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.

No abstract

pecies in the genus Aspergillus are of broad interest to medical 1 , applied 2,3 , and basic research 4. Members of Aspergillus section Nigri ('black aspergilli') are prolific producers of native and heterologous proteins 5,6 , organic acids (in particular citric acid 2,7,8), and secondary metabolites (including biopharmaceuticals and mycotoxins like ochratoxin A). Furthermore, the section members are generally very efficient producers of extracellular enzymes 9,10 ; they are the production organisms for 49 out of 260 industrial enzymes 11,12. Among the most important of these, in addition to A. niger, are A. tubingensis, A. aculeatus, and A. luchuensis (previously A. acidus, A. kawachii, and A. awamori 13-15 , respectively). Members of Aspergillus section Nigri are also known as destructive degraders of foods and feeds, and some isolates produce the potent mycotoxins ochratoxin A 16 and fumonisins 17-19. In addition, some species in this section have been proposed to be pathogenic to humans and other animals 20. It is thus of interest to further examine section Nigri for industrial exploitation, as well as prevention of food spoilage, toxin production, and pathogenicity caused by these fungi. A combined phylogenetic and phenotypic approach has shown that section Nigri contains at least 27 species 21-25. Recent results have shown that the section contains species with high diversity and may consist of two separate clades: the biseriate species and the uniseriate species 26 , which show differences in sexual states 27 , sclerotium formation 28 , and secondary metabolite production 29. In the section, only six species have had their genome sequenced: A. niger 2,8 , A. luchuensis 15,30 , A. carbonarius 31 , A. aculeatus 31 , A. tubingensis 31 , and A. brasiliensis 31. This section, with its combination of species richness and fungal species with a diverse impact on humanity, is thus particularly interesting for studying the diversification of fungi into species. In this study, we have de novo-sequenced the genomes of 20 species of section Nigri, thus completing a genome compendium of 26 described species in the section. Further, we have genome-sequenced three

BackgroundEconomical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts.ResultsIn this study, the carotenogenic yeast Rhodosporidium toruloides was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications. We found that R. toruloides can efficiently convert a mixture of glucose and xylose from hydrolyzed lignocellulose into these bioproducts, and unlike many conventional production hosts, its growth and productivity were enhanced in lignocellulosic hydrolysates relative to purified substrates. This organism was demonstrated to have superior growth in corn stover hydrolysates prepared by two different pretreatment methods, one using a novel biocompatible ionic liquid (IL) choline α-ketoglutarate, which produced 261 mg/L of bisabolene at bench scale, and the other using an alkaline pretreatment, which produced 680 mg/L of bisabolene in a high-gravity fed-batch bioreactor. Interestingly, R. toruloides was also observed to assimilate p-coumaric acid liberated from acylated grass lignin in the IL hydrolysate, a finding we verified with purified substrates. R. toruloides was also able to consume several additional compounds with aromatic motifs similar to lignin monomers, suggesting that this organism may have the metabolic potential to convert depolymerized lignin streams alongside lignocellulosic sugars.ConclusionsThis study highlights the natural compatibility of R. toruloides with bioprocess conditions relevant to lignocellulosic biorefineries and demonstrates its ability to produce non-native terpenes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0927-5) contains supplementary material, which is available to authorized users.