The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors

Abstract

One of the ways genomes respond to stress is by shedding extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole-circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat. We present a whole circularome sequencing study of the rice blast pathogen Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome containing many genes and showing evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs, which indicates that the presence of these genes on eccDNAs is selected against.