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Minio A, Figueroa-Balderas R, Cohen SP, Ali SS, Carriel D, Britto D, Stack C, Baruah IK, Marelli JP, Cantu D, Bailey BA. Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion. G3 (BETHESDA, MD.) 2023; 13:jkad125. [PMID: 37337677 PMCID: PMC10468315 DOI: 10.1093/g3journal/jkad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
- Genome Center, University of California Davis, 95616 Davis, CA, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Stephen P Cohen
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Denny Carriel
- Mars La Chola (MLCH), Mars Inc., Guayaquil 090103, Ecuador
| | - Dahyana Britto
- Mars Center for Cocoa Science, Mars Inc., Fazenda Almirante, Caixa Postal 55, Itajuípe, BA, CEP 45630-000, Brazil
| | - Conrad Stack
- Mars Digital Technologies, Mars Inc., Chicago 60642, IL, USA
| | - Indrani K Baruah
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
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de Novais DPS, Batista TM, Costa EA, Pirovani CP. Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review. Microorganisms 2023; 11:1567. [PMID: 37375069 DOI: 10.3390/microorganisms11061567] [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: 04/25/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of Theobroma cacao L. pathogens' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of T. cacao eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author's affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were Moniliophthora (105 studies), Phytophthora (59 studies) and Ceratocystis (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in T. cacao pathogen genomes. This review contributes to the knowledge about T. cacao diseases, providing an integrated discussion of T. cacao pathogens' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.
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Affiliation(s)
- Diogo Pereira Silva de Novais
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
- Bahia Federal Institute of Education, Science and Technology (IFBA), Porto Seguro 45810-000, BA, Brazil
| | - Thiago Mafra Batista
- Environmental Science Training Center, Federal University of Southern Bahia (UFSB), Porto Seguro 45810-000, BA, Brazil
| | - Eduardo Almeida Costa
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
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Neves Dos Santos F, Magalhães DMA, Luz EDMN, Eberlin MN, Simionato AVC. Metabolite mass spectrometry profiling of cacao genotypes reveals contrasting resistances to Ceratocystis cacaofunesta phytopathogen. Electrophoresis 2021; 42:2519-2527. [PMID: 34498763 DOI: 10.1002/elps.202100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/12/2022]
Abstract
Ceratocystis wilt is a lethal disease of cacao, and the search for resistant genotypes may provide the best way to deal with the disease. Resistance or susceptibility behavior of some cacao genotypes when infected by Ceratocystis cacaofunesta is not yet understood. Herein, we report an LC-MS metabolomic screening analysis based on high-resolution MS to obtain comprehensive metabolic profile associated with multivariate data analysis of PLS-DA, which was effective to classify CCN-51 and TSH-1188 as resistant genotypes to C. cacaofunesta fungus, while CEPEC2002 was classified as a susceptible one. Using reversed-phase LC method, electrospray interface, and high-resolution tandem MS by the quadrupole-TOF analyzer, the typical profiles of metabolites, such as phenylpropanoids, flavonoids, lipids, alkaloids, and amino acids, were obtained. Untargeted metabolite profiles were used to construct discriminant analysis by partial least squares (PLS-DA)-derived loading plots, which placed the cacao genotypes into two major clusters related to susceptible or resistant groups. Linolenic, linoleic, oleic, stearic, arachidonic, and asiatic acids were annotated metabolites of infected, susceptible, and resistant genotypes, while methyl jasmonate, jasmonic acid, hydroxylated jasmonic acid, caffeine, and theobromine were annotated as constituents of the resistant genotypes. Trends of these typical metabolites levels revealed that CCN51 is susceptible, CEPEC2002 is moderately susceptible, and TSH1188 is resistant to C. cacaofunesta. Therefore, profiles of major metabolites as screened by LC-MS offer an efficient tool to reveal the level of resistance of cacao genotypes to C. cacaofunesta present in any farm around the world.
