Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal GenusPisolithus

Abstract

The mutualistic ectomycorrhizal (ECM) fungal genus Pisolithus comprises 19 species defined to date which colonize the roots of >50 hosts worldwide suggesting that substantial genomic and functional evolution occurred during speciation. To better understand this intra-genus variation, we undertook a comparative multi-omic study of nine Pisolithus species sampled from North America, South America, Asia, and Australasia. We found that there was a small core set of genes common to all species (13%), and that these genes were more likely to be significantly regulated during symbiosis with a host than accessory or species-specific genes. Thus, the genetic ‘toolbox’ foundational to the symbiotic lifestyle in this genus is small. Transposable elements were located significantly closer to gene classes including effector-like small secreted proteins (SSPs). Poorly conserved SSPs were more likely to be induced by symbiosis, suggesting that they may be a class of protein that tune host specificity. The Pisolithus gene repertoire is characterized by divergent CAZyme profiles when compared to other fungi, both symbiotic and saprotrophic. This was driven by differences in enzymes associated with symbiotic sugar processing, although metabolomic analysis suggest that neither copy number nor expression of these genes is sufficient to predict sugar capture from a host plant or its metabolism in fungal hyphae. Our results demonstrate that intra-genus genomic and functional diversity within ectomycorrhizal fungi is greater than previously thought, underlining the importance of continued comparative studies within the fungal tree of life to refine our focus on pathways and evolutionary processes foundational to this symbiotic lifestyle.

Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis

“…Pisolithus stock isolates were maintained on full‐strength MMN media (10 g l −1 glucose; 0.5 g l −1 (NH 4 ) 2 HPO 4 ; 0.3 g l −1 KH 2 PO 4 ; 0.14 g l −1 MgSO4.7H 2 O; 1 ml l −1 of CaCl 2 5% w/v stock solution; 1 ml l −1 of NaCl 2.5% w/v stock solution; 1 ml l −1 of ZnSO 4 0.3% w/v stock solution; 133 μl l −1 of thiamine 0.1% w/v stock solution; 1 ml l −1 of citric acid + Fe EDTA 1.25% w/v stock solution; and 13 g l −1 agar in de‐ionised water, pH 5.5). Isolates used included Pisolithus microcarpus ((Cooke & Massee) G. Cunn) isolates G5, MD06, SI‐9, SI‐14, Wil3, R4, R10, MW3 and sub species B1, and P. albus ((Cooke & Massee) Priest) isolates SI‐12, Be‐1, Meg7, NPiso and 76A (Jourand et al ., 2010; Plett et al ., 2015; Plett et al ., 2023; NPiso collected in 2019, −33.61279, 150.74958). These isolates were selected based on their diversity of phenotypes based on previous studies.…”

“…RNA was extracted using the Spectrum Plant Total RNA extraction kit (Sigma) based on the manufacturer's directions and sequenced by Azenta Life Sciences (Burlington, MA, USA) using a NovaSeq Illumina platform. Raw reads were trimmed and mapped to either the P. microcarpus (Plett et al ., 2023) or E. grandis (Myberg et al ., 2014) genomes in CLC Workbench (v.22).…”

From populations to pan-genomes: investigating the role of ecology and genomic architecture in maintaining species boundaries in the porcini mushroom,Boletus edulis

“…However, it remains a matter of debate whether they only decompose organic material to “mine” nutrients for provision to plant hosts, or whether some EMF are “facultativesaprotrophs” and can acquire carbon through both decomposition and mycorrhizal mutualsm (Baldrian 2009; Jennifer M. Talbot et al 2013; Vaario et al 2019). Regardless, it is evident that decomposition is an important component of the EMF lifestyle (Kohler et al 2015; Jonathan M Plett et al 2023) and variation in saprotrophic capacity may contribute to lineage divergence.…”

“…Futhermore, host specialization at the level of species is considered scarce, with host associations thought to be more important at broader evolutionary scales (Ishida et al 2007). Lastly, within the genome, much recent work has documented patterns of that transposable elements (TEs) abundance that may play a role in the adaptive evolution of EMF (Jonathan M Plett et al 2023; Wu et al 2022). In particular, most EMF exhibit expanded TEs families and inflated genome sizes compared to their saprotrophic ancestors, and these TEs are often clustered around rapidly diverging genes such as effector proteins (Jonathan M Plett et al 2023; Wu et al 2022).…”

Ectomycorrhizal Community Shifts at a Former Uranium Mining Site

“…Betulaceae, Pinaceae, and Fagaceae are prominent trees in temperate forest ecosystems and provide promising candidates for such approaches [3][4][5]. The mutually beneficial symbiosis, in addition to the general traits of nutrient exchange, alleviates abiotic stress like drought or can protect from bioavailable heavy metals, as well as increasing resistance against pathogens [5][6][7]. The positive effects on tree growth and metabolism can raise the survival of plants during afforestation [8][9][10].…”