Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum grass

Zheng, Huakun; Zhong, Zhenhui; Shi, Mingyue; Zhang, Limei; Lin, Lian‐Yu; Hong, Yonghe; Tian, Fang; Zhu, Yangyan; Guo, Jiayuan; Zhang, Limin; Fang, Jie; Lin, Hui; Norvienyeku, Justice; Chen, Xiaofeng; Lu, Guodong; Hu, Hong; Wang, Zonghua

doi:10.1186/s12864-018-5222-8

Cited by 18 publications

(13 citation statements)

References 73 publications

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“…[157] and Neurospora crassa [158] were among the identified Sordariomycetes and they convert cellulose into ethanol. Magnaporthales such as Pyricularia penniseti convert isoamylalcohol into isovaleraldehyde while other Magnaporthales' species convert fumaryl-acetoacetate into fumarate and acetoacetate [159,160]. Other roles played by the Sordariomycetes' species include the metabolism of aromatic compounds through which, phenolics and aryl alcohols/aldehydes are converted into acetate, formate and ethanol [161,162].…”

Section: The Identified Fungal Biomesmentioning

confidence: 99%

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

et al. 2021

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The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities’ abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its’ productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.

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Section: The Identified Fungal Biomesmentioning

confidence: 99%

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

et al. 2021

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“…The filamentous fungus M. oryzae is the causal pathogen of rice blast disease, which leads to substantial losses in rice production annually (15,30). Our previous studies suggested that the host plant is the major force that shapes the M. oryzae genome (20,21,31). However, no real-time assays have been performed so far to investigate the occurrence and accumulation of mutations in M. oryzae populations in interaction with rice plants.…”

Section: Discussionmentioning

confidence: 99%

Genetic Variation Bias toward Noncoding Regions and Secreted Proteins in the Rice Blast Fungus Magnaporthe oryzae

et al. 2020

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The genomes of plant pathogens are highly variable and plastic. Pathogen gene repertoires change quickly with the plant environment, which results in a rapid loss of plant resistance shortly after the pathogen emerges in the field. Extensive studies have evaluated natural pathogen populations to understand their evolutionary effects; however, the number of studies that have examined the dynamic processes of the mutation and adaptation of plant pathogens to host plants remains limited. Here, we applied experimental evolution and high-throughput pool sequencing to Magnaporthe oryzae, a fungal pathogen that causes massive losses in rice production, to observe the evolution of genome variation. We found that mutations, including single-nucleotide variants (SNVs), insertions and deletions (indels), and transposable element (TE) insertions, accumulated very rapidly throughout the genome of M. oryzae during sequential plant inoculation and preferentially in noncoding regions, while such mutations were not frequently found in coding regions. However, we also observed that new TE insertions accumulated with time and preferentially accumulated at the proximal region of secreted protein (SP) coding genes in M. oryzae populations. Taken together, these results revealed a bias in genetic variation toward noncoding regions and SP genes in M. oryzae and may contribute to the rapid adaptive evolution of the blast fungal effectors under host selection. IMPORTANCE Plants “lose” resistance toward pathogens shortly after their widespread emergence in the field because plant pathogens mutate and adapt rapidly under resistance selection. Thus, the rapid evolution of pathogens is a serious threat to plant health. Extensive studies have evaluated natural pathogen populations to understand their evolutionary effects; however, the study of the dynamic processes of the mutation and adaptation of plant pathogens to host plants remains limited. Here, by performing an experimental evolution study, we found a bias in genetic variation toward noncoding regions and SPs in the rice blast fungus Magnaporthe oryzae, which explains the ability of the rice blast fungus to maintain high virulence variation to overcome rice resistance in the field.

