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Ray S, Singh PK, Gupta DK, Mahato AK, Sarkar C, Rathour R, Singh NK, Sharma TR. Analysis of Magnaporthe oryzae Genome Reveals a Fungal Effector, Which Is Able to Induce Resistance Response in Transgenic Rice Line Containing Resistance Gene, Pi54. FRONTIERS IN PLANT SCIENCE 2016; 7:1140. [PMID: 27551285 PMCID: PMC4976503 DOI: 10.3389/fpls.2016.01140] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/18/2016] [Indexed: 05/04/2023]
Abstract
Rice blast caused by Magnaporthe oryzae is one of the most important diseases of rice. Pi54, a rice gene that imparts resistance to M. oryzae isolates prevalent in India, was already cloned but its avirulent counterpart in the pathogen was not known. After decoding the whole genome of an avirulent isolate of M. oryzae, we predicted 11440 protein coding genes and then identified four candidate effector proteins which are exclusively expressed in the infectious structure, appresoria. In silico protein modeling followed by interaction analysis between Pi54 protein model and selected four candidate effector proteins models revealed that Mo-01947_9 protein model encoded by a gene located at chromosome 4 of M. oryzae, interacted best at the Leucine Rich Repeat domain of Pi54 protein model. Yeast-two-hybrid analysis showed that Mo-01947_9 protein physically interacts with Pi54 protein. Nicotiana benthamiana leaf infiltration assay confirmed induction of hypersensitive response in the presence of Pi54 gene in a heterologous system. Genetic complementation test also proved that Mo-01947_9 protein induces avirulence response in the pathogen in presence of Pi54 gene. Here, we report identification and cloning of a new fungal effector gene which interacts with blast resistance gene Pi54 in rice.
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Affiliation(s)
- Soham Ray
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Pankaj K. Singh
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Deepak K. Gupta
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Ajay K. Mahato
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Chiranjib Sarkar
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Rajeev Rathour
- Chaudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - Nagendra K. Singh
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology, Pusa CampusNew Delhi, India
- *Correspondence: Tilak R. Sharma,
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2
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Bryant MK, Schardl CL, Hesse U, Scott B. Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloë festucae. BMC Evol Biol 2009; 9:168. [PMID: 19615101 PMCID: PMC2717940 DOI: 10.1186/1471-2148-9-168] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 07/19/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Subtilisin-like proteases (SLPs) form a superfamily of enzymes that act to degrade protein substrates. In fungi, SLPs can play either a general nutritive role, or may play specific roles in cell metabolism, or as pathogenicity or virulence factors. RESULTS Fifteen different genes encoding SLPs were identified in the genome of the grass endophytic fungus Epichloë festucae. Phylogenetic analysis indicated that these SLPs belong to four different subtilisin families: proteinase K, kexin, pyrolysin and subtilisin. The pattern of intron loss and gain is consistent with this phylogeny. E. festucae is exceptional in that it contains two kexin-like genes. Phylogenetic analysis in Hypocreales fungi revealed an extensive history of gene loss and duplication. CONCLUSION This study provides new insights into the evolution of the SLP superfamily in filamentous fungi.
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Affiliation(s)
- Michelle K Bryant
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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3
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Novel bacterial artificial chromosome vector pUvBBAC for use in studies of the functional genomics of Listeria spp. Appl Environ Microbiol 2008; 74:1892-901. [PMID: 18223114 DOI: 10.1128/aem.00415-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial artificial chromosome (BAC) vectors are important tools for microbial genome research. We constructed a novel BAC vector, pUvBBAC, for replication in both gram-negative and gram-positive bacterial hosts. The pUvBBAC vector was used to generate a BAC library for the facultative intracellular pathogen Listeria monocytogenes EGD-e. The library had insert sizes ranging from 68 to 178 kb. We identified two recombinant BACs from the L. monocytogenes pUvBBAC library that each contained the entire virulence gene cluster (vgc) of L. monocytogenes and transferred them to a nonpathogenic Listeria innocua strain. Recombinant L. innocua strains harboring pUvBBAC+vgc1 and pUvBBAC+vgc2 produced the vgc-specific listeriolysin (LLO) and actin assembly protein ActA and represent the first reported cloning of the vgc locus in its entirety. The use of the novel broad-host-range BAC vector pUvBBAC extends the versatility of this technology and provides a powerful platform for detailed functional genomics of gram-positive bacteria as well as its use in explorative functional metagenomics.
