level analyses of AMF nuclei, which showed that ‘repressed’ regions of the AMF genome can become activated when in symbiosis with the plant host.
sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016;1:16033. Yildirir G, Sperschneider J, Malar M, Chen ECH, Iwasaki W et al. Long reads and Hi-C sequencing illuminate the two compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis . New Phytol 2022;233:1097–1107.
Genome biology of AMF: going beyond model species
While genome data from AMF are regularly published, the overall genome quality of those assemblies has until recently been rather poor. Most genome sequences obtained to date are highly fragmented and incomplete due to the presence of multiple and highly repeated sequences in these genomes. Recently, the use of chromatin-capture (Hi-C) sequencing has allowed for a complete view of AMF chromosomes in five model strains. This technique also uncovered the existence of two dominant chromosomal compartments (euchromatin vs heterochromatin) in AMF that carry distinct genes and repeat contents, as well as expression and methylation levels. These findings uncovered a higher order genome organisation that governs genome biology and evolution of model terrestrial symbionts and opened avenues to study the epigenetic mechanisms that modify chromosome folding during host–microbe interactions. While a fine-scale view of the AMF genome biology is now within reach for model species in the genus Rhizophagus , our knowledge in this area for non-model AMF taxa is non-existent. To tackle this, it is essential to now aim sequencing, particularly high-fidelity long-read and chromatin- capture sequencing at the entire AMF phylogeny, with a particular focus on early branching taxa such as P. occultum and those known to carry a unique symbiotic lifestyle such as the fungus-cyanobacterial species Geosiphon pyriformis . Ultimately, a complete understanding of genome biology across all the AMF phylogeny will improve our understanding of this widespread terrestrial mutualism and ensure a more sustainable and widespread application of these organisms as bio-stimulants in a green economy. Further reading Kokkoris V, Chagnon PL, Yildirir G, Clarke K, Goh D et al . Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi. Curr Biol 2021;31:1531–1538, e6. Kokkoris V, Stefani F, Dalpé Y, Dettman J, Corradi N. Nuclear dynamics in the arbuscular mycorrhizal fungi. Trends Plant Sci 2020;25:765–778. Ropars J, Toro KS, Noel J, Pelin A, Charron P et al . Evidence for the
About the author
Nicolas Corradi Professor and Chair in Microbial Genomics, Department of Biology, University of Ottawa, Ottawa, K1N 6N5, Ontario, Canada
ncorradi@uottawa.ca @Blunt_Microbe
Nicolas Corradi started his scientific career studying biology at the University of Geneva, Switzerland. He then went on to do a PhD, studying genome evolution in arbuscular mycorrhizal fungi at the University of Lausanne, Switzerland. Following his PhD, Nicolas received two consecutive postdoctoral fellowships from the Swiss National Foundation to work at the University of British Columbia, Canada, on the evolutionary genomics of intracellular parasites of animals called Microsporidia. It was here that Nicolas further developed his interest in genome analysis, which he applied to understand the biology of arbuscular mycorrhizal fungi and Microsporidia in his first academic PI position at the University of Ottawa, Canada. During 12 successful years as PI, Nicolas helped establish an internationally renowned research team studying microbial genomics and evolution of prominent plant symbionts and ubiquitous animal pathogens, receiving a Fellowship from the Canadian Institute for Advanced Research (CIFAR) and a University Chair in Microbial Genomics. What inspired you to start a career in scientific research? The ability to discover something no one else knew existed before, and shake long-held scientific beliefs. What advice would you give to early career researchers? Do not be afraid to question consensus/authority when contradictory evidence emerges from your work. Do not play ‘politics’, just always be true to yourself. Prioritise producing high-quality and reproducible work.
99 Microbiology Today October 2022 | microbiologysociety.org
Made with FlippingBook Online document maker