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Csikós A, Németh MZ, Frenkel O, Kiss L, Váczy KZ. A Fresh Look at Grape Powdery Mildew ( Erysiphe necator) A and B Genotypes Revealed Frequent Mixed Infections and Only B Genotypes in Flag Shoot Samples. PLANTS 2020; 9:plants9091156. [PMID: 32906683 PMCID: PMC7570353 DOI: 10.3390/plants9091156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 11/25/2022]
Abstract
Erysiphe necator populations, causing powdery mildew of grapes, have a complex genetic structure. Two genotypes, A and B, were identified in most vineyards across the world on the basis of fixed single nucleotide polymorphisms (SNPs) in several DNA regions. It was hypothesized that A populations overwinter as mycelia in grapevine buds, giving rise to so-called flag shoots in spring, and are more sensitive to fungicides than B populations, which overwinter as ascospores and become widespread later in the season. Other studies concluded that the biological significance of these genotypes is unclear. In the spring of 2015, there was a unique opportunity to collect E. necator samples from flag shoots in Hungary. The same grapevines were sampled in summer and autumn as well. A total of 182 samples were genotyped on the basis of β-tubulin (TUB2), nuclear ribosomal DNA (nrDNA) intergenic spacer (IGS), and internal transcribed spacer (ITS) sequences. Genotypes of 56 samples collected in 2009–2011 were used for comparison. Genotype A was not detected at all in spring, and was present in only 19 samples in total, mixed with genotype B, and sometimes with another frequently found genotype, designated as B2. These results did not support the hypothesis about temporal isolation of the two genotypes and indicated that these are randomly distributed in vineyards.
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Affiliation(s)
- Anett Csikós
- Food and Wine Research Institute, Eszterházy Károly University, H-3300 Eger, Hungary;
| | - Márk Z. Németh
- Plant Protection Institute, Centre for Agricultural Research, H-1525 Budapest, Hungary; (M.Z.N.); (L.K.)
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan 50250, Israel;
| | - Levente Kiss
- Plant Protection Institute, Centre for Agricultural Research, H-1525 Budapest, Hungary; (M.Z.N.); (L.K.)
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba 4350, Australia
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly University, H-3300 Eger, Hungary;
- Correspondence:
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Barsoum M, Kusch S, Frantzeskakis L, Schaffrath U, Panstruga R. Ultraviolet Mutagenesis Coupled with Next-Generation Sequencing as a Method for Functional Interrogation of Powdery Mildew Genomes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1008-1021. [PMID: 32370643 DOI: 10.1094/mpmi-02-20-0035-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Powdery mildews are obligate biotrophic fungal pathogens causing important diseases of plants worldwide. Very little is known about the requirements for their pathogenicity at the molecular level. This is largely due to the inability to culture these organisms in vitro or to modify them genetically. Here, we describe a mutagenesis procedure based on ultraviolet (UV) irradiation to accumulate mutations in the haploid genome of the barley powdery mildew pathogen Blumeria graminis f. sp. hordei. Exposure of B. graminis f. sp. hordei conidia to different durations of UV-C radiation (10 s to 12 min) resulted in a reduced number of macroscopically visible fungal colonies. B. graminis f. sp. hordei colony number was negatively correlated with exposure time and the total number of consecutive cycles of UV irradiation. Dark incubation following UV exposure further reduced fungal viability, implying that photoreactivation is an important component of DNA repair in B. graminis f. sp. hordei. After several rounds of UV mutagenesis, we selected two mutant isolates in addition to the parental B. graminis f. sp. hordei K1 isolate for whole-genome resequencing. By combining automated prediction of sequence variants and their manual validation, we identified unique UV-induced mutations in the genomes of the two isolates. Most of these mutations were in the up- or downstream regions of genes or in the intergenic space. Some of the variants detected in genes led to predicted missense mutations. As an additional insight, our bioinformatic analyses revealed a complex population structure within supposedly clonal B. graminis f. sp. hordei isolates.
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Affiliation(s)
- Mirna Barsoum
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringerweg 1, 52056 Aachen, Germany
| | - Stefan Kusch
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringerweg 1, 52056 Aachen, Germany
| | - Lamprinos Frantzeskakis
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringerweg 1, 52056 Aachen, Germany
| | - Ulrich Schaffrath
- RWTH Aachen University, Institute for Biology III, Worringerweg 1, 52056 Aachen, Germany
| | - Ralph Panstruga
- RWTH Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Worringerweg 1, 52056 Aachen, Germany
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Gent DH, Claassen BJ, Gadoury DM, Grünwald NJ, Knaus BJ, Radišek S, Weldon W, Wiseman MS, Wolfenbarger SN. Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. PHYTOPATHOLOGY 2020; 110:1105-1116. [PMID: 32091314 DOI: 10.1094/phyto-12-19-0448-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop. The disease was first reported in the Pacific Northwestern United States, the primary hop-growing region in this country, in the mid-1990s. More recently, the disease has reemerged in newly planted hopyards of the eastern United States, as hop production has expanded to meet demands of local craft brewers. The spread of strains virulent on previously resistant cultivars, the paucity of available fungicides, and the potential introduction of the MAT1-2 mating type to the western United States, all threaten sustainability of hop production. We sequenced the transcriptome of 104 isolates of P. macularis collected throughout the western United States, eastern United States, and Europe to quantify genetic diversity of pathogen populations and elucidate the possible origins of pathogen populations in the western United States. Discriminant analysis of principal components grouped isolates within three to five geographic populations, dependent on stringency of grouping criteria. Isolates from the western United States were phenotyped and categorized into one of three pathogenic races based on disease symptoms generated on differential cultivars. Western U.S. populations were clonal, irrespective of pathogenic race, and grouped with isolates originating from Europe. Isolates originating from wild hop plants in the eastern United States were genetically differentiated from all other populations, whereas isolates from cultivated hop plants in the eastern United States mostly grouped with isolates originating from the west, consistent with origins from nursery sources. Mating types of isolates originating from cultivated western and eastern U.S. hop plants were entirely MAT1-1. In contrast, a 1:1 ratio of MAT1-1 and MAT1-2 was observed with isolates sampled from wild plants or Europe. Within the western United States a set of highly differentiated loci were identified in P. macularis isolates associated with virulence to the powdery mildew R-gene R6. The weight of genetic and phenotypic evidence suggests a European origin of the P. macularis populations in the western United States, followed by spread of the pathogen from the western United States to re-emergent production regions in the eastern United States. Furthermore, R6 compatibility appears to have been selected from an extant isolate within the western United States. Greater emphasis on sanitation measures during propagation and quarantine policies should be considered to limit further spread of novel genotypes of the pathogen, both between and within production areas.
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Affiliation(s)
- David H Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Briana J Claassen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - David M Gadoury
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330, U.S.A
| | - Brian J Knaus
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | | | - William Weldon
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Michele S Wiseman
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - Sierra N Wolfenbarger
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
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Milo S, Harari-Misgav R, Hazkani-Covo E, Covo S. Limited DNA Repair Gene Repertoire in Ascomycete Yeast Revealed by Comparative Genomics. Genome Biol Evol 2020; 11:3409-3423. [PMID: 31693105 PMCID: PMC7145719 DOI: 10.1093/gbe/evz242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Ascomycota is the largest phylogenetic group of fungi that includes species important to human health and wellbeing. DNA repair is important for fungal survival and genome evolution. Here, we describe a detailed comparative genomic analysis of DNA repair genes in Ascomycota. We determined the DNA repair gene repertoire in Taphrinomycotina, Saccharomycotina, Leotiomycetes, Sordariomycetes, Dothideomycetes, and Eurotiomycetes. The subphyla of yeasts, Saccharomycotina and Taphrinomycotina, have a smaller DNA repair gene repertoire comparing to Pezizomycotina. Some genes were absent from most, if not all, yeast species. To study the conservation of these genes in Pezizomycotina, we used the Gain Loss Mapping Engine algorithm that provides the expectations of gain or loss of genes given the tree topology. Genes that were absent from most of the species of Taphrinomycotina or Saccharomycotina showed lower conservation in Pezizomycotina. This suggests that the absence of some DNA repair in yeasts is not random; genes with a tendency to be lost in other classes are missing. We ranked the conservation of DNA repair genes in Ascomycota. We found that Rad51 and its paralogs were less conserved than other recombinational proteins, suggesting that there is a redundancy between Rad51 and its paralogs, at least in some species. Finally, based on the repertoire of UV repair genes, we found conditions that differentially kill the wine pathogen Brettanomyces bruxellensis and not Saccharomyces cerevisiae. In summary, our analysis provides testable hypotheses to the role of DNA repair proteins in the genome evolution of Ascomycota.
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Affiliation(s)
- Shira Milo
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
| | - Reut Harari-Misgav
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
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Covo S. Genomic Instability in Fungal Plant Pathogens. Genes (Basel) 2020; 11:E421. [PMID: 32295266 PMCID: PMC7230313 DOI: 10.3390/genes11040421] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Fungi and fungal-like organisms (oomycetes) that cause diseases in plants have impacted human communities for centuries and probably from the dawn of agriculture. In modern agriculture, there is a constant race between new strategies to manage fungal plant pathogens and their ability to adapt. An important component in this race is fungal genetic diversity. Mechanisms such as sexual and parasexual recombination that contribute to the creation of novel allele combinations in fungal plant pathogens are briefly discussed in the first part of this review. Advances in genomics have enabled the investigation of chromosomal aberrations of agriculturally important fungal isolates at the nucleotide level. Some of these cases are summarized in the second part of this review; it is claimed that the effect of chromosomal aberrations on pathogenicity should be studied mechanistically. More data on the effect of gene copy number variations on phenotypes that are relevant to agriculture are especially needed. Genome rearrangements through translocations have shaped the genome of fungal plant pathogens by creating lineage-specific chromosome territories encoding for genes participating in plant diseases. Pathogenicity chromosomes are unique cases of such lineage-specific genetic elements, interestingly these chromosomes can be transferred horizontally and thus transforming a non-pathogenic strain to a pathogenic one. The third part of this review describes our attempts to reveal mutators in fungal plant pathogens by identifying fungi that lack important DNA repair genes or respond to DNA damage in an unconventional way. We found that a group of fungal plant pathogens lack conserved genes that are needed for an important Holliday junction resolution pathway. In addition, in Fusarium oxysporum, the rate-limiting step in dNTP production is not induced under DNA replication stress. This is very different from organisms from bacteria to humans. It remains to be seen if these mechanisms promote genetic instability in fungal plant pathogens.