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Affiliation(s)
- Fábio Neves Dos Santos
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Laboratory of Biomolecule Analysis Tiselius-LABi Tiselius, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Marcos Nogueira Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,MackMass Laboratory for Mass Spectrometry, School of Engineering-PPGEMN, Mackenzie Presbyterian University, São Paulo, São Paulo, Brazil
| | - Ana Valéria Colnaghi Simionato
- Laboratory of Biomolecule Analysis Tiselius-LABi Tiselius, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,National Institute of Science and Technology in Bioanalytics (INCTBio), Campinas, São Paulo, Brazil
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De Wever J, Tulkens D, Verwaeren J, Everaert H, Rottiers H, Dewettinck K, Lefever S, Messens K. A Combined RNA Preservation and Extraction Protocol for Gene Expression Studies in Cacao Beans. FRONTIERS IN PLANT SCIENCE 2020; 11:992. [PMID: 32695136 PMCID: PMC7338848 DOI: 10.3389/fpls.2020.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 06/17/2020] [Indexed: 05/23/2023]
Abstract
Despite the high economic importance of cacao beans, few RNA-based studies have been conducted on this plant material and hence no optimal RNA-extraction has been reported. Moreover, extraction of high-quality RNA from recalcitrant cacao bean tissue has shown many difficulties and requires optimization. Furthermore, cacao beans are mostly found at remote and under-resourced locations, which pressures the outsourcing of such analysis and thereby demands RNA-stable preservation and transportation of cacao beans. This study aims to select an appropriate RNA extraction and preservation/transportation method for cacao beans. For this purpose, three sample homogenization and five extraction protocols on cacao beans were compared. In addition, 13 preservation conditions-differing in tissue crushing degree, preservation method, duration, and temperature-were compared and evaluated. A comparative analysis revealed that CTAB-based homogenization and extraction outcompeted all tested commercial protocols in RNA yield and integrity, respectively. Preservation at -80°C affected RNA quality the least, whereas freeze-drying was most suitable for transportation at room temperature for maximum 1 week. The cacao bean RNA obtained from the selected methods were compatible for downstream applications. The results of this study will facilitate on-field sampling and transportation of genetically sensitive cacao material prior to cacao bean transcriptomic studies. In addition, valuable insights on sample homogenization, extraction, preservation, and transportation have been provided, which is of interest to every plant geneticist.
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Affiliation(s)
- Jocelyn De Wever
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Dieter Tulkens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Jan Verwaeren
- Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Helena Everaert
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hayley Rottiers
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Koen Dewettinck
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium
| | - Kathy Messens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Ali SS, Asman A, Shao J, Balidion JF, Strem MD, Puig AS, Meinhardt LW, Bailey BA. Genome and transcriptome analysis of the latent pathogen Lasiodiplodia theobromae, an emerging threat to the cacao industry. Genome 2019; 63:37-52. [PMID: 31580730 DOI: 10.1139/gen-2019-0112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were transcriptionally active and 1255 were more highly expressed in planta compared with cultured mycelia. The predicted genes differentially expressed during infection were mainly those involved in carbohydrate, pectin, and lignin catabolism, cytochrome P450, necrosis-inducing proteins, and putative effectors. These findings significantly expand our knowledge of the genome of L. theobromae and the genes involved in virulence and pathogenicity.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705, USA.,Department of Viticulture & Enology, University of California, Davis, CA 95616, USA
| | - Asman Asman
- Department of Plant Pests and Diseases, Faculty of Agriculture, Hasanuddin University, Makassar, Indonesia; Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Makassar, Indonesia
| | | | - Johnny F Balidion
- Institute of Weed Science, Entomology and Plant Pathology, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Mary D Strem
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705, USA
| | - Alina S Puig
- Subtropical Horticultural Research Station, USDA/ARS, Miami, FL 33158, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705, USA
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Marelli JP, Guest DI, Bailey BA, Evans HC, Brown JK, Junaid M, Barreto RW, Lisboa DO, Puig AS. Chocolate Under Threat from Old and New Cacao Diseases. PHYTOPATHOLOGY 2019; 109:1331-1343. [PMID: 31115251 DOI: 10.1094/phyto-12-18-0477-rvw] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Theobroma cacao, the source of chocolate, is affected by destructive diseases wherever it is grown. Some diseases are endemic; however, as cacao was disseminated from the Amazon rain forest to new cultivation sites it encountered new pathogens. Two well-established diseases cause the greatest losses: black pod rot, caused by several species of Phytophthora, and witches' broom of cacao, caused by Moniliophthora perniciosa. Phytophthora megakarya causes the severest damage in the main cacao producing countries in West Africa, while P. palmivora causes significant losses globally. M. perniciosa is related to a sister basidiomycete species, M. roreri which causes frosty pod rot. These Moniliophthora species only occur in South and Central America, where they have significantly limited production since the beginnings of cacao cultivation. The basidiomycete Ceratobasidium theobromae causing vascular-streak dieback occurs only in South-East Asia and remains poorly understood. Cacao swollen shoot disease caused by Cacao swollen shoot virus is rapidly spreading in West Africa. This review presents contemporary research on the biology, taxonomy and genomics of what are often new-encounter pathogens, as well as the management of the diseases they cause.
