Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae

• Published in: Genetics (Austin) Vol. 226; no. 4
• Main Authors: Joubert, Pierre M, Krasileva, Ksenia V
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 03-04-2024
• Subjects: Investigation; population genetics; structural variation; plant pathogen; fungi; Magnaporthe oryzae; presence-absence variation; Pyricularia oryzae; evolution; machine learning; comparative genomics
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1093/genetics/iyae012

Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation (PAV) contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether PAV patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying PAV because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene PAV in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that PAV genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of PAV and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between PAV genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience PAV with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that PAV genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene PAV can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.