Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle

Label-free based comparative proteomics approach revealed the changes in proteomic profiles driven by different maturities in two Chinese white truffles, Tuber panzhihuanense and Tuber latisporum

T. panzhihuanense and T. latisporum are white truffle species native to China, of which T. panzhihuanense has significant commercial potential, with high nutritional value and unique flavor. Maturity is an important factor affecting the nutrition and aroma of truffles, which determines their economic status. Here, a label-free-based comparative proteomics method was used to determine the proteomic profiles of T. panzhihuanense and T. latisporum at two different stages of maturity. The results showed that both maturity and species significantly affected the protein expression patterns. T. panzhihuanense responded stronger to maturity than T. latisporum, accompanied by a more complex interaction network between proteins. Some critical proteins were regulated by maturity and variety, including those involved in aroma formation, e.g., S-adenosyl-methionine synthetase. The enrichment of oxidation-reduction processes, glycolysis, and SNARE interactions in vesicular transport were driven by species and maturity. This study provides the first insights into the proteomic profiles of T. panzhihuanense and T. latisporum, revealing the roles of key proteins and biological processes in their maturation.

Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle

Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.

Investigation of the Proteomes of the Truffles Tuber albidum pico, T. aestivum, T. indicum, T. magnatum, and T. melanosporum

Truffles of the Tuber species are known as expensive foods, mainly for their distinct aroma and taste. This high price makes them a profitable target of food fraud, e.g., the misdeclaration of cheaper truffle species as expensive ones. While many studies investigated truffles on the metabolomic level or the volatile organic compounds extruded by them, research at the proteome level as a phenotype determining basis is limited. In this study, a bottom-up proteomic approach based on LC-MS/MS measurements in data-independent acquisition mode was performed to analyze the truffle species Tuber aestivum, Tuber albidum pico, Tuber indicum, Tuber magnatum, and Tuber melanosporum, and a protein atlas of the investigated species was obtained. The yielded proteomic fingerprints are unique for each of the of the five truffle species and can now be used in case of suspected food fraud. First, a comprehensive spectral library containing 9000 proteins and 50,000 peptides was generated by two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS). Then, samples of the truffle species were analyzed in data-independent acquisition (DIA) proteomics mode yielding 2715 quantified proteins present in all truffle samples. Individual species were clearly distinguishable by principal component analysis (PCA). Quantitative proteome fingerprints were generated from 2066 ANOVA significant proteins, and side-by-side comparisons of truffles were done by T-tests. A further aim of this study was the annotation of functions for the identified proteins. For Tuber magnatum and Tuber melanosporum conclusive links to their superior aroma were found by enrichment of proteins responsible for sulfur-metabolic processes in comparison with other truffles. The obtained data in this study may serve as a reference library for food analysis laboratories in the future to tackle food fraud by misdeclaration of truffles. Further identified proteins with their corresponding abundance values in the different truffle species may serve as potential protein markers in the establishment of targeted analysis methods. Lastly, the obtained data may serve in the future as a basis for deciphering the biochemistry of truffles more deeply as well, when protein databases of the different truffle species will be more complete.

Draft Genome Sequences of the Black Truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee

Tuber brumale and Tuber indicum (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. T. brumale is ubiquitous in Europe, and T. indicum is mainly found in China. Here, we present the draft genome sequences of T. brumale and T. indicum.

Tuber brumale and Tuber indicum (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. T. brumale is ubiquitous in Europe, and T. indicum is mainly found in China. Here, we present the draft genome sequences of T. brumale and T. indicum.

The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

Effects of biogenerated ferric hydroxides nanoparticles on truffle mycorrhized plants

Truffles are highly valuable ectomycorrhizal fungi that grow naturally in alkaline, calcareous soils. Iron deficiency chlorosis is a common problem in truffle (Tuber spp.) cultivation due to the high quantity of lime added to increase the pH of acidic soils. In this work, the effects of ferric hydroxide nanoparticles embedded in an exopolysaccharide (Fe-EPS NPs), extracted from cultures of Klebsiella oxytoca DSM 29614, were investigated on Quercus robur seedlings under greenhouse conditions. The plants were inoculated with Tuber borchii (the bianchetto truffle) and were cultivated with and without iron nanoparticle additions and compared with non-inoculated control plants. The seedlings were grown in limed soil in order to induce iron deficiency. Low doses of Fe-EPS NPs had a beneficial effect on the growth of the plants inoculated with T. borchii, increasing their height and reducing their leaf chlorosis 5 months after the first Fe-EPS NP treatment. Moreover, Fe-EPS NP treatments significantly increased the level of T. borchii mycorrhizal colonization and the ectomycorrhizal mantle thickness. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) applied to cross sections of mycorrhizas showed that Fe accumulated in the fungal mantle and apparently was slowly released serving as a resilient reservoir of iron for the plant. The results suggest that the application of Fe-EPS NPs is a promising technique in the production of Tuber mycorrhized plants in the nursery and could have future applications in the field.