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Affiliation(s)
- Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100001, Israel
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56
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Qiu PL, Liu SY, Bradshaw M, Rooney-Latham S, Takamatsu S, Bulgakov TS, Tang SR, Feng J, Jin DN, Aroge T, Li Y, Wang LL, Braun U. Multi-locus phylogeny and taxonomy of an unresolved, heterogeneous species complex within the genus Golovinomyces (Ascomycota, Erysiphales), including G. ambrosiae, G. circumfusus and G. spadiceus. BMC Microbiol 2020; 20:51. [PMID: 32138640 PMCID: PMC7059721 DOI: 10.1186/s12866-020-01731-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/21/2020] [Indexed: 01/26/2023] Open
Abstract
Background Previous phylogenetic analyses of species within the genus Golovinomyces (Ascomycota, Erysiphales), based on ITS and 28S rDNA sequence data, revealed a co-evolutionary relationship between powdery mildew species and hosts of certain tribes of the plant family Asteraceae. Golovinomyces growing on host plants belonging to the Heliantheae formed a single lineage, comprised of a morphologically differentiated complex of species, which included G. ambrosiae, G. circumfusus, and G. spadiceus. However, the lineage also encompassed sequences retrieved from Golovinomyces specimens on other Asteraceae tribes as well as other plant families, suggesting the involvement of a plurivorous species. A multilocus phylogenetic examination of this complex, using ITS, 28S, IGS (intergenic spacer), TUB2 (beta-tubulin), and CHS1 (chitin synthase I) sequence data was carried out to clarify the discrepancies between ITS and 28S rDNA sequence data and morphological differences. Furthermore, the circumscription of species and their host ranges were emended. Results The phylogenetic and morphological analyses conducted in this study revealed three distinct species named, viz., (1) G. ambrosiae emend. (including G. spadiceus), a plurivorous species that occurs on a multitude of hosts including, Ambrosia spp., multiple species of the Heliantheae and plant species of other tribes of Asteraceae including the Asian species of Eupatorium; (2) G. latisporus comb. nov. (≡ Oidium latisporum), the closely related, but morphologically distinct species confined to hosts of the Heliantheae genera Helianthus, Zinnia, and most likely Rudbeckia; and (3) G. circumfusus confined to Eupatorium cannabinum in Europe. Conclusions The present results provide strong evidence that the combination of multi-locus phylogeny and morphological analysis is an effective way to identify species in the genus Golovinomyces.
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Affiliation(s)
- Peng-Lei Qiu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Shu-Yan Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China.
| | - Michael Bradshaw
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Suzanne Rooney-Latham
- California Department of Food & Agriculture, Plany Pest Diagnostic Branch, 3294 Meadowview Road, Sacramento, CA, 95832-1448, USA
| | - Susumu Takamatsu
- Faculty of Bioresources, Mie University, Tsu, 514-8507, Japan.,Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Timur S Bulgakov
- Russian Research Institute of Floriculture and Subtropical Crops, 2/28 Yana Fabritsiusa Street, Sochi, 354002, Krasnodar Region, Russia
| | - Shu-Rong Tang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Jing Feng
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Dan-Ni Jin
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Temitope Aroge
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Yu Li
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Li-Lan Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, People's Republic of China
| | - Uwe Braun
- Martin Luther University, Institute of Biology, Geobotany and Botanical Garden, Herbarium, Neuwerk 21, 06099, Halle (Saale), Germany
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Gupta M, Sharma G, Saxena D, Budhwar R, Vasudevan M, Gupta V, Gupta A, Gupta R, Chandran D. Dual RNA-Seq analysis of Medicago truncatula and the pea powdery mildew Erysiphe pisi uncovers distinct host transcriptional signatures during incompatible and compatible interactions and pathogen effector candidates. Genomics 2019; 112:2130-2145. [PMID: 31837401 DOI: 10.1016/j.ygeno.2019.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/14/2019] [Accepted: 12/09/2019] [Indexed: 12/29/2022]
Abstract
Powdery mildew (PM) is a serious fungal disease of legumes. To gain novel insights into PM pathogenesis and host resistance/susceptibility, we used dual RNA-Seq to simultaneously capture host and pathogen transcriptomes at 1 d post-inoculation of resistant and susceptible Medicago truncatula genotypes with the PM Erysiphe pisi (Ep). Differential expression analysis indicates that R-gene mediated resistance against Ep involves extensive transcriptional reprogramming. Functional enrichment of differentially expressed host genes and in silico analysis of co-regulated promoters suggests that amplification of PTI, activation of the JA/ET signaling network, and regulation of growth-defense balance correlate with resistance. In contrast, processes that favor biotrophy, including suppression of defense signaling and programmed cell death, and weaker cell wall defenses are important susceptibility factors. Lastly, Ep effector candidates and genes with known/putative virulence functions were identified, representing a valuable resource that can be leveraged to improve our understanding of legume-PM interactions.
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Affiliation(s)
- Megha Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India; Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Gunjan Sharma
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Divya Saxena
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Roli Budhwar
- Bionivid Technology Pvt. Ltd., Kasturi Nagar, Bangalore, India
| | | | - Varsha Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Arunima Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Rashi Gupta
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India
| | - Divya Chandran
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India.
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Vondras AM, Minio A, Blanco-Ulate B, Figueroa-Balderas R, Penn MA, Zhou Y, Seymour D, Ye Z, Liang D, Espinoza LK, Anderson MM, Walker MA, Gaut B, Cantu D. The genomic diversification of grapevine clones. BMC Genomics 2019; 20:972. [PMID: 31830913 PMCID: PMC6907202 DOI: 10.1186/s12864-019-6211-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. Results Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. Conclusions These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome.
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Affiliation(s)
- Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Michael A Penn
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92617, USA
| | - Danelle Seymour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92617, USA
| | - Zirou Ye
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Dingren Liang
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Lucero K Espinoza
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Michael M Anderson
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA
| | - Brandon Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92617, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
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Pagliarani C, Boccacci P, Chitarra W, Cosentino E, Sandri M, Perrone I, Mori A, Cuozzo D, Nerva L, Rossato M, Zuccolotto P, Pezzotti M, Delledonne M, Mannini F, Gribaudo I, Gambino G. Distinct Metabolic Signals Underlie Clone by Environment Interplay in "Nebbiolo" Grapes Over Ripening. FRONTIERS IN PLANT SCIENCE 2019; 10:1575. [PMID: 31867031 PMCID: PMC6904956 DOI: 10.3389/fpls.2019.01575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/11/2019] [Indexed: 05/05/2023]
Abstract
Several research studies were focused to understand how grapevine cultivars respond to environment; nevertheless, the biological mechanisms tuning this phenomenon need to be further deepened. Particularly, the molecular processes underlying the interplay between clones of the same cultivar and environment were poorly investigated. To address this issue, we analyzed the transcriptome of berries from three "Nebbiolo" clones grown in different vineyards, during two ripening seasons. RNA-sequencing data were implemented with analyses of candidate genes, secondary metabolites, and agronomical parameters. This multidisciplinary approach helped to dissect the complexity of clone × environment interactions, by identifying the molecular responses controlled by genotype, vineyard, phenological phase, or a combination of these factors. Transcripts associated to sugar signalling, anthocyanin biosynthesis, and transport were differently modulated among clones, according to changes in berry agronomical features. Conversely, genes involved in defense response, such as stilbene synthase genes, were significantly affected by vineyard, consistently with stilbenoid accumulation. Thus, besides at the cultivar level, clone-specific molecular responses also contribute to shape the agronomic features of grapes in different environments. This reveals a further level of complexity in the regulation of genotype × environment interactions that has to be considered for orienting viticultural practices aimed at enhancing the quality of grape productions.
