Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains. In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear.Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic diversity in a group of obligate plant symbionts: the arbuscular mycorrhizal fungi (AMF).We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within-species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps reveal a 'checkerboard' pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A-compartment is more gene-dense and contains most core genes, while the Bcompartment 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 upregulated 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 model plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.

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.

There is a global industry built upon the production of “bioinoculants,” which include both bacteria and fungi. The recent increase in bioinoculant uptake by land users coincides with a drive for more sustainable land use practices. But are bioinoculants sustainable? These microbes are believed to improve plant performance, but knowledge of their effect on resident microbial communities is scant. Without a clear understanding of how they affect soil microbial communities (SMC), their utility is unclear. To assess how different inoculation practices may affect bioinoculant effects on SMC, we surveyed the existing literature. Our results show that bioinoculants significantly affect soil microbial diversity and that these effects are mediated by inoculant type, diversity, and disturbance regime. Further, these changes to soil microbes affect plant outcomes. Knowledge that these products may influence crop performance indirectly through changes to soil microbial diversity attests to the importance of considering the soil microbiome when assessing both bioinoculant efficacy and threats to soil ecosystems.

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