Highly dynamic supernumerary mini-chromosomes in a Magnaporthe oryzae strain contributes to cellular variance of genomic content

Abstract

Magnaporthe oryzae (syn. Pyricularia oryzae), the causative agent of devastating crop diseases, exhibits remarkable genomic plasticity that contributes to its adaptability and pathogenicity. Individual M. oryzae strains may contain supernumerary mini-chromosomes, which are dispensable and highly repetitive. Here, we explored the stability of two mini-chromosomes of a Lolium strain isolated in the US, TF05–1, in which one mini-chromosome contains sequences nearly identical to the mini-chromosome of the wheat isolate B71 from Bolivia. The discordance of their phylogenetic relationships based on genomic polymorphisms in core chromosomes and polymorphisms in mini-chromosomes indicated horizontal transfer of the mini-chromosome. Contour-clamped homogeneous electric field (CHEF) karyotyping and genome sequencing analysis found variation in numbers and sizes of mini-chromosomes among asexual monoconidial progeny of TF05–1. Optimization of a fluorescence in situ hybridization (FISH) protocol enabled single-cell karyotyping and revelation of drastic cellular variation in numbers of mini-chromosomes. In addition, rearrangement within mini-chromosomes occurred frequently in the TF05–1 progeny. We characterized an intrachromosomal rearrangement presumably mediated by a palindrome repeat. The rearrangement resulted in a 300-kb deletion and a 900-kb duplication. We found that, in contrast to Long Terminal Repeat (LTR) retrotransposons in core chromosomes, LTR retrotransposons in mini-chromosomes were more recently inserted, less methylated, and with higher G + C content. The data indicated that most LTR retrotransposons in mini-chromosomes retain high activity and have yet to be silenced by fungal genome defense mechanisms such as repeat-induced point mutation, which may contribute to highly dynamic mini-chromosome content in fungi.