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Affiliation(s)
| | - David I Guest
- 2Sydney Institute of Agriculture, School of Life and Environmental Sciences, the University of Sydney, NSW 2006, Australia
| | - Bryan A Bailey
- 3USDA-ARS/Sustainable Perennial Crops Lab, Beltsville, MD 20705, U.S.A
| | | | - Judith K Brown
- 5School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, U.S.A
| | - Muhammad Junaid
- 2Sydney Institute of Agriculture, School of Life and Environmental Sciences, the University of Sydney, NSW 2006, Australia
- 8Cocoa Research Group/Faculty of Agriculture, Hasanuddin University, 90245 Makassar, Indonesia
| | | | | | - Alina S Puig
- 7USDA-ARS/Subtropical Horticultural Research Station, Miami, FL 33131, U.S.A
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Bailey BA, Evans HC, Phillips‐Mora W, Ali SS, Meinhardt LW. Moniliophthora roreri, causal agent of cacao frosty pod rot. MOLECULAR PLANT PATHOLOGY 2018; 19:1580-1594. [PMID: 29194910 PMCID: PMC6638017 DOI: 10.1111/mpp.12648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Taxonomy: Moniliophthora roreri (Cif.) H.C. Evans et al. ; Phylum Basidiomycota; Class Agaricomycetes; Order Agaricales; Family Marasmiaceae; Genus Moniliophthora. Biology: Moniliophthora roreri attacks Theobroma and Herrania species causing frosty pod rot. Theobroma cacao (cacao) is the host of major economic concern. Moniliophthora roreri is a hemibiotroph with a long biotrophic phase (45-90 days). Spore masses, of apparent asexual origin, are produced on the pod surface after initiation of the necrotrophic phase. Spores are spread by wind, rain and human activity. Symptoms of the biotrophic phase can include necrotic flecks and, in some cases, pod malformation, but pods otherwise remain asymptomatic. Relationship to Moniliophthora perniciosa: Moniliophthora roreri and Moniliophthora perniciosa, causal agent of witches' broom disease of cacao, are closely related. Their genomes are similar, including many of the genes they carry which are considered to be important in the disease process. Moniliophthora perniciosa, also a hemibiotroph, has a typical basidiomycete lifestyle and morphology, forming clamp connections and producing mushrooms. Basidiospores infect meristematic tissues including flower cushions, stem tips and pods. Moniliophthora roreri does not form clamp connections or mushrooms and infects pods only. Both pathogens are limited to the Western Hemisphere and are a threat to cacao production around the world. Agronomic importance: Disease losses caused by frosty pod rot can reach 90% and result in field abandonment. Moniliophthora roreri remains in the invasive phase in the Western Hemisphere, not having reached Brazil, some islands within the Caribbean and a few specific regions within otherwise invaded countries. DISEASE MANAGEMENT The disease can be managed by a combination of cultural (for example, maintenance of tree height and removal of infected pods) and chemical methods. These methods benefit from regional application, but can be cost prohibitive. Breeding for disease resistance offers the greatest potential for frosty pod rot management and new tolerant materials are becoming available.
