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

Abstract

Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

“…AM fungi are multinucleate, obligate symbionts that exist in all terrestrial ecosystems ( Davison et al 2015 ) and engage in symbioses with a wide range of plant species, often simultaneously ( Bever 2002 ). While ecological and molecular mechanistic evidence suggest that the AM symbiosis relies on the reciprocal transfer of organic and inorganic nutrients through a permeable membranous interface ( Bonfante and Genre 2010 ), our understanding of the genomic basis of this symbiotic lifestyle remains limited by the fact that whole-genome sequencing data are available for a limited number of AM species ( Trepanier et al 2005 ; Kobayashi et al 2018 ; Morin et al 2019 ; Singh et al 2019 , 2021 ; Sun et al 2019 ; Venice et al 2020 ; Malar et al 2021 ; Montoliu-Nerin et al 2021 ; Sahraei et al 2022 ). These include genome assemblies of multiple isolates of the model species, Rhizophagus irregularis , and the homokaryotic laboratory strain DAOM197198 ( Fig.…”

Single-worm long-read sequencing reveals genome diversity in free-living nematodes

“…Such requirements are challenging to meet in microscopic organisms that cannot be cultured, leading to sampling bias and loss of their biological information on genetic and evolutionary studies ( 7–9 ). Recent advances in whole-genome amplification (WGA) have enabled single cells or limited samples to generate sufficient DNA for sequencing ( 10 , 11 ), and have been applied to eukaryotic microorganisms, including fungi ( 9 , 12 ), marine phytoplankton ( 13 ) and parasitic nematodes ( 14 , 15 ), for genomic and population genetic studies ( 9 , 16 ).…”

Single worm long read sequencing reveals genome diversity in free-living nematodes

“…Such requirements are challenging to meet in microscopic organisms that cannot be cultured, leading to sampling bias and loss of their biological information on genetic and evolutionary studies (7)(8)(9). Recent advances in whole genome amplification (WGA) have enabled single cells or limited samples to generate sufficient DNA for sequencing (10,11), and have been applied to eukaryotic microorganisms, including fungi (9,12), marine phytoplankton (13) and parasitic nematodes (14,15) for genomic and population genetic studies (9,16).…”