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Eaton CJ, Jourdain I, Foster SJ, Hyams JS, Scott B. Functional analysis of a fungal endophyte stress-activated MAP kinase. Curr Genet 2008; 53:163-74. [PMID: 18188569 DOI: 10.1007/s00294-007-0174-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 11/25/2022]
Abstract
The ability of fungi to sense and respond rapidly to environmental stress is crucial for their survival in the wild. One of the most important pathways involved in this response is the stress-activated MAP (mitogen-activated protein) kinase pathway. We report here on the isolation of the stress-activated MAP kinase, sakA, from the fungal endophyte Epichloë festucae. Complementation of the stress sensitivity and cell cycle defects of an Schizosaccharomyces pombe sty1Delta mutant with sakA confirmed it encodes a functional MAP kinase. Analysis of an E. festucae DeltasakA mutant revealed sakA is essential for growth under conditions of temperature and osmotic stress in culture, and for sensitivity to the fungicide fludioxonil. However, the DeltasakA mutant shows no increased sensitivity to hydrogen peroxide. Given sakA can rescue the sty1Delta mutant from sensitivity to oxidative stress, SakA has the potential to sense and transduce oxidative stress signals. The DeltasakA mutant is also defective in conidia formation, suggesting a role for SakA in asexual development of E. festucae. The detection of elevated hydrogen peroxide production in the DeltasakA mutant suggests there may be a link between MAP kinase and ROS (reactive oxygen species) signalling pathways in E. festucae.
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Affiliation(s)
- Carla J Eaton
- Institute of Molecular BioSciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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5
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Borenstein E, Shlomi T, Ruppin E, Sharan R. Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes. Nucleic Acids Res 2006; 35:e7. [PMID: 17158152 PMCID: PMC1802574 DOI: 10.1093/nar/gkl792] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The rate of conservation of a gene in evolution is believed to be correlated with its biological importance. Recent studies have devised various conservation measures for genes and have shown that they are correlated with several biological characteristics of functional importance. Specifically, the state-of-the-art propensity for gene loss (PGL) measure was shown to be strongly correlated with gene essentiality and its number of protein-protein interactions (PPIs). The observed correlation between conservation and functional importance varies however between conservation measures, underscoring the need for accurate and general measures for the rate of gene conservation. Here we develop a novel maximum-likelihood approach to computing the rate in which a gene is lost in evolution, motivated by the same principles as those underlying PGL. However, in difference to PGL which considers only the most parsimonious ancestral states of the internal nodes of the phylogenetic tree relating the species, our approach weighs in a probabilistic manner all possible ancestral states, and includes the branch length information as part of the probabilistic model. In application to data of 16 eukaryotic genomes, our approach shows higher correlations with experimental data than PGL, including data on gene lethality, level of connectivity in a PPI network and coherence within functionally related genes.
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Affiliation(s)
- Elhanan Borenstein
- School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
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6
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Jiang RHY, Tyler BM, Govers F. Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:1311-21. [PMID: 17153915 DOI: 10.1094/mpmi-19-1311] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Comparative analysis of two Phytophthora genomes revealed overall colinearity in four genomic regions consisting of a 1.5-Mb sequence of Phytophthora sojae and a 0.9-Mb sequence of P. ramorum. In these regions with conserved synteny, the gene order is largely similar; however, genome rearrangements also have occurred. Deletions and duplications often were found in association with genes encoding secreted proteins, including effectors that are important for interaction with host plants. Among secreted protein genes, different evolutionary patterns were found. Elicitin genes that code for a complex family of highly conserved Phytophthora-specific elicitors show conservation in gene number and order, and often are clustered. In contrast, the race-specific elicitor gene Avrlb-1 appeared to be missing from the region with conserved synteny, as were its five homologs that are scattered over the four genomic regions. Some gene families encoding secreted proteins were found to be expanded in one species compared with the other. This could be the result of either repeated gene duplications in one species or specific deletions in the other. These different evolutionary patterns may shed light on the functions of these secreted proteins in the biology and pathology of the two Phytophthora spp.
