Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Abstract

The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.

Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray

“…Fully developed Tuber melanosporum ectomycorrhizae and non-mycorrhizal root tips from the root systems of 1 year and a half old hazel plantlets (Corylus avellana L.), previously inoculated by a T. melanosporum mycelium slurry produced from a fruiting body (Martin et al 2010), and grown in the AGRITRUFFE greenhouse facilities (Saint-Maixant, France) have been sampled under a stereomicroscope. A section of one ectomycorrhiza representative of those used in this work is shown in Supplementary Fig.…”

“…Large-scale transcriptomic data were previously obtained from a T. melanosporum custom-exon expression array (4 × 72 K) manufactured by Roche Nimblegen Systems Limited (Madison, WI, USA) and from massive cDNA sequencing, with Illumina technology, of the samples of the free living mycelium and ectomycorrhizae, as described in detail in Martin et al (2010). Quantitative RT-PCR (RT-qPCR) experiments were conducted to validate the large-scale transcriptomic results.…”

“…The expression of PCWDEs in T. melanosporum was carried out for three growth conditions (ectomycorrhizal root tips; fruiting bodies and free-living mycelium) using RNA-Seq and cDNA arrays, as described in Martin et al (2010). These analyses have shown that several of these genes are regulated during the symbiotic stage (Martin et al 2010; Table 2).…”

“…It has recently been reported that the genomes of the ectomycorrhizal fungi Laccaria bicolor and Tuber melanosporum contain a reduced gene set involved in the production of enzymes that are active on plant cell-wall polysaccharides (Martin et al , 2010, in comparison with saprotrophic and pathogenic fungi (Martin and Selosse 2008). A reduced set of plant cell-wall degrading enzymes (PCWDEs) has also been reported for Amanita bisporigena by Nagendran et al (2009), who showed that this ectomycorrhizal fungus lacks the genomic potential to biosynthesize many extracellular enzymes that are active on the linkages in the plant cell wall and, in particular, exhibits a loss of several key cellulase genes.…”

“…This specific plant-fungus interaction has here been focused on as the hazelnut tree is a typical host plant for truffles, and in fact, it has also been used to analyse the T. melanosporum transcriptome during the symbiotic stage (Martin et al 2010;Tisserant et al 2011). Genes encoding putative PCWDEs were identified in the T. melanosporum genome, and previous large-scale transcriptomics data (Martin et al 2010) of candidate genes were validated, using RT-qPCR, on C. avellana/T.…”