- Anita Haegi
- Centro di Ricerca per la Patologia Vegetale, Rome, Italy
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16
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Mandelc S, Timperman I, Radišek S, Devreese B, Samyn B, Javornik B. Comparative proteomic profiling in compatible and incompatible interactions between hop roots and Verticillium albo-atrum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 68:23-31. [PMID: 23619241 DOI: 10.1016/j.plaphy.2013.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/26/2013] [Indexed: 05/26/2023]
Abstract
Verticillium wilt, caused by the soil borne fungal pathogen Verticillium albo-atrum, is a serious threat to hop (Humulus lupulus L.) production in several hop-growing regions. A proteomic approach was applied to analyse the response of root tissue in compatible and incompatible interactions between hop and V. albo-atrum at 10, 20 and 30 days after inoculation, using two-dimensional difference gel electrophoresis (2D-DIGE) coupled with de novo sequencing of derivatized peptides. Approximately 1200 reproducible spots were detected on the gels, of which 102 were identified. In the compatible interaction, 252 spots showed infection-specific changes in spot abundance and an accumulation of defence-related proteins, such as chitinase, β-glucanase, thaumatin-like protein, peroxidase and germin-like protein, was observed. However, no significant infection-specific changes were detected in the incompatible interaction. The results indicate that resistance in this pathosystem may be conferred by constitutive rather than induced defence mechanisms. The identification and high abundance of two mannose/glucose-specific lectin isoforms present only in the roots of the resistant cultivar suggests function of lectins in hop resistance against V. albo-atrum.
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Affiliation(s)
- Stanislav Mandelc
- Biotechnical Faculty, Department of Agronomy, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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Roig C, Fita A, Ríos G, Hammond JP, Nuez F, Picó B. Root transcriptional responses of two melon genotypes with contrasting resistance to Monosporascus cannonballus (Pollack et Uecker) infection. BMC Genomics 2012; 13:601. [PMID: 23134692 PMCID: PMC3542287 DOI: 10.1186/1471-2164-13-601] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/31/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. RESULTS Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. CONCLUSIONS As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.
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Affiliation(s)
- Cristina Roig
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Ana Fita
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - John P Hammond
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Fernando Nuez
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of the Agricultural Biodiversity, Universitat Politècnica de València (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
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Robust ordered mRNA differential display: an improved method for global gene expression profiling. Biotechniques 2012; 51:271-2, 274-5. [PMID: 21988694 DOI: 10.2144/000113752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 09/09/2011] [Indexed: 11/23/2022] Open
Abstract
Global gene expression profiling (GGEP) plays a pivotal role in biological research. We developed an improved GGEP method called "robust ordered mRNA differential display (RoDD)" by combining mRNA differential display (DD) and complementary DNA amplified fragment length polymorphisms (cDNA-AFLP) using elaborately designed primers and a poly (dT:A) replacement technique. Redundancy was minimized by bead-based isolation and coverage was improved by using restriction enzymes that recognized 4-bp sites. This method offers the common virtues of gel-based methods along with the reliability of cDNA-AFLP. The most significant advantage of RoDD over current gel-based methods is greatly improved coverage and minimized redundancy.
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