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Affiliation(s)
- Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | | | - Wilbert Phillips‐Mora
- Tropical Agricultural Research and Higher Education Center (CATIE)Turrialba 7170Costa Rica
| | - Shahin S. Ali
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
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Bailey BA, Ali SS, Strem MD, Meinhardt LW. Morphological variants of Moniliophthora roreri on artificial media and the biotroph/necrotroph shift. Fungal Biol 2018; 122:701-716. [PMID: 29880205 DOI: 10.1016/j.funbio.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 11/24/2022]
Abstract
Moniliophthora roreri (Mr) causes frosty pod rot of Theobroma cacao in a hemibiotrophic association. The Mr biotroph-like phase has not been studied in culture. Mr spores (isolates Co12, Co52, and B3) were germinated on high (V8) and low (BPMM) nutrients with different media hardness (0.5% to 3% agarose). Germination was high on V8 media. Hardness affected germination on BPMM. Most colonies on V8 were slow-growing, failing to sporulate. Colony morphology depended on the isolate. On BPMM, exaggerated mycelia formed of limited length with enlarged cells. On agarose, rapidly expanding sporulating necrotrophic colonies formed rarely. Co12 and B3 spores were germinated on V8 and BPMM with low melting point (LMP) agarose. Slow-growing colonies of B3 on BPMM were unstable on LMP agarose, often forming slow-growing/rapidly expanding hybrids. Slow-growing colonies are hypothesized to represent the biotrophic phase. One nucleus was common in Mr cells, other than spores. Binucleate cells were occasionally observed in aged cells of slow-growing mycelia. Co52 cells often had more than two nuclei per cell after germination. Mr mycelia cells typically carry a single nucleus, being considered haploid. Biotroph- and necrotroph-like mycelia displayed differential gene expression but results were inconsistent with published in vivo results and require further study.
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Affiliation(s)
- Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States.
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Mary D Strem
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
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Ngo Bieng MA, Alem L, Curtet C, Tixier P. Tree spacing impacts the individual incidence of Moniliophthora roreri disease in cacao agroforests. PEST MANAGEMENT SCIENCE 2017; 73:2386-2392. [PMID: 28581254 DOI: 10.1002/ps.4635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 05/25/2017] [Accepted: 05/28/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Using conventional pesticides in crop protection has raised serious environmental concerns and there is therefore a need for integrated pest management (IPM) methods. In this paper, we found that the spacing of trees can impact disease, which could result in a reduction in pesticide applications and may act as a potential IPM method. We studied Frosty Pod Rot (FPR) in 20 cacao agroforests in Costa Rica (Upala region). RESULTS Using a generalized linear mixed model, we analyzed the impact of the neighborhood composition and distance from a studied cacao individual on its individual FPR incidence. We found that the number of cacao tree neighbors in a radius of 3.7 m and the number of fruit trees in a radius of 4.3 m had a significant negative influence on the incidence of FPR on individual cacao trees. Moreover, cacao tree neighbors had the most significant local influence compared to the neighborhood of other taller categories such as fruit or forest trees. CONCLUSION The mechanisms involved are related to the barrier effect, due to the effectiveness of the cacao tree's architecture as an efficient barrier against FPR spore dispersal. This paper provides new insights into optimization of the spatial environment around each host as an original IPM method. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Marie Ange Ngo Bieng
- CIRAD, UMR SYSTEM, 30501 Turrialba, Costa Rica
- CIRAD, UMR SYSTEM, F-34398 Montpellier, France
- CATIE, 30501 Turrialba, Costa Rica
| | - Laudine Alem
- CIRAD, UMR SYSTEM, 30501 Turrialba, Costa Rica
- CIRAD, UMR SYSTEM, F-34398 Montpellier, France
- CATIE, 30501 Turrialba, Costa Rica
| | - Chloé Curtet
- CIRAD, UMR SYSTEM, 30501 Turrialba, Costa Rica
- CIRAD, UMR SYSTEM, F-34398 Montpellier, France
- CATIE, 30501 Turrialba, Costa Rica
| | - Philippe Tixier
- CATIE, 30501 Turrialba, Costa Rica
- CIRAD, UPR GECO, F-34398 Montpellier, France
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Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S. Codon optimization underpins generalist parasitism in fungi. eLife 2017; 6:e22472. [PMID: 28157073 PMCID: PMC5315462 DOI: 10.7554/elife.22472] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/28/2017] [Indexed: 01/04/2023] Open
Abstract
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.
