To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Summary: Arbuscular mycorrhizal (AM) fungi are ancient Zygomycetes, thought to have colonized the first land plants; today, they are associated with the roots of about 80% of plant species. The symbiosis they form is potentially valuable not only for developmental programmes based on low‐input agriculture, but also as a complex experimental model, where both fungal and host plant growth are regulated. Here we review some recent progress m the area of cell and molecular biology of arbuscular mycorrhizas. Particular attention is given to strategies followed by AM fungi when, as obligate biotrophs, they establish a successful symbiosis with their host plants. Four topics are analysed: (i) parameters controlling fungal growth in the absence and presence of the host root, Le. events of DNA replication and timing of the cell cycle; (ii) mechanical and enzymatic mechanisms which allow the fungus to colonize root tissues, maintaining host viability; (iii) morphological changes induced by AM fungus host cells and, in particular, the formationde novoof a subcellular compartment termed the interface, and (iv) modifications of plant gene expression during fungal colonization, including those involving structural, symbiotic and defence‐related genes. Contents Summary 3 I. Introduction 3 II. Fungal growth and activatioti of the cell cycle 5 III. Molecular basis of the colonization process 9 IV. Plant and fungal morphogenesis during the infection process 12 V. AM fungi change the pattern of gene expression in host plants 17 VI. Conclusions 18 Acknowledgements 470 References