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Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, Binnenhaven 5, NL-6709 PD Wageningen, The Netherlands
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7
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Thon MR, Pan H, Diener S, Papalas J, Taro A, Mitchell TK, Dean RA. The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol 2006; 7:R16. [PMID: 16507177 PMCID: PMC1431731 DOI: 10.1186/gb-2006-7-2-r16] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 01/16/2006] [Accepted: 01/31/2006] [Indexed: 11/16/2022] Open
Abstract
Analysis of the Magnaporthe oryzae chromosome 7 and comparison with syntenic regions in other fungal genomes suggests that transposable elements create localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution. Background Transposable elements are abundant in the genomes of many filamentous fungi, and have been implicated as major contributors to genome rearrangements and as sources of genetic variation. Analyses of fungal genomes have also revealed that transposable elements are largely confined to distinct clusters within the genome. Their impact on fungal genome evolution is not well understood. Using the recently available genome sequence of the plant pathogenic fungus Magnaporthe oryzae, combined with additional bacterial artificial chromosome clone sequences, we performed a detailed analysis of the distribution of transposable elements, syntenic blocks, and other features of chromosome 7. Results We found significant levels of conserved synteny between chromosome 7 and the genomes of other filamentous fungi, despite more than 200 million years of divergent evolution. Transposable elements are largely restricted to three clusters located in chromosomal segments that lack conserved synteny. In contradiction to popular evolutionary models and observations from other model organism genomes, we found a positive correlation between recombination rate and the distribution of transposable element clusters on chromosome 7. In addition, the transposable element clusters are marked by more frequent gene duplications, and genes within the clusters have greater sequence diversity to orthologous genes from other fungi. Conclusion Together, these data suggest that transposable elements have a profound impact on the M. oryzae genome by creating localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution.
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Affiliation(s)
- Michael R Thon
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Huaqin Pan
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
| | - Stephen Diener
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
| | - John Papalas
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
| | - Audrey Taro
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
| | - Thomas K Mitchell
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
| | - Ralph A Dean
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
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8
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Shiu SH, Shih MC, Li WH. Transcription factor families have much higher expansion rates in plants than in animals. PLANT PHYSIOLOGY 2005; 139:18-26. [PMID: 16166257 PMCID: PMC1203354 DOI: 10.1104/pp.105.065110] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcription factors (TFs), which are central to the regulation of gene expression, are usually members of multigene families. In plants, they are involved in diverse processes such as developmental control and elicitation of defense and stress responses. To investigate if differences exist in the expansion patterns of TF gene families between plants and other eukaryotes, we first used Arabidopsis (Arabidopsis thaliana) TFs to identify TF DNA-binding domains. These DNA-binding domains were then used to identify related sequences in 25 other eukaryotic genomes. Interestingly, among 19 families that are shared between animals and plants, more than 14 are larger in plants than in animals. After examining the lineage-specific expansion of TF families in two plants, eight animals, and two fungi, we found that TF families shared among these organisms have undergone much more dramatic expansion in plants than in other eukaryotes. Moreover, this elevated expansion rate of plant TF is not simply due to higher duplication rates of plant genomes but also to a higher degree of expansion compared to other plant genes. Further, in many Arabidopsis-rice (Oryza sativa) TF orthologous groups, the degree of lineage-specific expansion in Arabidopsis is correlated with that in rice. This pattern of parallel expansion is much more pronounced than the whole-genome trend in rice and Arabidopsis. The high rate of expansion among plant TF genes and their propensity for parallel expansion suggest frequent adaptive responses to selection pressure common among higher plants.
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Affiliation(s)
- Shin-Han Shiu
- Department of Ecology and Evolution, University of Chicago, Illinois 60637, USA
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9
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Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M, Fosker N, Fraser A, Harris D, Larke N, Murphy L, Humphray S, O'Neil S, Pertea M, Price C, Rabbinowitsch E, Rajandream MA, Salzberg S, Saunders D, Seeger K, Sharp S, Warren T, Denning DW, Barrell B, Hall N. Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genet Biol 2004; 41:443-53. [PMID: 14998527 DOI: 10.1016/j.fgb.2003.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Accepted: 12/05/2003] [Indexed: 11/25/2022]
Abstract
Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be approximately 30 Mb in size, we have sequenced a 922 kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922 kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.
