Long reads and Hi‐C sequencing illuminate the two‐compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

Abstract

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.

Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina

“…On one hand, the streamlined features of the P. occultum genome could indicate that the MRCA of Glomeromycotina was an obligate plant biotroph but also gene and repeat poor. If correct, then gene and repeat family expansions commonly attributed to these prominent plant symbionts must have emerged later in the more derived AMF lineages, possibly to improve their adaptability to environmental and host change [11, 62, 63]. On the other hand, it is possible that the Paraglomerales have undergone drastic and species-specific genome reductive processes and the observation of over 200 P. occultum specific gene losses support this view.…”

Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum

“…Nevertheless, it is possible that other aspects of genome organization not covered by gene annotations could differ between cultured and field collected strains. For instance, considerable chromosome length variation and structural rearrangements have been observed across three well studied strains of R. irregularis separately isolated from the same field (Yildirir et al 2022). Furthermore, we acknowledge that an appropriate comparison of genetic variation would require that field collected and cultured strains of the same species are analyzed.…”

“…As a consequence of cultivability, species and strains in the genus Rhizophagus, which can be grown in vitro in root-organ cultures, are among the genomically most wellstudied AM fungi (Kobayashi et al 2018;Lin et al 2014;Morin et al 2019;Tisserant et al 2013;Yildirir et al 2022). Genomes have also been successfully sequenced and assembled from representatives of the order Diversisporales, such as Diversispora epigaea which is an AM fungus that forms above-ground sporocarps from which genome assemblies can be generated using metagenomic approaches (Sun et al 2019) as well as two species in Gigasporales (Morin et al 2019;Venice et al 2020).…”

“…Some AM fungi can be grown in pot culture for extended periods of time. For example, the most well-sequenced strain of R. irregularis (Tisserant et al 2013;Yildirir et al 2022) has been maintained in laboratory conditions since the 80 s (Stockinger et al 2009). Emerging evidence suggests that growth under controlled conditions influences AM strains by selecting phenotypes that perform well under those conditions .…”

“…The genomic structure of genetic variation in AM fungi remains well studied; however, only in R. irregularis for which population sampling (Koch et al 2004) has allowed the discovery of mating type linked heterokaryosis (Ropars et al 2016). Furthermore, chromosome level assemblies has revealed genome structures with compartments of different variability (Yildirir et al 2022). The aim of this study was to test if whole genome assemblies suitable for phylogenomic analysis could be generated from individually amplified and sequenced nuclei isolated from AM fungal spores collected from the field.…”