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“…Many events have been driving the gain or loss of related-virulence and avirulence genes involved in pathogenicity. For example, mixed infections in shared hosts favors gene flow through sexual recombination or non-meiotic parasexual processes, (Talbot et al 1993a, b;Soanes et al 2002;Inoue et al 2017;Monsur and Kusaba 2018;Zheng et al 2018;Gómez Luciano et al 2019;Asuke et al 2019), mutations in avirulence genes through selecting frequently occurs (Orbach et al 2000), or through the moving of a Pot3 transposon across pathogenicity related-genes (Kang et al 2001). Pathogenic effector proteins have been under evolutive selection across blast populations (Sweigard et al 1995;Farman and Leong 1998;Jones and Dangl 2006;Avila-Adame 2014;Tosa et al 2016;Wang and Valent 2017;Inoue et al 2017Inoue et al , 2021Gladieux et al 2018;Langner et al 2018;Gómez Luciano et al 2019), which might explain the ability to infect a new host or the variable levels of aggressiveness across different hosts (Kato et al 2000;Tosa et al 2004;Castroagudín et al 2016;Perelló et al 2017;Urashima et al 2017;Reges et al 2018Reges et al , 2019Qi et al 2021).…”

Section: Taxonomy and Genetic Diversitymentioning

confidence: 99%

Taxonomic and pathogenic diversity of the blast pathogen populations infecting wheat and grasses in Minas Gerais

Ascari¹,

Ponte²

2021

Preprint

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The blast disease of Poaceae is caused by a large species complex, among which P. oryzae is composed of several host-specialized lineages. The Pyricularia oryzae Triticum pathotype (PoT) causes the blast disease in wheat, but is also capable of infecting other grasses, which may serve as an inoculum reservoir for epidemics in wheat. In Brazil, severe wheat blast epidemics are most common in the Cerrado region. The dominant hypothesis is that signal grass (Urochloa sp.) and other gramineous plants harbor the wheat blast pathogen, thus serving as a major reservoir of inoculum for epidemics in wheat. A two-year survey of the Pyricularia blast pathogens was conducted in both wheat and non-wheat areas as well as prior (February) and during (May) the wheat growing season in Minas Gerais. A total of 1,368 plant samples representative of 31 Poaceae species, including wheat, were collected and inspected for the presence of blast symptoms. During the isolations, 932 isolates were obtained, being one fourth obtained from gramineous plants. A subset of 572 isolates was selected for identification at the species level based on portions of the CH7-BAC9 gene sequences. Most of the isolates (n = 494) were P. oryzae, within which 68% were PoT and 32% non-PoT based on two PCR assays targeting (MoT3 and C17 PCR assays). The PoT lineage was found predominantly (97%) in wheat and rarely in the other hosts, even nearby wheat fields (2.1%), as well as at longer distances from wheat regions (0.1%). The blast pathogen population isolated from signal grass grouped in different clades from PoT, and therefore referred to Urochloa lineage (PoU). A series of cross-inoculation greenhouse experiments was conducted using wheat (cv. BRS Guamirim and BR 18-Terena) and signal grass (cv. Marandu) as host and 14 PoT and six PoU isolates as pathogen factor. In the first leaf-inoculation experiment, results showed a significant interaction between host and pathogen; PoT was strongly/weakly aggressive towards wheat/signal grass and PoU was strongly/weakly aggressive towards signal grass/wheat. In inoculated wheat heads, PoT was more aggressive (>91% infected spikelets) than PoU (52% infected spikelets). In a third experiment, four signal grass cultivars (Marandu, Basilisk, Piatã, and Xaraés) were inoculated with the same set of 20 isolates. Similarly, signal grass cultivars were generally more susceptible to PoU than PoT. Severity induced by PoU was twice (7.7% severity) as high as PoT (3.8%) and so was the number of conidia/leaf produced by PoU (47,500) and PoT (23,200). Two groups of signal grass cultivars were formed, the most susceptible composed of Marandu and Basilisk and the least susceptible composed of Piatã and Xaraés. Results of our study confirm the host-specialization and the shaping of the blast populations according to the host. We further suggest that grasses in general, especially signal grass, may not play a major role as an inoculum reservoir for PoT, as it harbors mainly the PoU population. However, due to the large extent of pasture-growing regions and cross-infection ability in wheat, signal grass may harbor amounts of PoT inoculum that are sufficient for initiating leaf and head blast epidemics in wheat blast in Minas Gerais state.

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Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum grass

Cited by 18 publications

References 73 publications

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya

Genetic Variation Bias toward Noncoding Regions and Secreted Proteins in the Rice Blast Fungus Magnaporthe oryzae

Taxonomic and pathogenic diversity of the blast pathogen populations infecting wheat and grasses in Minas Gerais

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