Abstract
Background One of the ways genomes respond to stress is by producing 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.
Results 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 in our data, which indicates that the presence of these genes on eccDNAs is selected against.
Conclusions Our study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
A new analysis of overlap between technical replicates, validation of 8 eccDNAs via PCR and validation of 2 eccDNA-absent gene via PCR. A new definition of eccDNA-associated genes that is more robust to variation between samples. A clearer view of the evidence supporting eccDNA forming regions. And many other minor changes throughout the manuscript. We also include a summary of concerns expressed by the community about this manuscript as well as a response to these concerns as a comment on the bioRxiv page for this manuscript.