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Affiliation(s)
- Arnab Pain
- The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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10
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Nowrousian M, Würtz C, Pöggeler S, Kück U. Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation. Fungal Genet Biol 2004; 41:285-92. [PMID: 14761789 DOI: 10.1016/j.fgb.2003.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 10/22/2003] [Indexed: 11/16/2022]
Abstract
One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.
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Affiliation(s)
- Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany
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11
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Kutil BL, Liu G, Vrebalov J, Wilkinson HH. Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloë festucae, a mutualistic fungal endophyte of grasses. Fungal Genet Biol 2004; 41:23-32. [PMID: 14643256 DOI: 10.1016/j.fgb.2003.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We constructed and characterized a bacterial artificial chromosome (BAC) library for Epichloë festucae, a genetically tractable fungal plant mutualist. The 6144 clone library with an average insert size of 87kb represents at least 18-fold coverage of the 29 Mb genome. We used the library to assemble a 110kb contig spanning the putative ornithine decarboxylase (odc) ortholog and subsequently expanded it to 228kb with a single walking step in each direction. Furthermore, we evaluated conservation of microsynteny between E. festucae and some model filamentous fungi by comparing sequence available from a 43kb region at the end of one BAC to publicly available fungal genome sequences. Orthologs to the 13 contiguous open reading frames (ORFs) identified in E. festucae are syntenic in Neurospora crassa and Magnaporthe grisea occurring in small sets of two, three or four colinear ORFs. This library is a valuable resource for research into traits important for the development and maintenance of a plant-fungus mutualistic symbiosis.
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Affiliation(s)
- Brandi L Kutil
- Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX 77845-2132, USA
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12
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Abstract
The blast fungus Magnaporthe grisea causes a serious disease on a wide variety of grasses including rice, wheat, and barley. Rice blast is the most serious disease of cultivated rice and therefore poses a threat to the world's most important food security crop. Here, I review recent progress toward understanding the molecular biology of plant infection by M. grisea, which involves development of a specialized cell, the appressorium. This dome-shaped cell generates enormous turgor pressure and physical force, allowing the fungus to breach the host cuticle and invade plant tissue. The review also considers the role of avirulence genes in M. grisea and the mechanisms by which resistant rice cultivars are able to perceive the fungus and defend themselves. Finally, the likely mechanisms that promote genetic diversity in M. grisea and our current understanding of the population structure of the blast fungus are evaluated.
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Affiliation(s)
- Nicholas J Talbot
- School of Biological Sciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter EX4 4QG, United Kingdom.
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13
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Dawe AL, McMains VC, Panglao M, Kasahara S, Chen B, Nuss DL. An ordered collection of expressed sequences from Cryphonectria parasitica and evidence of genomic microsynteny with Neurospora crassa and Magnaporthe grisea. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2373-2384. [PMID: 12949163 DOI: 10.1099/mic.0.26371-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cryphonectria parasitica, the causative agent of chestnut blight, has proven to be a tractable experimental system for studying fungal pathogenesis. Moreover, the development of infectious cDNA clones of C. parasitica hypoviruses, capable of attenuating fungal virulence, has provided the opportunity to examine molecular aspects of fungal plant pathogenesis in the context of biological control. In order to establish a genomic base for future studies of C. parasitica, the authors have analysed a collection of expressed sequences. A mixed cDNA library was prepared from RNA isolated from wild-type (virus-free) and hypovirus-infected C. parasitica strains. Plasmid DNA was recovered from individual transformants and sequenced from the 5' end of the insert. Contig analysis of the collected sequences revealed that they represented approximately 2200 individual ORFs. An assessment of functional diversity present in this collection was achieved by using the BLAST software utilities and the NCBI protein database. Candidate genes were identified with significant potential relevance to C. parasitica growth, development, pathogenesis and vegetative incompatibility. Additional investigations of a 12.9 kbp genomic region revealed microsynteny between C. parasitica and both Neurospora crassa and Magnaporthe grisea, two closely related fungi. These data represent the largest collection of sequence information currently available for C. parasitica and are now forming the basis of further studies using microarray analyses to determine global changes in transcription that occur in response to hypovirus infection.
