PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae

Bao, Jiandong; Chen, Meilian; Zhong, Zhenhui; Tang, Wei; Lin, Lian‐Yu; Zhang, Xingtan; Jiang, Haolang; Zhang, Deyu; Miao, Chenyong; Tang, Haibao; Zhang, Jishen; Lu, Guodong; Ming, Ray; Norvienyeku, Justice; Wang, Zonghua

doi:10.1016/j.molp.2017.08.008

Cited by 112 publications

(124 citation statements)

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“…S2) and by 50 single PacBio long reads. This rearrangement is not MoT specific because it was also observed in a MoO field isolate, evidenced by a long PacBio assembled sequence spanning both chromosome 1 and chromosome 6 of MG8 (BAO et al 2017). A large sequence in B71Ref1, from 1.3 to 2.9 Mb on chromosome 3, was absent in MG8.…”

Section: A Reference Genome Of the Mot Strain B71mentioning

confidence: 87%

Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus

Peng

Oliveira-Garcia

Lin

et al. 2018

Preprint

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Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. To understand genetic diversity in wheat-infecting strains, we report a near-finished reference genome of a recent field isolate generated using long read sequencing and a novel scaffolding approach with long-distance paired genomic sequences. The genome assemblage includes seven core chromosomes and sequences from a dispensable mini-chromosome that harbors effector genes normally found on the ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and two mini-chromosomes from another field isolate each contain different effector homologous genes and core chromosome end sequences. The minichromosome is highly repetitive and is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and non-dispensable core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome. Significance statementThe emerging blast disease on wheat is proving even harder to control than the ancient, stillproblematic rice blast disease. Potential wheat resistance identified using strains isolated soon after disease emergence are no longer effective in controlling recent aggressive field isolates from wheat in South America and South Asia. We report that recent wheat pathogens can contain 3 one or two highly-variable conditionally-dispensable mini-chromosomes, each with an amalgamation of effector sequences that are duplicated or absent from pathogen core chromosome ends. Well-studied effectors found on different core chromosomes in rice pathogens appear side-by-side in wheat pathogen mini-chromosomes. The rice pathogen often overcomes deployed resistance genes by deleting triggering effector genes. Localization of effectors on mini-chromosomes, which are unstably transmitted during growth, would accelerate pathogen adaptation in the field. aggressive wheat pathogens that are so far restricted to certain countries in South America and South Asia (Fig. 1A).Although little is known about wheat blast, studies on rice blast disease have identified numerous effector genes, generally encoding small proteins that are specifically expressed in planta and play roles in host invasion (GIRALDO AND VALENT 2013). Some effectors, termed avirulence (AVR) effectors, determine either rice cultivar or host species specificity through blocking infection upon recognition by corresponding cultivar-or species-specific resistance (R) genes and triggering hypersensitive resistance. For example, strains of several M. oryzae pathotypes are able to infect weeping lo...

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Section: A Reference Genome Of the Mot Strain B71mentioning

confidence: 87%

Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus

Peng

Oliveira-Garcia

Lin

et al. 2018

Preprint

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“…Table 1)). Raw sequencing reads were downloaded and mapped to the M. oryzae reference genome ( GUY-11 PacBio assembly [59] ) using bwa-mem V.0.7.12 [60] with default parameters.…”

Section: Datasets and Mappingmentioning

confidence: 99%

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Latorre

Reyes-Avila

Malmgren

et al. 2020

Preprint

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Background: Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia ) oryzae -the causal agent of blast disease of cereals-is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined multiple genomics datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries. Results: The global population of the rice blast fungus consists of a diverse set of individuals and three well-defined genetic groups. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in South East Asia followed by three independent clonal expansions that took place over the last~200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence/absence of candidate effector genes. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of effector presence/absence define each of the pandemic clonal lineages. Conclusions: Our analyses reconstruct the genetic history of the rice-infecting lineage of M. oryzae revealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence/absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.

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“…We used GFP-CenpA as a tool for molecular identification of centromeres in the M. oryzae genome. We utilized chromatin immunoprecipitation (ChIP) assays followed by deep sequencing (ChIP-seq) of GFP-CenpA-associated chromatin fragments and aligned the reads on the recently published PacBio genome assembly of the wild-type Guy11 strain of M. oryzae [42]. This analysis revealed seven distinct CenpA-rich regions across the genome, one each on seven different contigs (Fig 3, Table 1 and S4 Fig).…”

Section: Resultsmentioning

confidence: 99%

Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus

Yadav

Yang

Reza

et al. 2018

Preprint

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0A series of well-synchronized events mediated by kinetochore-microtubule interactions ensure 2 1 faithful chromosome segregation in eukaryotes. Centromeres scaffold kinetochore assembly and 2 2 3 1 strain of M. oryzae. The centromeres in M. oryzae are regional and span 57 to 109 kb 3 2 transcriptionally poor regions. No centromere-specific DNA sequence motif or repetitive 3 3 elements could be identified in these regions suggesting an epigenetic specification of 3 4 centromere function in M. oryzae. Highly AT-rich and heavily methylated DNA sequences were 3 5

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PacBio Sequencing Reveals Transposable Elements as a Key Contributor to Genomic Plasticity and Virulence Variation in Magnaporthe oryzae

Cited by 112 publications

References 11 publications

Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus

Effector Gene Reshuffling Involves Dispensable Mini-chromosomes in the Wheat Blast Fungus

Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus

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