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Affiliation(s)
- Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
- Council for Agricultural Research and Economics, Centre of Viticultural and Enology Research (CREA-VE), Conegliano, Italy
| | | | - Marco Sandri
- DMS StatLab, University of Brescia, Brescia, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Alessia Mori
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Danila Cuozzo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Luca Nerva
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
- Council for Agricultural Research and Economics, Centre of Viticultural and Enology Research (CREA-VE), Conegliano, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paola Zuccolotto
- Big&Open Data Innovation Laboratory, University of Brescia, Brescia, Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino, Italy
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Pirrello C, Mizzotti C, Tomazetti TC, Colombo M, Bettinelli P, Prodorutti D, Peressotti E, Zulini L, Stefanini M, Angeli G, Masiero S, Welter LJ, Hausmann L, Vezzulli S. Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview. FRONTIERS IN PLANT SCIENCE 2019; 10:1394. [PMID: 31824521 PMCID: PMC6883492 DOI: 10.3389/fpls.2019.01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/09/2019] [Indexed: 05/23/2023]
Abstract
The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Chiara Mizzotti
- Department of Biosciences, University of Milan, Milan, Italy
| | - Tiago C. Tomazetti
- Center of Agricultural Sciences, Federal University of Santa Catarina, Rodovia Admar Gonzaga, Florianópolis, Brazil
| | - Monica Colombo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Paola Bettinelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Daniele Prodorutti
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Elisa Peressotti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Luca Zulini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Gino Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milan, Italy
| | - Leocir J. Welter
- Department of Natural and Social Sciences, Federal University of Santa Catarina, Campus of Curitibanos, Rodovia Ulysses Gaboardi, Curitibanos, Brazil
| | - Ludger Hausmann
- Julius Kühn Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
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Sharma G, Aminedi R, Saxena D, Gupta A, Banerjee P, Jain D, Chandran D. Effector mining from the Erysiphe pisi haustorial transcriptome identifies novel candidates involved in pea powdery mildew pathogenesis. MOLECULAR PLANT PATHOLOGY 2019; 20:1506-1522. [PMID: 31603276 PMCID: PMC6804345 DOI: 10.1111/mpp.12862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pea powdery mildew (PM) is an important fungal disease caused by an obligate biotroph, Erysiphe pisi (Ep), which significantly impacts pea production worldwide. The phytopathogen secretes a plethora of effectors, primarily through specialized infection structures termed haustoria, to establish a dynamic relationship with its host. To identify Ep effector candidates, a cDNA library of enriched haustoria from Ep-infected pea leaves was sequenced. The Ep transcriptome encodes 622 Ep candidate secreted proteins (CSPs), of which 167 were predicted to be candidate secreted effector proteins (CSEPs). Phylogenetic analysis indicates that Ep CSEPs are highly diverse, but, unlike cereal PM CSEPs, exhibit extensive sequence similarity with effectors from other PMs. Quantitative real-time PCR of a subset of EpCSEP/CSPs revealed that the majority are preferentially expressed in haustoria and exhibit infection stage-specific expression patterns. The functional roles of EpCSEP001, EpCSEP009 and EpCSP083 were probed by host-induced gene silencing (HIGS) via a double-stranded (ds) RNA-mediated RNAi approach. Foliar application of individual EpCSEP/CSP dsRNAs resulted in a marked reduction in PM disease symptoms. These findings were consistent with microscopic and molecular studies, suggesting that these Ep CSEP/CSPs play important roles in pea PM pathogenesis. Homology modelling revealed that EpCSEP001 and EpCSEP009 are analogous to fungal ribonucleases and belong to the RALPH family of effectors. This is the first study to identify and functionally validate candidate effectors from the agriculturally relevant pea PM, and highlights the utility of transcriptomics and HIGS to elucidate the key proteins associated with Ep pathogenesis.
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Affiliation(s)
- Gunjan Sharma
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Raghavendra Aminedi
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Divya Saxena
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Arunima Gupta
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Priyajit Banerjee
- Transcription Regulation Lab, Regional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
- Kalinga Institute of Industrial TechnologyBhubaneswarOrissaIndia
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
| | - Divya Chandran
- Laboratory of Plant–Microbe InteractionsRegional Centre for BiotechnologyNCR Biotech Science ClusterFaridabadHaryanaIndia
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Hu Y, Gao YR, Yang LS, Wang W, Wang YJ, Wen YQ. The cytological basis of powdery mildew resistance in wild Chinese Vitis species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:244-253. [PMID: 31593897 DOI: 10.1016/j.plaphy.2019.09.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
The wild Chinese grapevines (Vitis spp.) show varying levels of resistance to powdery mildew caused by Erysiphe necator that is an economically important disease of cultivated grapevines (Vitis vinifera). However, little information is available regarding the cytological mechanisms of powdery mildew resistance in these wild relatives. Here, we studied the cytological responses of three wild Chinese grapevine accessions after they were infected with E. necator (En) NAFU1 in comparison to the susceptible V. vinifera cv. 'Thompson Seedless' grape. The hyphal growth and sporulation of En NAFU1 were significantly restricted in wild species compared to 'Thompson Seedless', which appears to be associated with early cell wall deposition at the attempt sites, encasement of haustoria, and hypersensitive response-like cell death of penetrated epidermal cells. Moreover, endogenous free salicylic acid (SA) was more abundant in wild Chinese Vitis species than in 'Thompson Seedless' under pathogen-free condition. During En NAFU1 colonization, SA conjugates accumulated higher in wild grapevines than in 'Thompson Seedless'. In addition, the species-specific expression patterns of defense-associated genes during En NAFU1 colonization indicated that mechanisms underlying powdery mildew resistance are divergent among different wild Chinese Vitis species. These results contribute to understanding of mechanisms underlying defense responses of wild Chinese Vitis species against powdery mildew.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Yu-Rong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Lu-Shan Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Yue-Jin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling, 712100, Shaanxi, China.
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The Parauncinula polyspora Draft Genome Provides Insights into Patterns of Gene Erosion and Genome Expansion in Powdery Mildew Fungi. mBio 2019; 10:mBio.01692-19. [PMID: 31551331 PMCID: PMC6759760 DOI: 10.1128/mbio.01692-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Powdery mildew fungi are widespread and agronomically relevant phytopathogens causing major yield losses. Their genomes have disproportionately large numbers of mobile genetic elements, and they have experienced a significant loss of highly conserved fungal genes. In order to learn more about the evolutionary history of this fungal group, we explored the genome of an Asian oak tree pathogen, Parauncinula polyspora, a species that diverged early during evolution from the remaining powdery mildew fungi. We found that the P. polyspora draft genome is comparatively compact, has a low number of protein-coding genes, and, despite the absence of a dedicated genome defense system, lacks the massive proliferation of repetitive sequences. Based on these findings, we infer an evolutionary trajectory that shaped the genomes of powdery mildew fungi. Due to their comparatively small genome size and short generation time, fungi are exquisite model systems to study eukaryotic genome evolution. Powdery mildew fungi present an exceptional case because of their strict host dependency (termed obligate biotrophy) and the atypical size of their genomes (>100 Mb). This size expansion is largely due to the pervasiveness of transposable elements on 70% of the genome and is associated with the loss of multiple conserved ascomycete genes required for a free-living lifestyle. To date, little is known about the mechanisms that drove these changes, and information on ancestral powdery mildew genomes is lacking. We report genome analysis of the early-diverged and exclusively sexually reproducing powdery mildew fungus Parauncinula polyspora, which we performed on the basis of a natural leaf epiphytic metapopulation sample. In contrast to other sequenced species of this taxonomic group, the assembled P. polyspora draft genome is surprisingly small (<30 Mb), has a higher content of conserved ascomycete genes, and is sparsely equipped with transposons (<10%), despite the conserved absence of a common defense mechanism involved in constraining repetitive elements. We speculate that transposable element spread might have been limited by this pathogen’s unique reproduction strategy and host features and further hypothesize that the loss of conserved ascomycete genes may promote the evolutionary isolation and host niche specialization of powdery mildew fungi. Limitations associated with this evolutionary trajectory might have been in part counteracted by the evolution of plastic, transposon-rich genomes and/or the expansion of gene families encoding secreted virulence proteins.
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Ellingham O, David J, Culham A. Enhancing identification accuracy for powdery mildews using previously underexploited DNA loci. Mycologia 2019; 111:798-812. [DOI: 10.1080/00275514.2019.1643644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Oliver Ellingham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, Surrey, GU23 6QB, UK
| | - Alastair Culham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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66
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Polonio Á, Seoane P, Claros MG, Pérez-García A. The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi. BMC Genomics 2019; 20:543. [PMID: 31272366 PMCID: PMC6611051 DOI: 10.1186/s12864-019-5938-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits and is responsible for important yield losses in these crops worldwide. Powdery mildew fungi are obligate biotrophs. In these parasites, biotrophy is determined by the presence of haustoria, which are specialized structures of parasitism developed by these fungi for the acquisition of nutrients and the delivery of effectors. Detailed molecular studies of powdery mildew haustoria are scarce due mainly to difficulties in their isolation. Therefore, their analysis is considered an important challenge for powdery mildew research. The aim of this work was to gain insights into powdery mildew biology by analysing the haustorial transcriptome of P. xanthii. Results Prior to RNA isolation and massive-scale mRNA sequencing, a flow cytometric approach was developed to isolate P. xanthii haustoria free of visible contaminants. Next, several commercial kits were used to isolate total RNA and to construct the cDNA and Illumina libraries that were finally sequenced by the Illumina NextSeq system. Using this approach, the maximum amount of information from low-quality RNA that could be obtained was used to accomplish the de novo assembly of the P. xanthii haustorial transcriptome. The subsequent analysis of this transcriptome and comparison with the epiphytic transcriptome allowed us to identify the importance of several biological processes for haustorial cells such as protection against reactive oxygen species, the acquisition of different nutrients and genetic regulation mediated by non-coding RNAs. In addition, we could also identify several secreted proteins expressed exclusively in haustoria such as cell adhesion proteins that have not been related to powdery mildew biology to date. Conclusions This work provides a novel approach to study the molecular aspects of powdery mildew haustoria. In addition, the results of this study have also allowed us to identify certain previously unknown processes and proteins involved in the biology of powdery mildews that could be essential for their biotrophy and pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5938-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31, 29071, Málaga, Spain. .,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur 31, 29071, Málaga, Spain.
