2020
DOI: 10.1186/s12915-020-00818-z
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Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

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 isolate… Show more

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Cited by 65 publications
(153 citation statements)
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References 80 publications
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“…Although the high sequence divergence and elevated mutation rates among HMA sequences precluded rigorous dating of the emergence of these key adaptations, the low level of total nucleotide polymorphisms among closely related Pik alleles-in particular, the very few synonymous substitutions among Pikp-and Pikm-related alleles-points to a very recent emergence of the adaptive polymorphisms. Given that the rice-infecting lineage of M. oryzae is estimated to have arisen about 7,000-9,000 years ago (Couch et al, 2005;Latorre et al, 2020), our findings are consistent with the view that Pik-1 alleles evolved during rice domestication as previously suggested (Kanzaki et al, 2012;Zhai et al, 2011). In addition, AVR-Pik is widespread in rice-infecting isolates but absent in other blast fungus lineages (Langner et al, 2020;Latorre et al, 2020;Yoshida et al, 2016).…”
Section: Discussionsupporting
confidence: 91%
See 1 more Smart Citation
“…Although the high sequence divergence and elevated mutation rates among HMA sequences precluded rigorous dating of the emergence of these key adaptations, the low level of total nucleotide polymorphisms among closely related Pik alleles-in particular, the very few synonymous substitutions among Pikp-and Pikm-related alleles-points to a very recent emergence of the adaptive polymorphisms. Given that the rice-infecting lineage of M. oryzae is estimated to have arisen about 7,000-9,000 years ago (Couch et al, 2005;Latorre et al, 2020), our findings are consistent with the view that Pik-1 alleles evolved during rice domestication as previously suggested (Kanzaki et al, 2012;Zhai et al, 2011). In addition, AVR-Pik is widespread in rice-infecting isolates but absent in other blast fungus lineages (Langner et al, 2020;Latorre et al, 2020;Yoshida et al, 2016).…”
Section: Discussionsupporting
confidence: 91%
“…Given that the rice-infecting lineage of M. oryzae is estimated to have arisen about 7,000-9,000 years ago (Couch et al, 2005;Latorre et al, 2020), our findings are consistent with the view that Pik-1 alleles evolved during rice domestication as previously suggested (Kanzaki et al, 2012;Zhai et al, 2011). In addition, AVR-Pik is widespread in rice-infecting isolates but absent in other blast fungus lineages (Langner et al, 2020;Latorre et al, 2020;Yoshida et al, 2016). Therefore, it is tempting to speculate that the rice agroecosystem has created the ecological context that led to Pik neofunctionalization towards recognition of the new pathogen threat imposed by the blast fungus.…”
Section: Discussionmentioning
confidence: 99%
“…Paired NLR receptors harbouring integrated domains are particularly prevalent in rice [31, 32], and account for some of the most well-characterised resistance genes against rice blast [33]. The effector complement of different blast strains shows signatures of rapid evolution, including presence/absence polymorphisms [34-37]. This allows the blast pathogen to break genetic resistance, producing disease outbreaks that threaten food production worldwide [1, 27, 38].…”
Section: Introductionmentioning
confidence: 99%
“…The sensor NLR Pik-1 harbours an integrated heavy metal associated (HMA) domain that directly binds AVR-Pik triggering immune responses [20, 21]. In contrast to other blast effectors such as AVR1-CO39 and AVR-Pii, which present presence/absence polymorphisms in blast genomes [34, 35, 42], AVR-Pik displays signatures of positive selection, and occurs as multiple effector variants [39, 43]. To date, six AVR-Pik variants (A to F) have been described [39, 44].…”
Section: Introductionmentioning
confidence: 99%
“…Disease monitoring is greatly facilitated by genome sequencing to characterize pathogen diversity (Hubbard et al, 2015) although a sequence-based prediction of virulence types remains challenging due to a rapid evolution of pathogen genomes (Lamour et al, 2012;Raffaele et al, 2010;Dong et al, 2015;Thordal-Christensen et al, 2018;Frantzeskakis et al, 2019). Sequencing data were used to track the epidemiology and demographic history of pathogens (e.g., Gladieux et al, 2018;Stam et al, 2019;Latorre et al, 2020) and to reconstruct introductions (Yoshida et al, 2013).…”
Section: Introductionmentioning
confidence: 99%