Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus

Abstract

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. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome 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 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.

Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus

“…Future experiments will tease out the degree to which the distinct effector repertoires of the clonal lineages of M. oryzae reflect their adaptation to the rice host and their evolutionary history. Such analyses will require new genomic resources that permit a more accurate identification of effectors in canonical chromosomes and minichromosomes [60,61]. To this aim, it will be fundamental to generate multiple reference genomes sequenced with long-read technologies in conjunction with a detailed characterization of structural variation and genomic rearrangements, which will include a per isolate inventory of mini-chromosome repertoires.…”

Pyricularia graminis‐tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2)

“…Comparison of reference genome sequences for Triticum and Oryza strains show seven conserved core chromosomes plus supernumerary minichromosomes (Peng et al. , ). Strains in different lineages, including the Oryza and Triticum lineages, are sexually fertile, producing abundant viable ascospores in laboratory studies (Tosa et al.…”

Expecting the unexpected: factors influencing the emergence of fungal and oomycete plant pathogens

“…The pathogen carries effector genes in one of four accessory chromosomes (Ma et al ., ), which are required for pathogenicity towards its tomato host (Vlaardingerbroek et al ., ). More recently, highly variable fast‐evolving mini‐chromosomes carrying effector sequences have also been identified in the wheat‐adapted lineage of M. oryzae (Peng et al ., ). The unstable transmission of these mini‐chromosomes between strains has been hypothesized to act as a mechanism to accelerate host adaptation for M. oryzae (Peng et al ., ).…”

“…More recently, highly variable fast‐evolving mini‐chromosomes carrying effector sequences have also been identified in the wheat‐adapted lineage of M. oryzae (Peng et al ., ). The unstable transmission of these mini‐chromosomes between strains has been hypothesized to act as a mechanism to accelerate host adaptation for M. oryzae (Peng et al ., ). From these examples it is clear that sexual recombination and the exchange of accessory chromosomes can play a central role in EPP outbreaks by facilitating the emergence of new pathogen strains with novel virulence combinations that can be crucial for adaptation to new hosts.…”