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67
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Wadl PA, Mack BM, Beltz SB, Moore GG, Baird RE, Rinehart TA, Molnar TJ, Staton ME, Hadziabdic D, Trigiano RN. Development of Genomic Resources for the Powdery Mildew, Erysiphe pulchra. PLANT DISEASE 2019; 103:804-807. [PMID: 30864941 DOI: 10.1094/pdis-05-18-0719-a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Powdery mildews (PMs) are important plant pathogens causing widespread damage. Here, we report the first draft genome of Erysiphe pulchra, the causative agent of PM of flowering dogwood, Cornus florida. The assembled genome was 63.5 Mbp and resulted in formation of 19,442 contigs (N50 = 11,686 bp) that contained an estimated 6,860 genes with a genome coverage of 62×. We found 102 candidate secreted effector proteins (CSEPs) in E. pulchra similar to E. necator genes that are potentially involved in disease development. This draft genome is an initial step for understanding the evolutionary history of the PMs and will also provide insight into evolutionary strategies that led to the wide host expansion and environmental adaptations so effectively employed by the PM lineages.
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Affiliation(s)
- Phillip A Wadl
- 1 USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Brian M Mack
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Shannon B Beltz
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Geromy G Moore
- 2 USDA-ARS, Southern Regional Research Center, New Orleans, LA 70124
| | - Richard E Baird
- 3 Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | | | - Thomas J Molnar
- 5 Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and
| | - Margaret E Staton
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Denita Hadziabdic
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Robert N Trigiano
- 6 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
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Bheri M, M Bhosle S, Makandar R. Shotgun proteomics provides an insight into pathogenesis-related proteins using anamorphic stage of the biotroph, Erysiphe pisi pathogen of garden pea. Microbiol Res 2019; 222:25-34. [PMID: 30928027 DOI: 10.1016/j.micres.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/30/2018] [Accepted: 02/08/2019] [Indexed: 01/16/2023]
Abstract
E. pisi is an ascomycete member causing powdery mildew disease of garden pea. It is a biotrophic pathogen, requiring a living host for its survival. Our understanding of molecular mechanisms underlying its pathogenesis is limited. The identification of proteins expressed in the pathogen is required to gain an insight into the functional mechanisms of an obligate biotrophic fungal pathogen. In this study, the proteome of the anamorphic stage of E. pisi pathogen has been elucidated through the nano LC-MS/MS approach. A total of 328 distinct proteins were detected from Erysiphe isolates infecting the susceptible pea cultivar, Arkel. The proteome is available via ProteomeXchange with identifier PXD010238. The functional classification of protein accessions based on Gene Ontology revealed proteins related to signal transduction, secondary metabolite formation and stress which might be involved in virulence and pathogenesis. The functional validation carried through differential expression of genes encoding G-protein beta subunit, a Cyclophilin (Peptidyl prolyl cis-transisomerase) and ABC transporter in a time course study confirmed their putative role in pathogenesis between resistant and susceptible genotypes, JI2480 and Arkel. The garden pea-powdery mildew pathosystem is largely unexplored, therefore, the identified proteome provides a first-hand information and will form a basis to analyze mechanisms involving pathogen survival, pathogenesis and virulence.
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Affiliation(s)
- Malathi Bheri
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India
| | - Sheetal M Bhosle
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad- 500046, India.
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Milo-Cochavi S, Pareek M, Delulio G, Almog Y, Anand G, Ma LJ, Covo S. The response to the DNA damaging agent methyl methanesulfonate in a fungal plant pathogen. Fungal Biol 2019; 123:408-422. [PMID: 31053330 DOI: 10.1016/j.funbio.2019.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
DNA damage can cause mutations that in fungal plant pathogens lead to hypervirulence and resistance to pesticides. Almost nothing is known about the response of these fungi to DNA damage. We performed transcriptomic and phosphoproteomic analyses of Fusarium oxysporum exposed to methyl methanesulfonate (MMS). At the RNA level we observe massive induction of DNA repair pathways including the global genome nucleotide excision. Cul3, Cul4, several Ubiquitin-like ligases and components of the proteasome are significantly induced. In agreement, we observed drug synergism between a proteasome inhibitor and MMS. While our data suggest that Yap1 and Xbp1 networks are similarly activated in response to damage in yeast and F. oxysporum we were able to observe modules that were MMS-responsive in F. oxysporum and not in yeast. These include transcription/splicing modules that are upregulated and respiration that is down-regulated. In agreement, MMS treated cells are much more sensitive to a respiration inhibitor. At the phosphoproteomic level, Adenylate cyclase, which generates cAMP, is phosphorylated in response to MMS and forms a network of phosphorylated proteins that include cell cycle regulators and several MAPKs. Our analysis provides a starting point in understanding how genomic changes in response to DNA damage occur in Fusarium species.
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Affiliation(s)
- Shira Milo-Cochavi
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Manish Pareek
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Gregory Delulio
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Yael Almog
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Gautam Anand
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, 7610001, Israel.
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Liang P, Liu S, Xu F, Jiang S, Yan J, He Q, Liu W, Lin C, Zheng F, Wang X, Miao W. Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. Front Microbiol 2018; 9:3160. [PMID: 30619222 PMCID: PMC6305591 DOI: 10.3389/fmicb.2018.03160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/05/2018] [Indexed: 01/08/2023] Open
Abstract
Powdery mildew is a widespread plant disease caused by obligate biotrophic fungal pathogens involving species-specific interactions between host and parasite. To gain genomic insights into the underlying obligate biotrophic mechanisms, we analyzed 15 microbial genomes covering powdery and downy mildews and rusts. We observed a genome-wide, massive contraction of multiple gene families in powdery mildews, such as enzymes in the carbohydrate metabolism pathway, when compared with ascomycete phytopathogens, while the fatty acid metabolism pathway maintained its integrity. We also observed significant differences in candidate secreted effector protein (CSEP) families between monocot and dicot powdery mildews, perhaps due to different selection forces. While CSEPs in monocot mildews are likely subject to positive selection causing rapid expansion, CSEP families in dicot mildews are shrinking under strong purifying selection. Our results not only illustrate obligate biotrophic mechanisms of powdery mildews driven by gene family evolution in nutrient metabolism, but also demonstrate how the divergence of CSEPs between monocot and dicot lineages might contribute to species-specific adaption.
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Affiliation(s)
- Peng Liang
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China.,Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Songyu Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Xu
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Shuqin Jiang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jun Yan
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Qiguang He
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Wenbo Liu
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Chunhua Lin
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Fucong Zheng
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Weiguo Miao
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
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Wu Y, Ma X, Pan Z, Kale SD, Song Y, King H, Zhang Q, Presley C, Deng X, Wei CI, Xiao S. Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew. BMC Genomics 2018; 19:705. [PMID: 30253736 PMCID: PMC6156980 DOI: 10.1186/s12864-018-5069-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici. RESULTS We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification. CONCLUSIONS Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.
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Affiliation(s)
- Ying Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xianfeng Ma
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, 410128 China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiv D. Kale
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Yi Song
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Harlan King
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Qiong Zhang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Christian Presley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cheng-I Wei
- College of Agriculture & Natural Resources, University of Maryland, College Park, MD 20742 USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
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72
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Kusch S, Frantzeskakis L, Thieron H, Panstruga R. Small RNAs from cereal powdery mildew pathogens may target host plant genes. Fungal Biol 2018; 122:1050-1063. [PMID: 30342621 DOI: 10.1016/j.funbio.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
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74
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Martínez-Cruz J, Romero D, de la Torre FN, Fernández-Ortuño D, Torés JA, de Vicente A, Pérez-García A. The Functional Characterization of Podosphaera xanthii Candidate Effector Genes Reveals Novel Target Functions for Fungal Pathogenicity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:914-931. [PMID: 29513627 DOI: 10.1094/mpmi-12-17-0318-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Podosphaera xanthii is the main causal agent of powdery mildew disease in cucurbits. In a previous study, we determined that P. xanthii expresses approximately 50 Podosphaera effector candidates (PECs), identified based on the presence of a predicted signal peptide and the absence of functional annotation. In this work, we used host-induced gene silencing (HIGS), employing Agrobacterium tumefaciens as a vector for the delivery of the silencing constructs (ATM-HIGS), to identify genes involved in early plant-pathogen interaction. The analysis of seven selected PEC-encoding genes showed that six of them, PEC007, PEC009, PEC019, PEC032, PEC034, and PEC054, are required for P. xanthii pathogenesis, as revealed by reduced fungal growth and increased production of hydrogen peroxide by host cells. In addition, protein models and protein-ligand predictions allowed us to identify putative functions for these candidates. The biochemical activities of PEC019, PEC032, and PEC054 were elucidated using their corresponding proteins expressed in Escherichia coli. These proteins were confirmed as phospholipid-binding protein, α-mannosidase, and cellulose-binding protein. Further, BLAST searches showed that these three effectors are widely distributed in phytopathogenic fungi. These results suggest novel targets for fungal effectors, such as host-cell plasma membrane, host-cell glycosylation, and damage-associated molecular pattern-triggered immunity.
