Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?

Abstract

The ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the most diverse lineages of ectomycorrhizal fungi. We present comparative analyses of the pangenome and gene repertoires of 21 species across the order Russulales, including a closely related saprotrophic member of Russulaceae. The ectomycorrhizal Russulaceae is inferred to have originated around the Cretaceous-Paleogene extinction event (73.6-60.1 million years ago (MY)). The genomes of the ectomycorrhizal Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of genes coding for certain secreted proteins with TE "nests". The saprotrophic sister group of the ectomycorrhizal Russulaceae, Gloeopeniophorella convolvens, possesses some of these aspects (e.g., loss of PCWDE and protease orthologs, TE expansion, reduction in secondary metabolism clusters), resulting from an accelerated rate of gene evolution in the shared ancestor of Russulaceae that predates the evolution of the ectomycorrhizal habit. Genomes of Russulaceae possess a high degree of synteny, including a conserved set of terpene secondary metabolite gene clusters. We hypothesize that the evolution of the ectomycorrhizal habit requires premodification of the genome for plant root association followed by an accelerated rate of gene evolution within the secretome for host-defense circumvention and symbiosis establishment.

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

“…In Agaricales, Russulales, Thelephorales and Pezizales the transition from saprotrophy to the symbiotic ecology coincided with the loss of most hydrolytic enzymes acting on lignocellulose (Kohler et al, 2015;Hess et al, 2018;Murat et al 2018;Miyauchi et al, 2020;Looney et al, 2021;Marqués-Gálvez et al, 2021). Our analyses of the largest set of ectomycorrhizal Boletales genomes to date support the view that transitions from brown-rot to symbiosis entailed the widespread losses of PCWDEs acting on lignin, cellulose, hemicellulose and pectins.…”

“…Compared to their saprotrophic cousins, all ectomycorrhizal Boletales lack the set of enzymes required for efficient cellulose degradation consisting of cellobiohydrolases from families GH6 and GH7, and cellulose-binding module CBM1 appended to cellulases and endoglucanases. The absence of the synergistically acting GH7 and GH6 enzymes, acting on cellulose reducing and non-reducing ends, is a hallmark of ectomycorrhizal species in Agaricales and Russulales (Kohler et al, 2015;Wolfe et al 2012;Looney et al, 2021).…”

“…In the latter ectomycorrhizal symbionts, the host tree actively controls the decomposing activities of the associated fungi by controlling the amount of photosynthetic carbon provided to the fungus. These genomic features are shared with ectomycorrhizal Agaricales and Russulales (Miyauchi et al, 2020;Looney et al, 2021). It is tempting to speculate that TEs accelerated the evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases.…”

“…We measured the mean TE-to-gene distances with statistical support with the R package regioneR (Gel et al, 2016). Macrosynteny with combined genomic features among the selected species was visualized and evaluated with a custom script, Visually Integrated Numerous Genres of Omics (VINGO), incorporating the R package karyoploteR (Looney et al, 2021;Gel & Serra, 2017). We assessed and displayed associations between TEs and genes using the R package vegan (Oksanen et al 2019) and PCAtools (Blighe & Lun, 2020).…”

“…Functional traits, such as gene copy numbers for PCWDEs, nitrogen and phosphate acquisition pathways, MiSSPs and TEs, within a fungal family across functional guilds (e.g. saprotrophs vs. symbiotrophs) have been investigated within the Amanitaceae, Endogonaceae, Russulaceae, Suillaceae, Tuberaceae (Wolfe et al, 2012;Murat et al, 2018;Chang et al, 2019;Loftgren et al, 2021;Looney et al, 2021). These studies have shown that the abovementioned hallmarks of the ectomycorrhizal ecology are recapitulated at the family level, although idiosyncrasies have been identified in each of these fungal families, e.g.…”