The dark matter of genomics: mini-chromosomes as drivers of host adaptation in the blast fungus

Eukaryotic genomes are often organized into compartments to facilitate transcriptional regulation, recombination, and adaptation. In many plant pathogens, growing evidence suggest that compartmentalization of effectors into mini- or accessory chromosomes facilitates adaptive evolution. The blast fungus Magnaporthe oryzaecauses the most devastating rice disease worldwide and infects more than 50 grass species, including the staple crops rice, wheat and millet. Host adaptation is linked to presence/absence polymorphisms of effectors, possibly as the result of genetic material exchange and recombination associated with repeats and transposable elements. This gene flow can lead to new structural variants potentially involved in host jumps and disease outbreaks. We set out to study genomic structural variation in host specific lineages of M. oryzaecombining nanopore MinION sequencing and pulse-field gel electrophoresis. Almost every isolate contained a specific set of mini-chromosomes ranging in size from 500 kb–3 MB suggesting massive structural variation even in clonal lineages. We established a workflow to sequence isolated mini-chromosomes and a bioinformatics pipeline to identify them in nanopore assemblies. We found that mini-chromosomes contain effector genes and seem to be involved in large scale genomic rearrangements. This raises the possibility that mini-chromosomes are part of a mechanism that facilitates structural diversification of the blast fungus genome.