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Affiliation(s)
- Angus L Dawe
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
| | - Vanessa C McMains
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
| | - Maria Panglao
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
| | - Shin Kasahara
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
| | - Baoshan Chen
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
| | - Donald L Nuss
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, MD 20742, USA
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14
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Silar P, Barreau C, Debuchy R, Kicka S, Turcq B, Sainsard-Chanet A, Sellem CH, Billault A, Cattolico L, Duprat S, Weissenbach J. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing. Fungal Genet Biol 2003; 39:250-63. [PMID: 12892638 DOI: 10.1016/s1087-1845(03)00025-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.
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MESH Headings
- Amino Acid Sequence
- Centromere/chemistry
- Centromere/genetics
- Chromosomes, Artificial, Bacterial
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- DNA, Intergenic/analysis
- Gene Rearrangement
- Genes, Fungal
- Genes, rRNA
- Genome, Fungal
- Genomic Library
- Introns
- Molecular Sequence Data
- Physical Chromosome Mapping
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Sordariales/genetics
- Synteny
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Affiliation(s)
- Philippe Silar
- Institut de Génétique et Microbiologie, UMR CNRS 8621, Bât. 400, Université de Paris Sud, 91405 Orsay Cedex, France.
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15
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K Mitchell T, Thon MR, Jeong JS, Brown D, Deng J, Dean RA. The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens. THE NEW PHYTOLOGIST 2003; 159:53-61. [PMID: 33873673 DOI: 10.1046/j.1469-8137.2003.00787.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fungi have an astounding and diverse impact on this planet. While they are agents of human diseases and the cause of allergic reactions, factories for the conversion of carbon in environmental and industrially adapted systems, and potential biological weapons, their importance as plant pathogens is unparalleled. In plants alone, fungi cause tens of thousands of different diseases and are responsible for massive losses of food, fiber and forestry at an estimated annual cost of hundreds of billions of dollars. These losses are not only realized in the incomes of individual farmers and state economies, but contribute significantly to world hunger problems and issues relating to safeguarding a global food supply. Our collective understanding of how fungi, particularly plant pathogens, grow, reproduce, identify a host and cause disease is still at a formative stage. There is an equal lack of detailed knowledge about how a plant recognizes that it is being attacked and then mounts an adequate defense response. The advent of genomic technologies has given researchers an unprecedented opportunity to address these mysteries in a powerful and more holistic manner. Where the genetic revolution of only a few years ago allowed for the characterization of single genes, today's genomic technologies are facilitating the evaluation of the entire complement of genes in an organism and the discovery of the suites of genes that act during any one time or particular condition. This review will describe the recent development of tools for whole or partial genome analysis and multigenome comparisons. Th discussion focuses on the rice blast pathosystem as a case study.
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Affiliation(s)
- Thomas K Mitchell
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
| | - Michael R Thon
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
| | - Jun-Seop Jeong
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
| | - Doug Brown
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
| | - Jixin Deng
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
| | - Ralph A Dean
- North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Box 7251, Raleigh, NC 27695, USA
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Keon J, Curtis R, Cabrera H, Hargreaves J. A genomics approach to crop pest and disease research. PEST MANAGEMENT SCIENCE 2003; 59:143-148. [PMID: 12587867 DOI: 10.1002/ps.571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genome-wide analyses of gene function and gene expression are beginning to yield valuable information in many areas of biological research, and these genomic tools are now being applied to crop pest and disease research. DNA sequencing of cDNA libraries to generate sets of expressed sequence tags (ESTs) are allowing gene compendiums for crop diseases to be compiled. Annotation of such data collections is also providing a wealth of functional information about gene products through similarities to proteins with known function. The next phase of the functional genomics era will be to employ large-scale techniques to knock out or silence genes in order to synthesize gene-specific mutants for phenotypic analysis and to use micro-array methodology to analyze global gene expression, protein turnover and protein processing during the processes of parasitism and colonization. Application of these technologies promises to accelerate the pace that biological information relevant to crop protection accrues. The ability of researchers to assimilate this information into complex models and workable hypotheses is, thus, set to revolutionize the way we study pests and diseases of crop plants.
