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Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

Published on Dec 1, 2018in Scientific Reports 4.01
· DOI :10.1038/s41598-018-24301-6
Ning Zhang24
Estimated H-index: 24
(RU: Rutgers University),
Guohong Cai13
Estimated H-index: 13
(USDA: United States Department of Agriculture)
+ 12 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
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Abstract
The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.
  • References (75)
  • Citations (2)
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References75
Newest
Published on Aug 1, 2017in Molecular Plant Pathology 4.38
William Sharpee2
Estimated H-index: 2
,
Yeonyee Oh8
Estimated H-index: 8
+ 5 AuthorsRalph A. Dean44
Estimated H-index: 44
Phytopathogenic microorganisms including the fungal pathogen Magnaporthe oryzae secrete a myriad of effector proteins to facilitate infection. Utilizing transient expression of candidate effectors in the leaves of the model plant N. benthamiana, we identified 11 suppressors of plant cell death (SPD) effectors from M. oryzae that are able to block the host cell death reaction induced by the Nep1 gene. Ten of these 11 are also able to suppress BAX mediated plant cell death. Five of the eleven SPD ...
7 Citations Source Cite
Published on Dec 1, 2016in BMC Biology 6.72
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University),
Guohong Cai13
Estimated H-index: 13
(USDA: United States Department of Agriculture)
+ 2 AuthorsNing Zhang24
Estimated H-index: 24
(RU: Rutgers University)
Background Horizontal gene transfer (HGT) plays an important role in the adaptation of lineages to changing environments. The extent of this process in eukaryotes, however, remains controversial. The most well-known and dramatic form of HGT represents intracellular gene transfer from endosymbionts to the host nuclear genome. Such episodes of transfer typically involve hundreds of genes and are thought to be possible only in the case of endosymbiosis.
16 Citations Source Cite
Published on Aug 1, 2016in Molecular Biology and Evolution 14.80
Jennifer H. Wisecaver15
Estimated H-index: 15
(Vandy: Vanderbilt University),
William G. Alexander8
Estimated H-index: 8
(Great Lakes Bioenergy Research Center)
+ 2 AuthorsAntonis Rokas53
Estimated H-index: 53
(Vandy: Vanderbilt University)
Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in b...
12 Citations Source Cite
Published on May 1, 2016in Molecular Ecology 5.86
Adrien Rieux12
Estimated H-index: 12
(UCL: University College London),
Francois Balloux54
Estimated H-index: 54
(UCL: University College London)
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution. All molecular-dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast-evolving genomes such as viruses an...
32 Citations Source Cite
William G. Alexander8
Estimated H-index: 8
(Great Lakes Bioenergy Research Center),
Jennifer H. Wisecaver15
Estimated H-index: 15
(Vandy: Vanderbilt University)
+ 1 AuthorsChris Todd Hittinger25
Estimated H-index: 25
(Great Lakes Bioenergy Research Center)
Horizontal gene transfer (HGT) among bacteria, archaea, and viruses is widespread, but the extent of transfers from these lineages into eukaryotic organisms is contentious. Here we systematically identify hundreds of genes that were likely acquired horizontally from a variety of sources by the early-diverging fungal phyla Microsporidia and Cryptomycota. Interestingly, the Microsporidia have acquired via HGT several genes involved in nucleic acid synthesis and salvage, such as those encoding thym...
20 Citations Source Cite
Published on Feb 19, 2016in Frontiers in Plant Science 4.11
Ki-Tae Kim5
Estimated H-index: 5
(SNU: Seoul National University),
Jongbum Jeon7
Estimated H-index: 7
(SNU: Seoul National University)
+ 5 AuthorsYong-Hwan Lee49
Estimated H-index: 49
Fungal secretome consists of various functional groups of proteins, many of which participate in nutrient acquisition, self-protection, or manipulation of the environment and neighboring organisms. The least characterized component of the secretome is small secreted proteins (SSPs). Some SSPs have been reported to function as effectors, but most remain to be characterized. The composition of major secretome components, such as carbohydrate-active enzymes, proteases, lipases, and oxidoreductases,...
42 Citations Source Cite
Published on Dec 1, 2015in G3: Genes, Genomes, Genetics 2.63
Laura H. Okagaki9
Estimated H-index: 9
(NCSU: North Carolina State University),
Cristiano C. Nunes6
Estimated H-index: 6
(NCSU: North Carolina State University)
+ 19 AuthorsBrian J. Haas62
Estimated H-index: 62
(Broad Institute)
Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae. These three fungi cause widespread disease and loss in cereal and grass crops, including rice blast disease (M. oryzae), take-all disease in wheat and other grasses (G. graminis), and summer patch disease in turf grasses (M. poae). Here, we present the finished genome sequence for M. oryzae and draft sequences for M. po...
13 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 14.03
David Emms9
Estimated H-index: 9
(University of Oxford),
Steven L. Kelly55
Estimated H-index: 55
(University of Oxford)
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by pro...
449 Citations Source Cite
Published on Aug 1, 2015in Scientific Reports 4.01
Jing Luo18
Estimated H-index: 18
,
Huan Qiu18
Estimated H-index: 18
+ 3 AuthorsNing Zhang5
Estimated H-index: 5
The order Magnaporthales (Ascomycota, Fungi) includes devastating pathogens of cereals, such as the rice blast fungus Pyricularia (Magnaporthe) oryzae, which is a model in host-pathogen interaction studies. Magnaporthales also includes saprotrophic species associated with grass roots and submerged wood. Despite its scientific and economic importance, the phylogenetic position of Magnaporthales within Sordariomycetes and the interrelationships of its constituent taxa, remain controversial. In thi...
23 Citations Source Cite
Published on May 1, 2015in Scientific Reports 4.01
Xi-Hui Xu3
Estimated H-index: 3
,
Zhen-Zhu Su5
Estimated H-index: 5
+ 7 AuthorsChulong Zhang14
Estimated H-index: 14
The fungus Harpophora oryzae is a close relative of the pathogen Magnaporthe oryzae and a beneficial endosymbiont of wild rice. Here, we show that H. oryzae evolved from a pathogenic ancestor. The overall genomic structures of H. and M. oryzae were found to be similar. However, during interactions with rice, the expression of 11.7% of all genes showed opposing trends in the two fungi, suggesting differences in gene regulation. Moreover, infection patterns, triggering of host defense responses, s...
31 Citations Source Cite
Cited By2
Newest
Published on Jun 1, 2019in Molecular Biology and Evolution 14.80
Luis B Gómez Luciano (AS: Academia Sinica), Isheng Jason Tsai (AS: Academia Sinica)+ 7 AuthorsWen-Hsiung Li94
Estimated H-index: 94
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Published on May 1, 2019in Journal of General Plant Pathology 0.89
Kenichi Ikeda15
Estimated H-index: 15
(Kobe University),
Pyoyun Park21
Estimated H-index: 21
(Kobe University),
Hitoshi Nakayashiki26
Estimated H-index: 26
(Kobe University)
During infection of the host plant, various biological processes facilitate host invasion, including the physical invasion of the host, and subsequent adaptation to the host’s internal environment. During these processes, cellular biological changes result in host adhesion, morphogenetic differentiation via the sensing of plant-derived signals, and maturation of infection structures via reorientation of the cytoskeleton. Changes in lipid and sugar metabolism in fungi generate energy for survival...
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