Two ectomycorrhizal truffles, Tuber melanosporum and T. aestivum, endophytically colonise roots of non-ectomycorrhizal plants in natural environments

Serendipitous findings and studies on Tuber species suggest that some ectomycorrhizal fungi, beyond their complex interaction with ectomycorrhizal hosts, also colonise roots of nonectomycorrhizal plants in a loose way called endophytism. Here, we investigate endophytism of T. melanosporum and T. aestivum. We visualised endophytic T. melanosporum hyphae by fluorescent in situ hybridisation on nonectomycorrhizal plants. For the two Tuber species, microsatellite genotyping investigated the endophytic presence of the individuals whose mating produced nearby ascocarps. We quantified the expression of four T. aestivum genes in roots of endophyted, non-ectomycorrhizal plants. Tuber melanosporum hyphae colonised the apoplast of healthy roots, confirming endophytism. Endophytic Tuber melanosporum and T. aestivum contributed to nearby ascocarps, but only as maternal parents (forming the flesh). Paternal individuals (giving only genes found in meiotic spores of ascocarps) were not detected. Gene expression of T. aestivum in non-ectomycorrhizal plants confirmed a living status. Tuber species, and likely other ectomycorrhizal fungi found in nonectomycorrhizal plant roots in this study, can be root endophytes. This is relevant for the ecology (brûlé formation) and commercial production of truffles. Evolutionarily speaking, endophytism may be an ancestral trait in some ectomycorrhizal fungi that evolved from root endophytes.

Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments

BACKGROUND

Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments.

RESULTS

Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source.

CONCLUSIONS

Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.

Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea

Sphaerosporella brunnea is a pioneer ectomycorrhizal fungus with facultative saprophytic capacities. Here, we sequenced the genome of S. brunnea strain Sb_GMNB300, which is estimated at 51.6 Mb in size with 872 assembled contigs accounting for 12,597 predicted coding genes. This genome will be useful for comparative studies of Pezizales ectomycorrhizal symbioses.

At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.

Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery

BACKGROUND

Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).

RESULTS

The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.

CONCLUSIONS

We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.

Ascoma genotyping and mating type analyses of mycorrhizas and soil mycelia of Tuber borchii in a truffle orchard established by mycelial inoculated plants

Tuber borchii (the Bianchetto truffle) is a heterothallic Ascomycete living in symbiotic association with trees and shrubs. Maternal and paternal genotype dynamics have already been studied for the black truffles Tuber melanosporum and Tuber aestivum but not yet for T. borchii. In this study, we analysed maternal and paternal genotypes in the first truffle orchard realized with plants inoculated with five different T. borchii mycelia. Our aims were to test the persistence of the inoculated mycelia, if maternal and/or paternal genotypes correspond to inoculated mycelia and to assess the hermaphroditism of T. borchii. The mating type of each isolate as well as those of mycorrhizas, ascomata and extraradical soil mycelia was determined. Moreover, simple sequence repeat (SSR) profiles of maternal and paternal genotypes were assessed in 18 fruiting bodies to investigate the sexual behaviour of this truffle. The maternal genotypes of the fruiting bodies corresponded to those of the inoculated mycelia with only two exceptions. This confirmed that the inoculated mycelia persisted 9 years after plantation. As regards paternal partner, only two had the same genotype as those of the inoculated mycelia, suggesting hermaphroditism. Most of the new paternal genotypes originated from a recombination of those of inoculated mycelia.

Pindara revisited - evolution and generic limits in Helvellaceae

The Helvellaceae encompasses taxa that produce some of the most elaborate apothecial forms, as well as hypogeous ascomata, in the class Pezizomycetes (Ascomycota). While the circumscription of the Helvellaceae is clarified, evolutionary relationships and generic limits within the family are debatable. A robust phylogeny of the Helvellaceae, using an increased number of molecular characters from the LSU rDNA, RPB2 and EF-1α gene regions (4 299 bp) and a wide representative sampling, is presented here. Helvella s.lat. was shown to be polyphyletic, because Helvella aestivalis formed a distant monophyletic group with hypogeous species of Balsamia and Barssia. All other species of Helvella formed a large group with the enigmatic Pindara (/Helvella) terrestris nested within it. The ear-shaped Wynnella constitutes an independent lineage and is recognised with the earlier name Midotis. The clade of the hypogeous Balsamia and Barssia, and H. aestivalis is coherent in the three-gene phylogeny, and considering the lack of phenotypic characters to distinguish Barssia from Balsamia we combine species of Barssia, along with H. aestivalis, in Balsamia. The closed/tuberiform, sparassoid H. astieri is shown to be a synonym of H. lactea; it is merely an incidental folded form of the saddle-shaped H. lactea. Pindara is a sister group to a restricted Helvella, i.e., excluding the /leucomelaena lineage, on a notably long branch. We recognise Pindara as a separate genus and erect a new genus Dissingia for the /leucomelaena lineage, viz. H. confusa, H. crassitunicata, H. leucomelaena and H. oblongispora. Dissingia is supported by asci that arise from simple septa; all other species of Helvellaceae have asci that arise from croziers, with one exception being the /alpina-corium lineage of Helvella s.str. This suggests ascus development from croziers is the ancestral state for the Helvellaceae and that ascus development from simple septa has evolved at least twice in the family. Our phylogeny does not determine the evolutionary relationships within Helvella s.str., but it is most parsimonious to infer that the ancestor of the helvelloids produced subsessile or shortly stipitate, cup-shaped apothecia. This shape has been maintained in some lineages of Helvella s.str. The type species of Underwoodia, Underwoodia columnaris, is a sister lineage to the rest of the Helvellaceae.