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Affiliation(s)
- John Keon
- IACR-Long Ashton, University of Bristol, Long Ashton, Bristol BS41 9AF, UK
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Kimura M, Tokai T, Matsumoto G, Fujimura M, Hamamoto H, Yoneyama K, Shibata T, Yamaguchi I. Trichothecene nonproducer Gibberella species have both functional and nonfunctional 3-O-acetyltransferase genes. Genetics 2003; 163:677-84. [PMID: 12618405 PMCID: PMC1462466 DOI: 10.1093/genetics/163.2.677] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The trichothecene 3-O-acetyltransferase gene (FgTri101) required for trichothecene production by Fusarium graminearum is located between the phosphate permease gene (pho5) and the UTP-ammonia ligase gene (ura7). We have cloned and sequenced the pho5-to-ura7 regions from three trichothecene nonproducing Fusarium (i.e., F. oxysporum, F. moniliforme, and Fusarium species IFO 7772) that belong to the teleomorph genus Gibberella. BLASTX analysis of these sequences revealed portions of predicted polypeptides with high similarities to the TRI101 polypeptide. While FspTri101 (Fusarium species Tri101) coded for a functional 3-O-acetyltransferase, FoTri101 (F. oxysporum Tri101) and FmTri101 (F. moniliforme Tri101) were pseudogenes. Nevertheless, F. oxysporum and F. moniliforme were able to acetylate C-3 of trichothecenes, indicating that these nonproducers possess another as yet unidentified 3-O-acetyltransferase gene. By means of cDNA expression cloning using fission yeast, we isolated the responsible FoTri201 gene from F. oxysporum; on the basis of this sequence, FmTri201 has been cloned from F. moniliforme by PCR techniques. Both Tri201 showed only a limited level of nucleotide sequence similarity to FgTri101 and FspTri101. The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species.
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Affiliation(s)
- Makoto Kimura
- Laboratory for Remediation Research, Plant Science Center, RIKEN, Wako, Saitama 351-0198, Japan.
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Seiboth B, Karaffa L, Sándor E, Kubicek C. The Hypocrea jecorina gal10 (uridine 5'-diphosphate-glucose 4-epimerase-encoding) gene differs from yeast homologues in structure, genomic organization and expression. Gene 2003; 295:143-9. [PMID: 12242021 DOI: 10.1016/s0378-1119(02)00834-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As part of a comprehensive study on lactose metabolism in Hypocrea jecorina (anamorph: Trichoderma reesei), a genomic clone of the gal10 gene encoding H. jecorina uridine 5'-diphosphate (UDP)-glucose 4-epimerase has been cloned and sequenced. It contains an open reading frame of 1548-base pair, interrupted by three introns, and encoding a 370-amino acids protein with similarity to pro- and eukaryotic UDP-glucose-4-epimerases. H. jecorina Gal10 does not contain the C-terminal mutarotase domain which is present in yeast Gal10 proteins but is able to functionally complement a corresponding Saccharomyces cerevisiae gal10 mutant. gal10 is not clustered with other H. jecorina gal genes (gal7, gene encoding galactose-1-phosphate uridylyltransferase and gal1, gene encoding galactokinase). The genomic location of H. jecorina gal10 and gal7 was syntenic with that in Neurospora crassa and colinear over an area of 6 and 3.5-kilobase. gal10 is constitutively expressed, and--unlike H. jecorina gal7--not further stimulated by D-galactose or L-arabinose or its corresponding polyols.
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Affiliation(s)
- Bernhard Seiboth
- Mikrobielle Biochemie und Gentechnik, Institut für Verfahrenstechnik, Umwelttechnik und Technische Biowissenschaften, TU Wien, Getreidemarkt 9, A-1060 Vienna, Austria.
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Abstract
Summary The rice blast fungus Magnaporthe grisea causes one of the most destructive diseases of rice. Genetic studies of this important pathogen during the past decade have made it an excellent system for investigating fungal-plant interactions. Recently, the well coordinated efforts by the rice blast community have also made significant progresses in genomics studies of M. grisea. BAC contigs were assembled and integrated with the high density genetic map, and 12 674 BAC-ends were sequenced as genome survey sequences. Over ten BAC clones have been sequenced by the shot-gun approach. Preliminary analysis with one completely sequenced BAC clone indicated that M. grisea may have a gene density of 4.2 kb/gene and contain approximately 9000 genes. In addition, > 10 000 ESTs have been sequenced from several cDNA libraries representing different stages of fungal growth, differentiation and plant infection. Currently, there are ongoing projects to sequence additional ESTs, telomeres, and 6X coverage of the M. grisea genome. A large-scale functional genomics project on M. grisea and its interaction with rice is also underway. It is an exciting time for genomics studies in M. grisea, and the resources generated in these studies will certainly enhance our understanding of fungal pathogenicity.