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Affiliation(s)
- Jesús Martínez-Cruz
- 1 Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Diego Romero
- 1 Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Fernando N de la Torre
- 2 Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and
| | - Dolores Fernández-Ortuño
- 3 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750 Algarrobo-Costa, Málaga, Spain
| | - Juan A Torés
- 3 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29750 Algarrobo-Costa, Málaga, Spain
| | - Antonio de Vicente
- 1 Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandro Pérez-García
- 1 Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga and Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
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75
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Massonnet M, Morales-Cruz A, Minio A, Figueroa-Balderas R, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum. Front Microbiol 2018; 9:1784. [PMID: 30150972 PMCID: PMC6099105 DOI: 10.3389/fmicb.2018.01784] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022] Open
Abstract
The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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76
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Cherrad S, Charnay A, Hernandez C, Steva H, Belbahri L, Vacher S. Emergence of boscalid-resistant strains of Erysiphe necator in French vineyards. Microbiol Res 2018; 216:79-84. [PMID: 30269859 DOI: 10.1016/j.micres.2018.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/22/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
Abstract
The grapevine powdery mildew Erysiphe necator (E. necator) is an obligate pathogen. Powdery mildew-diseased vines show an important reduction in plant size, winter hardiness and grape yield. Even a low-level infection with powdery mildew was shown to taint wine and ultimately reduce wine quality. For many years, succinate dehydrogenase inhibitor (SDHI) fungicides, mainly the new generation active ingredients (AIs) boscalid, penthiopyrad and fluopyram, have been widely used to control powdery mildew in grapevines. The repeated use of fungicides (mainly boscalid) has resulted in the emergence of resistant microorganisms such as Botrytis cinerea (B. cinerea). However, boscalid resistance was never observed in E. necator. In this study, a large-scale survey of French grapevine field populations of E. necator revealed many field populations with low sensitivity to boscalid. Single spore strains originating from collected resistant populations showed Half maximal effective concentration (EC50) values greater than 100 mg L-1, and strains originating from boscalid sensitive populations showed EC50 values lower than 1 mg L-1. The complete nucleotide sequences of the EnSdhB succinate dehydrogenase of sensitive and resistant single spore strains revealed that H242R and H242Y substitutions in the EnSdhB succinate dehydrogenase subunit conferred E. necator resistance to boscalid. No cross-resistance of E. necator strains bearing H242R and H242Y substitutions in EnSdhB succinate dehydrogenase to fluxapyroxad and fluopyram was noticed. Therefore, our results highlight the emergence of resistance to boscalid activity in French vineyards and warrant the need of the implementation of risk assessment strategies to maintain effective grapevine protection against powdery mildew.
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Affiliation(s)
- Semcheddine Cherrad
- CONIDIA, Parc d'activités en Chuel, Route de Chasselay, 69650 Quincieux, France.
| | - Aline Charnay
- CONIPHY, Parc d'activités en Chuel, Route de Chasselay, 69650 Quincieux, France
| | - Catalina Hernandez
- CONIPHY, Parc d'activités en Chuel, Route de Chasselay, 69650 Quincieux, France
| | - Herve Steva
- CJH SARL, 21 C Chemin de la Girotte, 33650 La Brede, France
| | - Lassaad Belbahri
- Laboratory of Soil Biology, Department of Biology, University of Neuchâtel, 11 Rue Emile Argand, CH-2000, Neuchâtel, Switzerland; NextBiotech, 98 Rue Ali Belhouane, 3030 Agareb, Tunisia
| | - Sébastien Vacher
- CONIPHY, Parc d'activités en Chuel, Route de Chasselay, 69650 Quincieux, France
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77
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Keymer A, Gutjahr C. Cross-kingdom lipid transfer in arbuscular mycorrhiza symbiosis and beyond. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:137-144. [PMID: 29729528 DOI: 10.1016/j.pbi.2018.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
Arbuscular mycorrhiza (AM) is a widespread symbiosis between most land plants and fungi of the Glomeromycotina, which has existed for more than 400million years. AM fungi (AMF) improve plant nutrition with mineral nutrients and conversely, their growth and development is fueled by organic carbon supplied from their host. Recent studies demonstrated independently and with different experimental approaches that lipids are transferred from plants to fungi in addition to sugars, and that AMF are dependent on this lipid supply because they lack genes encoding fatty acid synthase I subunits. Dependence on host lipids or lipid parasitism occur in a range of interorganismic associations with participants from almost all kingdoms. Thus, these phenomena seem rather common in mutualistic and parasitic interactions.
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Affiliation(s)
- Andreas Keymer
- Faculty of Biology, Genetics, LMU Munich, Biocenter Martinsried, Großhaderner Str. 2-4, 82152 Martinsried, Germany; Plant Genetics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany
| | - Caroline Gutjahr
- Plant Genetics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354 Freising, Germany.
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Chang HX, Noel ZA, Sang H, Chilvers MI. Annotation resource of tandem repeat-containing secretory proteins in sixty fungi. Fungal Genet Biol 2018; 119:7-19. [PMID: 30026018 DOI: 10.1016/j.fgb.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/06/2018] [Accepted: 07/15/2018] [Indexed: 11/17/2022]
Abstract
Fungal secretory proteins that interact with host plants are regarded as effectors. Because fungal effectors rarely contain conserved sequence features, identification and annotation of fungal effectors from predicted secretory proteins are difficult using outward comparison methods such as BLAST or hidden Markov model. In desire of more sequence features to prioritize research interests of fungal secretory proteins, this study developed a pipeline to identify tandem repeat (TR) domain within putative secretory proteins and tested a hypothesis that at least one type of TR domain in non-orthologous secretory proteins has emerged from convergent evolution for plant pathogenicity. There were 2804 types of TR domains and a total of 2925 TR-containing secretory proteins found from 60 fungi. There was no conserved type of TR domain shared only by plant pathogens, indicating functional divergence for different types of TR domain and TR-containing secretory proteins. The annotation resource of putative fungal TR-containing secretory proteins provides new sequence features that will be useful for the community interested in fungal effector biology.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Zachary A Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Hyunkyu Sang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States.
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Ilc T, Arista G, Tavares R, Navrot N, Duchêne E, Velt A, Choulet F, Paux E, Fischer M, Nelson DR, Hugueney P, Werck-Reichhart D, Rustenholz C. Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome. PLoS One 2018; 13:e0199902. [PMID: 29953551 PMCID: PMC6023221 DOI: 10.1371/journal.pone.0199902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/15/2018] [Indexed: 12/26/2022] Open
Abstract
Cytochromes P450 are enzymes that participate in a wide range of functions in plants, from hormonal signaling and biosynthesis of structural polymers, to defense or communication with other organisms. They represent one of the largest gene/protein families in the plant kingdom. The manual annotation of cytochrome P450 genes in the genome of Vitis vinifera PN40024 revealed 579 P450 sequences, including 279 complete genes. Most of the P450 sequences in grapevine genome are organized in physical clusters, resulting from tandem or segmental duplications. Although most of these clusters are small (2 to 35, median = 3), some P450 families, such as CYP76 and CYP82, underwent multiple duplications and form large clusters of homologous sequences. Analysis of gene expression revealed highly specific expression patterns, which are often the same within the genes in large physical clusters. Some of these genes are induced upon biotic stress, which points to their role in plant defense, whereas others are specifically activated during grape berry ripening and might be responsible for the production of berry-specific metabolites, such as aroma compounds. Our work provides an exhaustive and robust annotation including clear identification, structural organization, evolutionary dynamics and expression patterns for the grapevine cytochrome P450 families, paving the way to efficient functional characterization of genes involved in grapevine defense pathways and aroma biosynthesis.
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Affiliation(s)
- Tina Ilc
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Gautier Arista
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon 1, Lyon, France
| | - Nicolas Navrot
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Eric Duchêne
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Frédéric Choulet
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Etienne Paux
- Laboratoire Structure et Evolution du Génome du Blé, Institut National de la Recherche Agronomique, Université Blaise Pascal, Clermont-Ferrand, France
| | - Marc Fischer
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | | | - Danièle Werck-Reichhart
- Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Camille Rustenholz
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
- * E-mail:
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Frantzeskakis L, Kracher B, Kusch S, Yoshikawa-Maekawa M, Bauer S, Pedersen C, Spanu PD, Maekawa T, Schulze-Lefert P, Panstruga R. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 2018; 19:381. [PMID: 29788921 PMCID: PMC5964911 DOI: 10.1186/s12864-018-4750-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Background Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). Results The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. Conclusions The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens. Electronic supplementary material The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamprinos Frantzeskakis
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Barbara Kracher
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stefan Kusch
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Makoto Yoshikawa-Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Saskia Bauer
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Pietro D Spanu
- Imperial College, Department of Life Sciences, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Takaki Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
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Hu Y, Li Y, Hou F, Wan D, Cheng Y, Han Y, Gao Y, Liu J, Guo Y, Xiao S, Wang Y, Wen YQ. Ectopic expression of Arabidopsis broad-spectrum resistance gene RPW8.2 improves the resistance to powdery mildew in grapevine (Vitis vinifera). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:20-31. [PMID: 29362096 DOI: 10.1016/j.plantsci.2017.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/03/2017] [Accepted: 11/11/2017] [Indexed: 05/08/2023]
Abstract
Powdery mildew is the most economically important disease of cultivated grapevines worldwide. Here, we report that the Arabidopsis broad-spectrum disease resistance gene RPW8.2 could improve resistance to powdery mildew in Vitis vinifera cv. Thompson Seedless. The RPW8.2-YFP fusion gene was stably expressed in grapevines from either the constitutive 35S promoter or the native promoter (NP) of RPW8.2. The grapevine shoots and plantlets transgenic for 35S::RPW8.2-YFP showed reduced rooting and reduced growth at later development stages in the absence of any pathogens. Infection tests with an adapted grapevine powdery mildew isolate En NAFU1 showed that hyphal growth and sporulation were significantly restricted in transgenic grapevines expressing either of the two constructs. The resistance appeared to be attributable to the ectopic expression of RPW8.2, and associated with the enhanced encasement of the haustorial complex (EHC) and onsite accumulation of H2O2. In addition, the RPW8.2-YFP fusion protein showed focal accumulation around the fungal penetration sites. Transcriptome analysis revealed that ectopic expression of RPW8.2 in grapevines not only significantly enhanced salicylic acid-dependent defense signaling, but also altered expression of other phytohormone-associated genes. Taken together, our results indicate that RPW8.2 could be utilized as a transgene for improving resistance against powdery mildew in grapevines.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Fengjuan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Dongyan Wan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yuan Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yongtao Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yurong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ye Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research & Department of Plant Science and Landscape Architecture, University of Maryland College Park, Rockville, MD 20850, USA
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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Morales‐Cruz A, Allenbeck G, Figueroa‐Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D. Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. MOLECULAR PLANT PATHOLOGY 2018; 19:490-503. [PMID: 28218463 PMCID: PMC6638111 DOI: 10.1111/mpp.12544] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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Affiliation(s)
- Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Gabrielle Allenbeck
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Vanessa E. Ashworth
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Renaud Travadon
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Rhonda J. Smith
- University of California Cooperative Extension, Sonoma CountySanta RosaCA95403USA
| | - Kendra Baumgartner
- United States Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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83
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Massonnet M, Morales‐Cruz A, Figueroa‐Balderas R, Lawrence DP, Baumgartner K, Cantu D. Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. MOLECULAR PLANT PATHOLOGY 2018; 19:21-34. [PMID: 27608421 PMCID: PMC6637977 DOI: 10.1111/mpp.12491] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single-molecule real-time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co-expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co-regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Kendra Baumgartner
- US Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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Mestre P, Arista G, Piron M, Rustenholz C, Ritzenthaler C, Merdinoglu D, Chich J. Identification of a Vitis vinifera endo-β-1,3-glucanase with antimicrobial activity against Plasmopara viticola. MOLECULAR PLANT PATHOLOGY 2017; 18:708-719. [PMID: 27216084 PMCID: PMC6638254 DOI: 10.1111/mpp.12431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Inducible plant defences against pathogens are stimulated by infections and comprise several classes of pathogenesis-related (PR) proteins. Endo-β-1,3-glucanases (EGases) belong to the PR-2 class and their expression is induced by many pathogenic fungi and oomycetes, suggesting that EGases play a role in the hydrolysis of pathogen cell walls. However, reports of a direct effect of EGases on cell walls of plant pathogens are scarce. Here, we characterized three EGases from Vitis vinifera whose expression is induced during infection by Plasmopara viticola, the causal agent of downy mildew. Recombinant proteins were expressed in Escherichia coli. The enzymatic characteristics of these three enzymes were measured in vitro and in planta. A functional assay performed in vitro on germinated P. viticola spores revealed a strong anti-P. viticola activity for EGase3, which strikingly was that with the lowest in vitro catalytic efficiency. To our knowledge, this work shows, for the first time, the direct effect against downy mildew of EGases of the PR-2 family from Vitis.
