Daucus carrota root colonized by Rhizophagus irregularis C2 strain, photo by Gökalp Yıldırır.

The Rhizophagus irregularis B3 genome sequence and gene models have not been determined by the JGI, but were received from the laboratory of Nicolas Corradi at University of Ottawa on March 05, 2024. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 3802 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All of the original published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by the Corradi lab and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into MycoCosm. The JGI Annotation Pipeline was used to add functional annotation to the genes.

Arbuscular mycorrhizal fungi (AMF), found within the fungal subphylum Glomeromycotina, are mutualistic symbionts for the majority of vascular plant species, having developed a mutualistic bond with their roots. Within this symbiosis, these fungi improve their host's nutrient and water absorption capabilities while receiving sugars and lipids in return, as well as providing enhanced protection against pathogens. The fragmented nature of AMF genome assemblies have significantly impeded efforts to identify the mechanisms governing the relationships between genome structure and function. The regulation of genes driven by compartmentalization underscores the crucial epigenetic role of chromosome folding in genome biology. However, such structural knowledge has been lacking in the previous genome assemblies. This study utilized a combination of Nanopore (ONT) sequencing and chromatin conformation capture sequencing (Hi-C) to unveil chromosome and epigenetic diversity between AMF strains.

The findings reveal that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis (A1, C2, B3, 4401 and DAOM197198) carry 33 chromosomes with substantial variability in size, gene content, and repeat content within the species. Strain-specific Hi-C contact maps unveil a distinctive 'checkerboard' pattern, highlighting two predominant euchromatin (compartment A) and heterochromatin (compartment B) genome regions. Each compartment exhibits differences in gene transcription levels, regulation of candidate effectors, and methylation frequencies. The A-compartment is more gene-dense and contains most of the core genes, whereas the B-compartment is richer in repeats and experiences higher rates of chromosomal rearrangements. Despite being transcriptionally repressed, the B-compartment harbors significantly more secreted proteins and candidate effectors upregulated in planta, hinting at a potential host-induced alteration in chromosome conformation.

Overall, this study offers a detailed insight into the genome biology and evolution of these model plant symbionts, and it paves the way for investigating the epigenetic mechanisms that influence chromosome folding during host-microbe interactions.