Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes

Abstract

Contents Summary 1129 I. Introduction 1129 II. Intraspecific phenotypic variation and the plant host 1130 III. High inter-isolate genetic diversity in model AMF 1130 IV. Genome diversity within the model AM fungus Rhizophagus irregularis 1131 V. Pangenomes and the future of AMF ecological genomics 1131 Acknowledgements 1133 References 1133 SUMMARY: Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant symbionts with an intriguing population biology. Conspecific AMF strains can vary substantially at the genetic and phenotypic levels, leading to direct and quantifiable variation in plant growth. Recent studies have shown that high intraspecific diversity is very common in AMF, and not only found in model species. Studies have also revealed how the phenotype of conspecific isolates varies depending on the plant host, highlighting the functional relevance of intraspecific phenotypic plasticity for the AMF ecology and mycorrhizal symbiosis. Recent work has also demonstrated that conspecific isolates of the model AMF Rhizophagus irregularis harbor large and highly variable pangenomes, highlighting the potential role of intraspecific genome diversity for the ecological adaptation of these symbionts.

Fungal evolution: cellular, genomic and metabolic complexity

“…Even so, nuclear competition and population dynamics have been described and studied in Heterobasidion (Garbelotto et al ., ; James et al ., ; James, Johansson & Johannesson, ; Garbelotto & Gonthier, ; Giordano et al ., ) and Termitomyces (Nobre et al ., ). Arbuscular mycorrhizal fungi also seem to show high levels of heterokaryosis in nature (Bever & Wang, ; Boon et al ., ; Wyss et al ., ; Mathieu et al ., ), forming nuclear populations that are mantained over time through the production of highly multinucleated spores (Bever & Wang, ; Jany & Pawlowska, ; Chagnon, ; Boon et al ., ). However, there are considerable discrepancies among studies and methods and in the amount of estimated divergence (Kuo et al ., ; Lin et al ., ; Ropars & Corradi, ).…”

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts

“…The genome sequence also provided the first indication that AM fungi are fatty acid auxotrophs (Wewer et al ., ). A comparison of several strains of Rhizophagus irregularis indicates substantial genetic and physiological diversity (Chen et al ., ; Mathieu et al ., ). Across the Glomeromycotina, with 288 AM fungal species defined by morphological and sequence characteristics (Öpik & Davison, ) and many more defined at the level of operational taxonomic units (Davison et al ., ), there is considerable evidence for functional diversity (Jakobsen et al ., ).…”

The Infection Unit: An Overlooked Conceptual Unit for Arbuscular Mycorrhizal Function

“…On the other hand, plant roots closely interact with the native fungal partners that may have genetically recorded beneficial traits for adapting to the local environment. The specific phenotype (functionality) of native AMFs may be conferred by accessory genes that are not shared by all members of a species [64]. However, due to the complexity of the genetic basis of AMF individuals, it is difficult to understand which AMF genes are really functional in the roots.…”