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Affiliation(s)
- Pere Mestre
- SVQV, INRA, Université de StrasbourgColmarF‐68000France
| | | | | | | | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg12 rue du Général ZimmerStrasbourg67084France
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85
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Abstract
Aspergillus species are ubiquitous fungal saprophytes found in diverse ecological niches worldwide. Among them, Aspergillus fumigatus is the most prevalent and is largely responsible for the increased incidence of invasive aspergillosis with high mortality rates in some immunocompromised hosts. Azoles are the first-line drugs in treating diseases caused by Aspergillus spp. However, increasing reports in A. fumigatus azole resistance, both in the clinical setting and in the environment, are threatening the effectiveness of clinical and agricultural azole drugs. The azole target is the 14-α sterol demethylase encoded by cyp51A gene and the main mechanisms of resistance involve the integration of tandem repeats in its promoter and/or single point mutations in this gene. In A. fumigatus, azole resistance can emerge in two different scenarios: a medical route in which azole resistance is generated during long periods of azole treatment in the clinical setting and a route of resistance derived from environmental origin due to extended use of demethylation inhibitors in agriculture. The understanding of A. fumigatus azole resistance development and its evolution is needed in order to prevent or minimize its impact. In this article, we review the current situation of azole resistance epidemiology and the predominant molecular mechanisms described based on the resistance acquisition routes. In addition, the clinical implications of A. fumigatus azole resistance and future research are discussed.
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86
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Feehan JM, Scheibel KE, Bourras S, Underwood W, Keller B, Somerville SC. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing. J Vis Exp 2017. [PMID: 28448006 DOI: 10.3791/55463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.
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Affiliation(s)
- Joanna M Feehan
- Department of Plant and Microbial Biology, University of California Berkeley; John Innes Centre, Norwich Research Park
| | | | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich
| | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich
| | - Shauna C Somerville
- Department of Plant and Microbial Biology, University of California Berkeley;
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87
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Teixeira M, Moreno L, Stielow B, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané J, Priest M, Souza R, Young S, Ferreira K, Zeng Q, da Cunha M, Gladki A, Barker B, Vicente V, de Souza E, Almeida S, Henrissat B, Vasconcelos A, Deng S, Voglmayr H, Moussa T, Gorbushina A, Felipe M, Cuomo C, de Hoog GS. Exploring the genomic diversity of black yeasts and relatives ( Chaetothyriales, Ascomycota). Stud Mycol 2017; 86:1-28. [PMID: 28348446 PMCID: PMC5358931 DOI: 10.1016/j.simyco.2017.01.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
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Affiliation(s)
- M.M. Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - L.F. Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - B.J. Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - A. Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - M. Hainaut
- Université Aix-Marseille (CNRS), Marseille, France
| | - L. Gonzaga
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | | | - J.S.L. Patané
- Department of Biochemistry, University of São Paulo, Brazil
| | - M. Priest
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - R. Souza
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Young
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - K.S. Ferreira
- Department of Biological Sciences, Federal University of São Paulo, Diadema, SP, Brazil
| | - Q. Zeng
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - M.M.L. da Cunha
- Núcleo Multidisciplinar de Pesquisa em Biologia UFRJ-Xerém-NUMPEX-BIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A. Gladki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - B. Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - V.A. Vicente
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
| | - E.M. de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - S. Almeida
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, SP, Brazil
| | - B. Henrissat
- Université Aix-Marseille (CNRS), Marseille, France
| | - A.T.R. Vasconcelos
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - H. Voglmayr
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - T.A.A. Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - A. Gorbushina
- Federal Institute for Material Research and Testing (BAM), Berlin, Germany
| | - M.S.S. Felipe
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - C.A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Xu Q, Xu X, Shi Y, Qi X, Chen X. Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm5.1 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling. BMC Genomics 2017; 18:21. [PMID: 28056792 PMCID: PMC5217421 DOI: 10.1186/s12864-016-3438-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8. RESULTS Whole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers. This led to the identification of a ~6.8 Mb substituted segment predicted to contain 856 genes. RNA-seq was used to study gene expression differences in PM treated (plants harvested 48 h after inoculation) and untreated (control) SSL508-28 and D8 lines. Exactly 1,248 and 1,325 differentially expressed genes (DEGs) were identified in SSL508-28 and D8, respectively. Of those, 88 DEGs were located in the ~6.8 Mb segment interval. Based on expression data and annotation, we identified 8 potential candidate genes that may participate in PM resistance afforded by Pm5.1, including two tandemly arrayed genes encoding receptor protein kinases, two transcription factors, two genes encoding remorin proteins, one gene encoding a P-type ATPase and one gene encoding a 70 kDa heat shock protein. The transcriptome data also revealed a complex regulatory network for Pm5.1-mediated PM resistance that may involve multiple signal regulators and transducers, cell wall modifications and the salicylic acid signaling pathway. CONCLUSION These findings shed light on the cucumber PM defense mechanisms mediated by Pm5.1 and provided valuable information for the fine mapping of Pm5.1 and breeding of cucumber with enhanced resistance to PM.
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Affiliation(s)
- Qiang Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuewen Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Yang Shi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xiaohua Qi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuehao Chen
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
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Short DPG, O'Donnell K, Stajich JE, Hulcr J, Kijimoto T, Berger MC, Macias AM, Spahr EJ, Bateman CC, Eskalen A, Lynch SC, Cognato AI, Cooperband MF, Kasson MT. PCR Multiplexes Discriminate Fusarium Symbionts of Invasive Euwallacea Ambrosia Beetles that Inflict Damage on Numerous Tree Species Throughout the United States. PLANT DISEASE 2017; 101:233-240. [PMID: 30682305 DOI: 10.1094/pdis-07-16-1046-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Asian Euwallacea ambrosia beetles vector Fusarium mutualists. The ambrosial fusaria are all members of the ambrosia Fusarium clade (AFC) within the Fusarium solani species complex (FSSC). Several Euwallacea-Fusarium mutualists have been introduced into nonnative regions and have caused varying degrees of damage to orchard, landscape, and forest trees. Knowledge of symbiont fidelity is limited by current identification methods, which typically requires analysis of DNA sequence data from beetles and the symbionts cultured from their oral mycangia. Here, polymerase chain reaction (PCR)-based diagnostic tools were developed to identify the six Fusarium symbionts of exotic Euwallacea spp. currently known within the United States. Whole-genome sequences were generated for representatives of six AFC species plus F. ambrosium and aligned to the annotated genome of F. euwallaceae. Taxon-specific primer-annealing sites were identified that rapidly distinguish the AFC species currently within the United States. PCR specificity, reliability, and sensitivity were validated using a panel of 72 Fusarium isolates, including 47 reference cultures. Culture-independent multiplex assays accurately identified two AFC fusaria using DNA isolated from heads of their respective beetle partners. The PCR assays were used to show that Euwallacea validus is exclusively associated with AF-4 throughout its sampled range within eastern North America. The rapid assay supports federal and state agency efforts to monitor spread of these invasive pests and mitigate further introductions.
