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. 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...

Pyricularia graminis-tritici, a new Pyricularia species causing wheat blast

“…The analyses of complete genomes of Oryza, Setaria, Triticum and Eleusine isolates showed that more than 88% of the genes involved in the interaction with the plant, including putative effectors, have homologues in all genomes (Chiapello et al, 2015;Yoshida et al, 2016). Comparison of reference genome sequences for Triticum and Oryza strains show seven conserved core chromosomes plus supernumerary minichromosomes (Peng et al, 2018). Strains in different lineages, including the Oryza and Triticum lineages, are sexually fertile, producing abundant viable ascospores in laboratory studies (Tosa et al, 2006.…”

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

“…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, 2018). 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, 2018). 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.…”

Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences

“…The alignments passing the filtering were used for the variant discovery with "showsnps". B71 whole genome sequencing using Nanopore MinION B71 nuclear genomic DNA was prepared as described previously (28). Genomic DNA was subjected to 20kb size selection using Bluepippin cassette kit BLF7510 with High-Pass protocol (Sage Science, USA), followed by library preparation with the SQK-LSK109 kit (Oxford Nanopore, UK).…”

“…Pilon used bwa alignments and polish assembled sequences with the parameters of (--minmq 40 --minqual 15). Assembled contigs were renamed based on their similarity to the assembly of B71Ref1 (28). We also manually fixed a misassembly that joined a previously identified minichromosome's sequence with chromosome 6.…”

“…The assembly and polishing procedure resulted in ONTv0.14. The same Pilon procedure was applied to further polish the PacBio assembly B71Ref1 (28) with Illumina reads, resulting in a new assembly PBRef1.3.…”