2020
DOI: 10.1101/2020.01.09.900308
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Recently expanded clonal lineages of the rice blast fungus display distinct patterns of presence/absence of effector genes

Abstract: 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 isolat… Show more

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Cited by 8 publications
(12 citation statements)
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“…We therefore tested whether eccDNA formation is associated with genes prone to presence-absence variation in 162 rice-infecting M. oryzae isolates (Supplemental Data File 25). As expected from previous studies 38, 39 , our analysis indicated that predicted effectors were more likely to experience presence-absence variation (Supplemental Figure 18; X-squared = 146.33, df = 1, p-value < 2.2e-16). We also found that eccDNA-associated genes were more likely to be prone to presence-absence variation (Figure 4B and Supplemental Data File 19; X-squared = 28.511, df = 2, p-value = 6.44e-07).…”
Section: Resultssupporting
confidence: 87%
“…We therefore tested whether eccDNA formation is associated with genes prone to presence-absence variation in 162 rice-infecting M. oryzae isolates (Supplemental Data File 25). As expected from previous studies 38, 39 , our analysis indicated that predicted effectors were more likely to experience presence-absence variation (Supplemental Figure 18; X-squared = 146.33, df = 1, p-value < 2.2e-16). We also found that eccDNA-associated genes were more likely to be prone to presence-absence variation (Figure 4B and Supplemental Data File 19; X-squared = 28.511, df = 2, p-value = 6.44e-07).…”
Section: Resultssupporting
confidence: 87%
“…Records of rice blast disease in China date back to the early 17 th century and until today it is recognized as one of the most threatening and widely distributed rice diseases [39]. Recent population genetics studies revealed that the rice-infecting lineage of M. oryzae consists of both a recombining population and multiple, clonally expanded lineages [42][43][44]. In Europe, the rice blast fungus population consists of only one of three major clonal lineages and it is possible that mating type isolation led to local asexual expansions.…”
Section: Introductionmentioning
confidence: 99%
“…The Kenyan and Diverse clusters were excluded from the second analysis to omit most recombination signals that were not incorporated in the BEAST approach, following (13). However, we added the reference, because the clonal lineages covered only a narrow window of sampling time differences (in time and mutations) between individuals and showed more noisy posterior estimates for split times, see SI Appendix Table S4 and Text E for more details.…”
Section: Methodsmentioning
confidence: 99%
“…Disease monitoring is greatly facilitated by genome sequencing to characterize pathogen diversity (5) although a sequence-based prediction of virulence types remains challenging due to a rapid evolution of pathogen genomes (6)(7)(8)(9)(10). Sequencing data were used to track the epidemiology and demographic history of pathogens (e.g., [11][12][13] and to reconstruct introductions (14). However, the relative importance of demographic effects versus selection-driven adaptation to cultivation conditions or plant resistance genes is still little understood.…”
Section: Introductionmentioning
confidence: 99%
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