Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains (TADs). In mammals, these domains undergo preferential interactions and regulate gene expression, however in fungi the role of chromosome folding in genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome diversity in a group of obligate plant symbionts with a multinucleate mycelium; the arbuscular mycorrhizal fungi (AMF). We find that phylogenetically distinct strains of the model AMF Rhizophagus irregularis all carry 33 chromosomes. Homologous chromosomes show within species variability in size, as well as in gene and repeat content. Strain-specific Hi-C sequencing reveals that all strains have a 3D genome organization that resembles a checkerboard structure with two distinct (A/B) chromatin compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation rate. The A-compartment is more gene-dense and contains most core genes, while the B-compartment is more repeat-rich and has higher rates of chromosomal rearrangement. While the B-compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta up-regulated candidate effectors suggesting a possible host-induced change in chromosome conformation. Overall, this study provides a fine-scale view into the genome biology and evolution of prominent plant symbionts, and opens avenues to study the mechanisms that generate and modify chromosome folding during host-microbe interactions.

We report here a 3.2-Mb draft assembled genome of Lactobacillus casei Lbs2. The bacterium shows probiotic and immunomodulatory activities. The genome assembly and annotation will help to identify molecules and pathways responsible for interaction between the host immune system and the microbe.