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Affiliation(s)
- Thomas Badet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Remi Peyraud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Malick Mbengue
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Mark Derbyshire
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Major phytopathogens and strains from cocoa (Theobroma cacao L.) are differentiated by MALDI-MS lipid and/or peptide/protein profiles. Anal Bioanal Chem 2016; 409:1765-1777. [PMID: 28028594 DOI: 10.1007/s00216-016-0133-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/30/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
Abstract
Phytopathogens are the main disease agents that promote attack of cocoa plantations in all tropical countries. The similarity of the symptoms caused by different phytopathogens makes the reliable identification of the diverse species a challenge. Correct identification is important in the monitoring and management of these pests. Here we show that matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis is able to rapidly and reliably differentiate cocoa phytopathogens, namely Moniliophthora perniciosa, Phytophthora palmivora, P. capsici, P. citrophthora, P. heveae, Ceratocystis cacaofunesta, C. paradoxa, and C. fimbriata. MALDI-MS reveals unique peptide/protein and lipid profiles which differentiate these phytopathogens at the level of genus, species, and single strain coming from different hosts or cocoa tissues collected in several plantations/places. This fast methodology based on molecular biomarkers is also shown to be sufficiently reproducible and selective and therefore seems to offer a suitable tool to guide the correct application of sanitary defense approaches for infected cocoa plantations. International trading of cocoa plants and products could also be efficiently monitored by MALDI-MS. It could, for instance, prevent the entry of new phytopathogens into a country, e.g., as in the case of Moniliophthora roreri fungus that is present in all cocoa plantations of countries bordering Brazil, but that has not yet attacked Brazilian plantations. Graphical Abstract Secure identification of phytopathogens attacking cocoa plantations has been demonstrated via typical chemical profiles provided by mass spectrometric screening.
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12
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Jaimes YY, Gonzalez C, Rojas J, Cornejo OE, Mideros MF, Restrepo S, Cilas C, Furtado EL. Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia. PLANT DISEASE 2016; 100:1548-1558. [PMID: 30686241 DOI: 10.1094/pdis-12-15-1498-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Frosty pod rot (FPR) disease on cocoa, caused by Moniliophthora roreri, is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple-sequence repeats (SSR) markers. In total, 117 different multilocus genotypes were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association (IA and řd) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoing sporadic recombination or partial recombination through parasexuality. A Bayesian clustering analysis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geographical differentiation among isolates. Similar results were obtained by a discriminant analysis of principal components, a principal coordinate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did contribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.