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Affiliation(s)
- Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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Soanes DM, Skinner W, Keon J, Hargreaves J, Talbot NJ. Genomics of phytopathogenic fungi and the development of bioinformatic resources. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:421-427. [PMID: 12036272 DOI: 10.1094/mpmi.2002.15.5.421] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Genomic resources available to researchers studying phytopathogenic fungi are limited. Here, we briefly review the genomic and bioinformatic resources available and the current status of fungal genomics. We also describe a relational database containing sequences of expressed sequence tags (ESTs) from three phytopathogenic fungi, Blumeria graminis, Magnaporthe grisea, and Mycosphaerella graminicola, and the methods and underlying principles required for its construction. The database contains significant annotation for each EST sequence and is accessible at http://cogeme.ex.ac.uk. An easy-to-use interface allows the user to identify gene sequences by using simple text queries or homology searches. New querying functions and large sequence sets from a variety of phytopathogenic species will be incorporated in due course.
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Affiliation(s)
- Darren M Soanes
- School of Biological Sciences, University of Exeter, Washington Singer Laboratories, UK
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Lo SCC, Hamer L, Hamer JE. Molecular characterization of a cystathionine beta-synthase gene, CBS1, in Magnaporthe grisea. EUKARYOTIC CELL 2002; 1:311-4. [PMID: 12455965 PMCID: PMC118034 DOI: 10.1128/ec.1.2.311-314.2002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
CBS1 from Magnaporthe grisea is a structural and functional homolog of the cystathionine beta-synthase (CBS) gene from Saccharomyces cerevisiae. Our studies indicated that M. grisea can utilize homocysteine and methionine through a CBS-independent pathway. The results also revealed responses of M. grisea to homocysteine that are reminiscent of human homocystinuria.
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Affiliation(s)
- Sze Chung Clive Lo
- Microbial Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709, USA.
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Pedersen C, Rasmussen SW, Giese H. A genetic map of Blumeria graminis based on functional genes, avirulence genes, and molecular markers. Fungal Genet Biol 2002; 35:235-46. [PMID: 11929213 DOI: 10.1006/fgbi.2001.1326] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A genetic map of the powdery mildew fungus, Blumeria graminis f. sp. hordei, an obligate biotrophic pathogen of barley, is presented. The linkage analysis was conducted on 81 segregating haploid progeny isolates from a cross between 2 isolates differing in seven avirulence genes. A total of 359 loci were mapped, comprising 182 amplified fragment length polymorphism markers, 168 restriction fragment length polymorphism markers including 42 LTR-retrotransposon loci and 99 expressed sequence tags (ESTs), all the seven avirulence genes, and a marker closely linked to the mating type gene. The markers are distributed over 34 linkage groups covering a total of 2114 cM. Five avirulence genes were found to be linked and mapped in clusters of three and two, and two were unlinked. The Avr(a6) gene was found to be closely linked to markers suitable for a map-based cloning approach. A linkage between ESTs allowed us to demonstrate examples of synteny between genes in B. graminis and Neurospora crassa.
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Affiliation(s)
- Carsten Pedersen
- Plant Research Department, Risø National Laboratory, Roskilde, DK-4000, Denmark.
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Guiliano DB, Hall N, Jones SJM, Clark LN, Corton CH, Barrell BG, Blaxter ML. Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol 2002; 3:RESEARCH0057. [PMID: 12372145 PMCID: PMC134624 DOI: 10.1186/gb-2002-3-10-research0057] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2002] [Revised: 07/19/2002] [Accepted: 08/22/2002] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi. RESULTS An 83 kb region flanking the gene for Bm-mif-1 (macrophage migration inhibitory factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. CONCLUSIONS We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements of neighboring genes.
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Affiliation(s)
- DB Guiliano
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - N Hall
- Pathogen Sequencing Unit, The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - SJM Jones
- Genome Sequence Centre, British Columbia Cancer Research Centre, Vancouver V5Z 4E6, Canada
| | - LN Clark
- Pathogen Sequencing Unit, The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - CH Corton
- Pathogen Sequencing Unit, The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - BG Barrell
- Pathogen Sequencing Unit, The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - ML Blaxter
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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