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Affiliation(s)
- Dylan P G Short
- Division of Plant and Soil Sciences, West Virginia University, Morgantown
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture (USDA)-Agricultural Research Service, Peoria IL
| | - Jason E Stajich
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California, Riverside
| | - Jiri Hulcr
- School of Forest Resources and Conservation, University of Florida, Gainesville
| | - Teiya Kijimoto
- Division of Plant and Soil Sciences, West Virginia University
| | | | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia University
| | - Ellie J Spahr
- Division of Plant and Soil Sciences, West Virginia University
| | - Craig C Bateman
- Department of Entomology and Nematology, University of Florida
| | - Akif Eskalen
- Department of Plant Pathology and Microbiology, University of California
| | - Shannon C Lynch
- Department of Plant Pathology and Microbiology, University of California
| | | | - Miriam F Cooperband
- Otis Laboratory, USDA Animal and Plant Health Inspection Service-Plant Protection and Quarantine-Center for Plant Health Science and Technology, Buzzards Bay, MA
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90
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Casida JE, Durkin KA. Pesticide Chemical Research in Toxicology: Lessons from Nature. Chem Res Toxicol 2016; 30:94-104. [DOI: 10.1021/acs.chemrestox.6b00303] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- John E. Casida
- Environmental Chemistry and Toxicology Laboratory, Department of
Environmental Science, Policy, and Management, University of California, Berkeley 94720, United States
| | - Kathleen A. Durkin
- Molecular Graphics and Computational Facility, College of Chemistry, University of California, Berkeley 94720, United States
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91
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Vela-Corcía D, Bautista R, de Vicente A, Spanu PD, Pérez-García A. De novo Analysis of the Epiphytic Transcriptome of the Cucurbit Powdery Mildew Fungus Podosphaera xanthii and Identification of Candidate Secreted Effector Proteins. PLoS One 2016; 11:e0163379. [PMID: 27711117 PMCID: PMC5053433 DOI: 10.1371/journal.pone.0163379] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/06/2016] [Indexed: 01/09/2023] Open
Abstract
The cucurbit powdery mildew fungus Podosphaera xanthii is a major limiting factor for cucurbit production worldwide. Despite the fungus’s agronomic and economic importance, very little is known about fundamental aspects of P. xanthii biology, such as obligate biotrophy or pathogenesis. To design more durable control strategies, genomic information about P. xanthii is needed. Powdery mildews are fungal pathogens with large genomes compared with those of other fungi, which contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. To reduce genome complexity, in this work we aimed to obtain and analyse the epiphytic transcriptome of P. xanthii as a starting point for genomic research. Total RNA was isolated from epiphytic fungal material, and the corresponding cDNA library was sequenced using a 454 GS FLX platform. Over 676,562 reads were obtained and assembled into 37,241 contigs. Annotation data identified 8,798 putative genes with different orthologues. As described for other powdery mildew fungi, a similar set of missing core ascomycete genes was found, which may explain obligate biotrophy. To gain insight into the plant-pathogen relationships, special attention was focused on the analysis of the secretome. After this analysis, 137 putative secreted proteins were identified, including 53 candidate secreted effector proteins (CSEPs). Consistent with a putative role in pathogenesis, the expression profile observed for some of these CSEPs showed expression maxima at the beginning of the infection process at 24 h after inoculation, when the primary appressoria are mostly formed. Our data mark the onset of genomics research into this very important pathogen of cucurbits and shed some light on the intimate relationship between this pathogen and its host plant.
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Affiliation(s)
- David Vela-Corcía
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC), Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Edificio de Bioinnovación, Parque Tecnológico de Andalucía, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC), Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Pietro D. Spanu
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC), Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
- * E-mail:
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92
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Pap D, Riaz S, Dry IB, Jermakow A, Tenscher AC, Cantu D, Oláh R, Walker MA. Identification of two novel powdery mildew resistance loci, Ren6 and Ren7, from the wild Chinese grape species Vitis piasezkii. BMC PLANT BIOLOGY 2016; 16:170. [PMID: 27473850 PMCID: PMC4966781 DOI: 10.1186/s12870-016-0855-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 07/14/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grapevine powdery mildew Erysiphe necator is a major fungal disease in all grape growing countries worldwide. Breeding for resistance to this disease is crucial to avoid extensive fungicide applications that are costly, labor intensive and may have detrimental effects on the environment. In the past decade, Chinese Vitis species have attracted attention from grape breeders because of their strong resistance to powdery mildew and their lack of negative fruit quality attributes that are often present in resistant North American species. In this study, we investigated powdery mildew resistance in multiple accessions of the Chinese species Vitis piasezkii that were collected during the 1980 Sino-American botanical expedition to the western Hubei province of China. RESULTS A framework genetic map was developed using simple sequence repeat markers in 277 seedlings of an F1 mapping population arising from a cross of the powdery mildew susceptible Vitis vinifera selection F2-35 and a resistant accession of V. piasezkii DVIT2027. Quantitative trait locus analyses identified two major powdery mildew resistance loci on chromosome 9 (Ren6) and chromosome 19 (Ren7) explaining 74.8 % of the cumulative phenotypic variation. The quantitative trait locus analysis for each locus, in the absence of the other, explained 95.4 % phenotypic variation for Ren6, while Ren7 accounted for 71.9 % of the phenotypic variation. Screening of an additional 259 seedlings of the F1 population and 910 seedlings from four pseudo-backcross populations with SSR markers defined regions of 22 kb and 330 kb for Ren6 and Ren7 in the V. vinifera PN40024 (12X) genome sequence, respectively. Both R loci operate post-penetration through the induction of programmed cell death, but vary significantly in the speed of response and degree of resistance; Ren6 confers complete resistance whereas Ren7 confers partial resistance to the disease with reduced colony size. A comparison of the kinetics of induction of powdery mildew resistance mediated by Ren6, Ren7 and the Run1 locus from Muscadinia rotundifolia, indicated that the speed and strength of resistance conferred by Ren6 is greater than that of Run1 which, in turn, is superior to that conferred by Ren7. CONCLUSIONS This is the first report of mapping powdery mildew resistance in the Chinese species V. piasezkii. Two distinct powdery mildew R loci designated Ren6 and Ren7 were found in multiple accessions of this Chinese grape species. Their location on different chromosomes to previously reported powdery mildew resistance R loci offers the potential for grape breeders to combine these R genes with existing powdery mildew R loci to produce grape germplasm with more durable resistance against this rapidly evolving fungal pathogen.
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Affiliation(s)
- Dániel Pap
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Ian B. Dry
- CSIRO Agriculture, Glen Osmond, SA Australia
| | | | - Alan C. Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Róbert Oláh
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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93
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Pessina S, Lenzi L, Perazzolli M, Campa M, Dalla Costa L, Urso S, Valè G, Salamini F, Velasco R, Malnoy M. Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine. HORTICULTURE RESEARCH 2016; 3:16016. [PMID: 27390621 PMCID: PMC4935963 DOI: 10.1038/hortres.2016.16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 05/16/2023]
Abstract
Erysiphe necator is the causal agent of powdery mildew (PM), one of the most destructive diseases of grapevine. PM is controlled by sulfur-based and synthetic fungicides, which every year are dispersed into the environment. This is why PM-resistant varieties should become a priority for sustainable grapevine and wine production. PM resistance can be achieved in other crops by knocking out susceptibility S-genes, such as those residing at genetic loci known as MLO (Mildew Locus O). All MLO S-genes of dicots belong to the phylogenetic clade V, including grapevine genes VvMLO7, 11 and 13, which are upregulated during PM infection, and VvMLO6, which is not upregulated. Before adopting a gene-editing approach to knockout candidate S-genes, the evidence that loss of function of MLO genes can reduce PM susceptibility is necessary. This paper reports the knockdown through RNA interference of VvMLO6, 7, 11 and 13. The knockdown of VvMLO6, 11 and 13 did not decrease PM severity, whereas the knockdown of VvMLO7 in combination with VvMLO6 and VvMLO11 reduced PM severity up to 77%. The knockdown of VvMLO7 and VvMLO6 seemed to be important for PM resistance, whereas a role for VvMLO11 does not seem likely. Cell wall appositions (papillae) were present in both resistant and susceptible lines in response to PM attack. Thirteen genes involved in defense were less upregulated in infected mlo plants, highlighting the early mlo-dependent disruption of PM invasion.
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Affiliation(s)
- Stefano Pessina
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Luisa Lenzi
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
- Department of Ecological and Biological Sciences, Università della Tuscia, Via San Camillo de Lellis, Viterbo 01100, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
| | - Manuela Campa
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
| | - Lorenza Dalla Costa
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
| | - Simona Urso
- Council for Agricultural Research and Economics (CREA), Rice Research Unit, S.S. 11 per Torino km 25, Vercelli 13100, Italy
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via San Protaso, 302, 29017, Fiorenzuola d’Arda, Piacenza, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA), Rice Research Unit, S.S. 11 per Torino km 25, Vercelli 13100, Italy
- Council for Agricultural Research and Economics (CREA), Genomics Research Centre, Via San Protaso, 302, 29017, Fiorenzuola d’Arda, Piacenza, Italy
| | - Francesco Salamini
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010 San Michele all’Adige, Italy
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94
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Armijo G, Schlechter R, Agurto M, Muñoz D, Nuñez C, Arce-Johnson P. Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios. FRONTIERS IN PLANT SCIENCE 2016; 7:382. [PMID: 27066032 PMCID: PMC4811896 DOI: 10.3389/fpls.2016.00382] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/13/2016] [Indexed: 05/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important fruit crop worldwide. Commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. Among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. While plant-pathogen interactions are cycles of resistance and susceptibility, resistance traits from natural resources are selected and may be used for breeding purposes and for a sustainable agriculture. In this context, here we summarize some of the most important diseases affecting V. vinifera together with their causal agents. The aim of this work is to bring a comprehensive review of the infection strategies deployed by significant types of pathogens while understanding the host response in both resistance and susceptibility scenarios. New approaches being used to uncover grapevine status during biotic stresses and scientific-based procedures needed to control plant diseases and crop protection are also addressed.