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Affiliation(s)
- Yeirme Y Jaimes
- Corpoica, Research Center La Suiza, Rionegro-Santander, Colombia; CAPES PEC-PG Fellow; and Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
| | | | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Maria F Mideros
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Christian Cilas
- CIRAD, UR Bioagresseurs, Campus de Baillarguet, TA A-106/D, 34398 Montpellier Cedex 5, France
| | - E L Furtado
- CNPq Fellow, Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
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13
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Tata A, Perez C, Campos ML, Bayfield MA, Eberlin MN, Ifa DR. Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging for Monitoring Secondary Metabolites Production during Antagonistic Interaction of Fungi. Anal Chem 2015; 87:12298-305. [PMID: 26637047 DOI: 10.1021/acs.analchem.5b03614] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Direct analysis of microbial cocultures grown on agar media by desorption electrospray ionization mass spectrometry (DESI-MS) is quite challenging. Due to the high gas pressure upon impact with the surface, the desorption mechanism does not allow direct imaging of soft or irregular surfaces. The divots in the agar, created by the high-pressure gas and spray, dramatically change the geometry of the system decreasing the intensity of the signal. In order to overcome this limitation, an imprinting step, in which the chemicals are initially transferred to flat hard surfaces, was coupled to DESI-MS and applied for the first time to fungal cocultures. Note that fungal cocultures are often disadvantageous in direct imaging mass spectrometry. Agar plates of fungi present a complex topography due to the simultaneous presence of dynamic mycelia and spores. One of the most devastating diseases of cocoa trees is caused by fungal phytopathogen Moniliophthora roreri. Strategies for pest management include the application of endophytic fungi, such as Trichoderma harzianum, that act as biocontrol agents by antagonizing M. roreri. However, the complex chemical communication underlying the basis for this phytopathogen-dependent biocontrol is still unknown. In this study, we investigated the metabolic exchange that takes place during the antagonistic interaction between M. roreri and T. harzianum. Using imprint-DESI-MS imaging we annotated the secondary metabolites released when T. harzianum and M. roreri were cultured in isolation and compared these to those produced after 3 weeks of coculture. We identified and localized four phytopathogen-dependent secondary metabolites, including T39 butenolide, harzianolide, and sorbicillinol. In order to verify the reliability of the imprint-DESI-MS imaging data and evaluate the capability of tape imprints to extract fungal metabolites while maintaining their localization, six representative plugs along the entire M. roreri/T. harzianum coculture plate were removed, weighed, extracted, and analyzed by liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Our results not only provide a better understanding of M. roreri-dependent metabolic induction in T. harzianum, but may seed novel directions for the advancement of phytopathogen-dependent biocontrol, including the generation of optimized Trichoderma strains against M. roreri, new biopesticides, and biofertilizers.
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Affiliation(s)
- Alessandra Tata
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada.,ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Rua Josué Castro, s/n Cidade Universitária, CEP 13083-970 Campinas, São Paulo, Brazil
| | - Consuelo Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
| | - Michel L Campos
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada.,Department of Natural Active Principles and Toxicology, School of Pharmaceutical Sciences, São Paulo State University , Rodovia Araraquara-Jaú, km 1, CEP 14 801-902 Araraquara, São Paulo, Brazil
| | - Mark A Bayfield
- Department of Biology, York University , 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
| | - Marcos N Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas , Rua Josué Castro, s/n Cidade Universitária, CEP 13083-970 Campinas, São Paulo, Brazil
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University , Chemistry Building, 4700 Keele Street, M3J 1P3 Toronto, Ontario, Canada
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Liu JJ, Sturrock RN, Sniezko RA, Williams H, Benton R, Zamany A. Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors. BMC Genomics 2015; 16:678. [PMID: 26338692 PMCID: PMC4559923 DOI: 10.1186/s12864-015-1861-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Background The fungus Cronartium ribicola (Cri) is an economically and ecologically important forest pathogen that causes white pine blister rust (WPBR) disease on five-needle pines. To cause stem cankers and kill white pine trees the fungus elaborates a life cycle with five stages of spore development on five-needle pines and the alternate host Ribes plants. To increase our understanding of molecular WP-BR interactions, here we report genome-wide transcriptional profile analysis of C. ribicola using RNA-seq. Results cDNA libraries were constructed from aeciospore, urediniospore, and western white pine (Pinus monticola) tissues post Cri infection. Over 200 million RNA-seq 100-bp paired-end (PE) reads from rust fungal spores were de novo assembled and a reference transcriptome was generated with 17,880 transcripts that were expressed from 13,629 unigenes. A total of 734 unique proteins were predicted as a part of the Cri secretome from complete open reading frames (ORFs), and 41 % of them were Cronartium-specific. This study further identified a repertoire of candidate effectors and other pathogenicity determinants. Differentially expressed genes (DEGs) were identified to gain an understanding of molecular events important during the WPBR fungus life cycle by comparing Cri transcriptomes at different infection stages. Large-scale changes of in planta gene expression profiles were observed, revealing that multiple fungal biosynthetic pathways were enhanced during mycelium growth inside infected pine stem tissues. Conversely, many fungal genes that were up-regulated at the urediniospore stage appeared to be signalling components and transporters. The secreted fungal protein genes that were up-regulated in pine needle tissues during early infection were primarily associated with cell wall modifications, possibly to mask the rust pathogen from plant defenses. Conclusion This comprehensive transcriptome profiling substantially improves our current understanding of molecular WP-BR interactions. The repertoire of candidate effectors and other putative pathogenicity determinants identified here are valuable for future functional analysis of Cri virulence and pathogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1861-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Rona N Sturrock
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA.
