Abstract
Supernumerary mini-chromosomes-a unique type of genomic structural variation-have been implicated in the emergence of virulence traits in plant pathogenic fungi. However, the mechanisms that facilitate the emergence and maintenance of mini-chromosomes across fungi remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), mini-chromosomes have been first described in the early 1990s but, until very recently, have been overlooked in genomic studies. Here we investigated structural variation in four isolates of the blast fungus M. oryzae from different grass hosts and analyzed the sequences of mini-chromosomes in the rice, foxtail millet and goosegrass isolates. The mini-chromosomes of these isolates turned out to be highly diverse with distinct sequence composition. They are enriched in repetitive elements and have lower gene density than core-chromosomes. We identified several virulence-related genes in the mini-chromosome of the rice isolate, including the virulence-related polyketide synthase Ace1 and two variants of the effector gene AVR-Pik. Macrosynteny analyses around these loci revealed structural rearrangements, including inter-chromosomal translocations between core- and mini-chromosomes. Our findings provide evidence that mini-chromosomes emerge from structural rearrangements and segmental duplication of core-chromosomes and might contribute to adaptive evolution of the blast fungus.
Highlights
Genomes of plant pathogens are highly dynamic and typically exhibit an architecture that facilitates rapid adaptation to their hosts
Nanopore sequencing reads were deposited under accession numbers ERR2612751 (BR32), ERR2612749 (FR13), ERR2612750 (US71), and ERR2612752 (CD156)
Considering that structural genomic variation has emerged as a common feature of fungal plant pathogens, we re-examined 4 previously sequenced M. oryzae genomes of the host specific isolates FR13, US71, CD156, and BR32
Summary
Genomes of plant pathogens are highly dynamic and typically exhibit an architecture that facilitates rapid adaptation to their hosts. Various types of genome architecture have been observed in different species These include effector gene clusters [4,5], lineage-specific genomic regions that are rich in transposable elements [6,7,8,9,10], or enrichment of virulence related genes in specific genomic regions, e.g. unstable telomeric and sub-telomeric regions [11]. These genomic compartments display higher rates of adaptive mutations compared to the rest of the genome [12]. The diversity of supernumerary chromosomes across plant pathogens and their contribution to genome plasticity is still poorly known
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