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Affiliation(s)
| | | | | | | | | | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
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95
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Rallos LEE, Baudoin AB. Co-Occurrence of Two Allelic Variants of CYP51 in Erysiphe necator and Their Correlation with Over-Expression for DMI Resistance. PLoS One 2016; 11:e0148025. [PMID: 26839970 PMCID: PMC4740414 DOI: 10.1371/journal.pone.0148025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/12/2016] [Indexed: 01/15/2023] Open
Abstract
Demethylation inhibitors (DMIs) have been an important tool in the management of grapevine powdery mildew caused by Erysiphe necator. Long-term, intensive use of DMIs has resulted in reduced sensitivity in field populations. To further characterize DMI resistance and understand resistance mechanisms in this pathogen, we investigated the cyp51 sequence of 24 single-spored isolates from Virginia and surrounding states and analyzed gene expression in isolates representing a wide range of sensitivity. Two cyp51 alleles were found with respect to the 136th codon of the predicted EnCYP51 sequence: the wild-type (TAT) and the mutant (TTT), which results in the known Y136F amino acid change. Some isolates possessed both alleles, demonstrating gene duplication or increased gene copy number and possibly a requirement for at least one mutant copy of CYP51 for resistance. Cyp51 was over-expressed 1.4- to 19-fold in Y136F-mutant isolates. However, the Y136F mutation was absent in one isolate with moderate to high resistance factor. Two additional synonymous mutations were detected as well, one of which, A1119C was present only in isolates with high cyp51 expression. Overall, our results indicate that at least two mechanisms, cyp51 over-expression and the known target-site mutation in CYP51, contribute to resistance in E. necator, and may be working in conjunction with each other.
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Affiliation(s)
- Lynn Esther E. Rallos
- Department of Plant Pathology, Physiology and Weed Science, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Anton B. Baudoin
- Department of Plant Pathology, Physiology and Weed Science, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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96
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Rallos LEE, Baudoin AB. Co-Occurrence of Two Allelic Variants of CYP51 in Erysiphe necator and Their Correlation with Over-Expression for DMI Resistance. PLoS One 2016; 11:e0148025. [PMID: 26839970 DOI: 10.1371/journal.pone.014802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/12/2016] [Indexed: 05/26/2023] Open
Abstract
Demethylation inhibitors (DMIs) have been an important tool in the management of grapevine powdery mildew caused by Erysiphe necator. Long-term, intensive use of DMIs has resulted in reduced sensitivity in field populations. To further characterize DMI resistance and understand resistance mechanisms in this pathogen, we investigated the cyp51 sequence of 24 single-spored isolates from Virginia and surrounding states and analyzed gene expression in isolates representing a wide range of sensitivity. Two cyp51 alleles were found with respect to the 136th codon of the predicted EnCYP51 sequence: the wild-type (TAT) and the mutant (TTT), which results in the known Y136F amino acid change. Some isolates possessed both alleles, demonstrating gene duplication or increased gene copy number and possibly a requirement for at least one mutant copy of CYP51 for resistance. Cyp51 was over-expressed 1.4- to 19-fold in Y136F-mutant isolates. However, the Y136F mutation was absent in one isolate with moderate to high resistance factor. Two additional synonymous mutations were detected as well, one of which, A1119C was present only in isolates with high cyp51 expression. Overall, our results indicate that at least two mechanisms, cyp51 over-expression and the known target-site mutation in CYP51, contribute to resistance in E. necator, and may be working in conjunction with each other.
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Affiliation(s)
- Lynn Esther E Rallos
- Department of Plant Pathology, Physiology and Weed Science, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Anton B Baudoin
- Department of Plant Pathology, Physiology and Weed Science, College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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97
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Enguita FJ, Costa MC, Fusco-Almeida AM, Mendes-Giannini MJ, Leitão AL. Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next-Generation Sequencing Methods. J Fungi (Basel) 2016; 2:jof2010007. [PMID: 29376924 PMCID: PMC5753088 DOI: 10.3390/jof2010007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/12/2015] [Accepted: 12/12/2015] [Indexed: 12/22/2022] Open
Abstract
Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific transcriptional program in their host cells. The detailed knowledge of this transcriptional program will allow for a better understanding of the infection process and consequently will help in the future design of more efficient therapeutic strategies. Simultaneous transcriptomic studies of pathogen and host by high-throughput sequencing (dual RNA-seq) is an unbiased protocol to understand the intricate regulatory networks underlying the infectious process. This protocol is starting to be applied to the study of the interactions between fungal pathogens and their hosts. To date, our knowledge of the molecular basis of infection for fungal pathogens is still very limited, and the putative role of regulatory players such as non-coding RNAs or epigenetic factors remains elusive. The wider application of high-throughput transcriptomics in the near future will help to understand the fungal mechanisms for colonization and survival, as well as to characterize the molecular responses of the host cell against a fungal infection.
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Affiliation(s)
- Francisco J Enguita
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, Lisboa 1649-028, Portugal.
| | - Marina C Costa
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, Lisboa 1649-028, Portugal.
| | - Ana Marisa Fusco-Almeida
- Núcleo de Proteômica, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista-UNESP, Rodovia Araraquara-Jaú Km 1, Araraquara 14801-902, São Paulo, Brazil.
| | - Maria José Mendes-Giannini
- Núcleo de Proteômica, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista-UNESP, Rodovia Araraquara-Jaú Km 1, Araraquara 14801-902, São Paulo, Brazil.
| | - Ana Lúcia Leitão
- MEtRICs, Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica 2829-516, Portugal.
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98
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Gao YR, Han YT, Zhao FL, Li YJ, Cheng Y, Ding Q, Wang YJ, Wen YQ. Identification and utilization of a new Erysiphe necator isolate NAFU1 to quickly evaluate powdery mildew resistance in wild Chinese grapevine species using detached leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 98:12-24. [PMID: 26590705 DOI: 10.1016/j.plaphy.2015.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 05/01/2023]
Abstract
The most economically important disease of cultivated grapevines worldwide is powdery mildew caused by the biotrophic fungal pathogen Erysiphe necator. To integrate effective genetic resistance into cultivated grapevines, numerous disease resistance screens of diverse Vitis germplasm, including wild species, have been conducted to identify powdery mildew resistance, but the results have been inconsistent. Here, a new powdery mildew isolate that is infectious on grapevines, designated Erysiphe necator NAFU1 (En. NAFU1), was identified and characterized by phylogeny inferred from the internal transcribed spacer (ITS) of pathogen ribosomal DNA sequences. Three classical methods were compared for the maintenance of En. NAFU1, and the most convenient method was maintenance on detached leaves and propagation by contact with infected leaves. Furthermore, controlled inoculations of En. NAFU1 were performed using detached leaves from 57 wild Chinese grapevine accessions to quickly evaluate powdery mildew resistance based on trypan blue staining of leaf sections. The results were compared with previous natural epidemics in the field. Among the screened accessions inoculated with En. NAFU1, 22.8% were resistant, 33.3% were moderately resistant, and 43.9% were susceptible. None of the accessions assessed herein were immune from infection. These results support previous findings documenting the presence of race-specific resistance to E. necator in wild Chinese grapevine. The resistance of wild Chinese grapevine to En. NAFU1 could be due to programmed cell death. The present results suggest that En. NAFU1 isolate could be used for future large-scale screens of resistance to powdery mildew in diverse Vitis germplasms and investigations of the interaction between grapevines and pathogens.
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Affiliation(s)
- Yu-Rong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yong-Tao Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Feng-Li Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Ya-Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yuan Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Qin Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yue-Jin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
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99
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Bindschedler LV, Panstruga R, Spanu PD. Mildew-Omics: How Global Analyses Aid the Understanding of Life and Evolution of Powdery Mildews. FRONTIERS IN PLANT SCIENCE 2016; 7:123. [PMID: 26913042 PMCID: PMC4753294 DOI: 10.3389/fpls.2016.00123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/22/2016] [Indexed: 05/21/2023]
Abstract
The common powdery mildew plant diseases are caused by ascomycete fungi of the order Erysiphales. Their characteristic life style as obligate biotrophs renders functional analyses in these species challenging, mainly because of experimental constraints to genetic manipulation. Global large-scale ("-omics") approaches are thus particularly valuable and insightful for the characterisation of the life and evolution of powdery mildews. Here we review the knowledge obtained so far from genomic, transcriptomic and proteomic studies in these fungi. We consider current limitations and challenges regarding these surveys and provide an outlook on desired future investigations on the basis of the various -omics technologies.
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Affiliation(s)
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen UniversityAachen, Germany
- *Correspondence: Ralph Panstruga,
| | - Pietro D. Spanu
- Department of Life Sciences, Imperial College LondonLondon, UK
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Amselem J, Vigouroux M, Oberhaensli S, Brown JKM, Bindschedler LV, Skamnioti P, Wicker T, Spanu PD, Quesneville H, Sacristán S. Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics 2015; 16:917. [PMID: 26556056 PMCID: PMC4641428 DOI: 10.1186/s12864-015-2185-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avrk1 and Avra10) gene family. Results We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5 % of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. Conclusions Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2185-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joelle Amselem
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France. .,INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, 78850, Thiverval-Grignon, France.
| | | | - Simone Oberhaensli
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - Pari Skamnioti
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, TK 11855, Athens, Greece.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK.
| | - Hadi Quesneville
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France.
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
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