| | - Holly Williams
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Ross Benton
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Arezoo Zamany
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
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15
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Ali SS, Shao J, Strem MD, Phillips-Mora W, Zhang D, Meinhardt LW, Bailey BA. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality. Front Microbiol 2015; 6:850. [PMID: 26379633 PMCID: PMC4550789 DOI: 10.3389/fmicb.2015.00850] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023] Open
Abstract
Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population may allow the population to adapt to changing environmental conditions and adapt to enhanced resistance in the host plant. The present study developed single nucleotide polymorphism (SNP) markers from RNASeq results for 13 M. roreri isolates and validated the markers for their ability to reveal genetic diversity in an international M. roreri collection. The SNP resources reported herein represent the first study of RNA sequencing (RNASeq)-derived SNP validation in M. roreri and demonstrates the utility of RNASeq as an approach for de novo SNP identification in M. roreri. A total of 88 polymorphic SNPs were used to evaluate the genetic diversity of 172 M. roreri cacao isolates resulting in 37 distinct genotypes (including 14 synonymous groups). Absence of heterozygosity for the 88 SNP markers indicates reproduction in M. roreri is clonal and likely due to a homothallic life style. The upper Magdalena Valley of Colombia showed the highest levels of genetic diversity with 20 distinct genotypes of which 13 were limited to this region, and indicates this region as the possible center of origin for M. roreri.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
| | - Jonathan Shao
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
| | - Mary D Strem
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
| | - Wilberth Phillips-Mora
- Departamento de Agricultura y Agroforestería, Centro Agronómico Tropica de Investigación y Enseñanza Turrialba, Costa Rica
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, United States Department of Agriculture/Agricultural Research Service, Beltsville Agricultural Research Center-West Beltsville, MD, USA
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Ali SS, Melnick RL, Crozier J, Phillips-Mora W, Strem MD, Shao J, Zhang D, Sicher R, Meinhardt L, Bailey BA. Successful pod infections by Moniliophthora roreri result in differential Theobroma cacao gene expression depending on the clone's level of tolerance. MOLECULAR PLANT PATHOLOGY 2014; 15:698-710. [PMID: 24528440 PMCID: PMC6638783 DOI: 10.1111/mpp.12126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An understanding of the tolerance mechanisms of Theobroma cacao used against Moniliophthora roreri, the causal agent of frosty pod rot, is important for the generation of stable disease-tolerant clones. A comparative view was obtained of transcript populations of infected pods from two susceptible and two tolerant clones using RNA sequence (RNA-Seq) analysis. A total of 3009 transcripts showed differential expression among clones. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of differentially expressed genes indicated shifts in 152 different metabolic pathways between the tolerant and susceptible clones. Real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) analyses of 36 genes verified the differential expression. Regression analysis validated a uniform progression in gene expression in association with infection levels and fungal loads in the susceptible clones. Expression patterns observed in the susceptible clones diverged in tolerant clones, with many genes showing higher expression at a low level of infection and fungal load. Principal coordinate analyses of real-time qRT-PCR data separated the gene expression patterns between susceptible and tolerant clones for pods showing malformation. Although some genes were constitutively differentially expressed between clones, most results suggested that defence responses were induced at low fungal load in the tolerant clones. Several elicitor-responsive genes were highly expressed in tolerant clones, suggesting rapid recognition of the pathogen and induction of defence genes. Expression patterns suggested that the jasmonic acid-ethylene- and/or salicylic acid-mediated defence pathways were activated in the tolerant clones, being enhanced by reduced brassinosteroid (BR) biosynthesis and catabolic inactivation of both BR and abscisic acids. Finally, several genes associated with hypersensitive response-like cell death were also induced in tolerant clones.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, 20705, USA
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