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Data released on November 03, 2014

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data of black truffle, Tuber melanosporum.

Chen, P; Jaroszewicz, A; Liao, W; Lopez, D; Montanini, B; Morselli, M; Ottonello, S; Pellegrini, M (2014): A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data of black truffle, Tuber melanosporum. GigaScience Database. RIS BibTeX Text

Tuber melanosporum, a plant-symbiotic macrofungus and a highly appreciated gastronomic delicacy (“truffle”), features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (>58%). The main purpose of DNA methylation in fungi is TE silencing. As obligate outcrossing organisms, truffles are bound to a sexual mode of propagation, which together with TEs is thought to represent a major force driving the evolution of DNA methylation. It was thus of interest to examine if and how T. melanosporum exploits DNA methylation to maintain genome integrity.
We performed whole-genome DNA bisulfite sequencing (BS-seq) and mRNA sequencing (RNA-seq) on different developmental stages of T. melanosporum; namely, fruitbody (“truffle”), free-living mycelium and ectomycorrhiza. The data revealed a high rate of cytosine methylation (>44%), selectively targeting TEs rather than genes with a strong preference for CpG sites. Whole genome DNA sequencing (WG-seq) uncovered multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs, almost exclusively in in-vitro propagated free-living mycelium. Treatment of mycelia with 5-azacytidine partially reduced DNA methylation and increased TE transcription. Our transcriptome assembly also resulted in the identification of a set of novel transcripts from 614 genes. The present datasets provide valuable and comprehensive (epi)genomic information that can be of interest for evolutionary genomics studies of multicellular (filamentous) fungi, in particular Ascomycetes belonging to the Pezizomycotina.

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Read the peer-reviewed publication(s):

Chen, P.-Y., Montanini, B., Liao, W.-W., Morselli, M., Jaroszewicz, A., Lopez, D., … Pellegrini, M. (2014). A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum. GigaScience, 3(1). doi:10.1186/2047-217x-3-25
Montanini, B., Chen, P.-Y., Morselli, M., Jaroszewicz, A., Lopez, D., Martin, F., … Pellegrini, M. (2014). Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome Biology, 15(8). doi:10.1186/s13059-014-0411-5

Accessions (data not in GigaDB):

GEO: GSE49700

Genomic, Epigenomic, Transcriptomic

Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Aspergillus nidulans162425  Aspergillus nidulans Genotype:wild type
ECM39416French trufflePerigord truffleTuber melanosporum Body site:ectomycorrhiza
Genotype:wild type
FB39416French trufflePerigord truffleTuber melanosporum Body site:fruitbody
Genotype:wild type
FLM39416French trufflePerigord truffleTuber melanosporum Body site:mycelium
Genotype:wild type
Neurospora crassa5141  Neurospora crassa Genotype:wild type
Saccharomyces cerevisiae4932brewer's yeastbaker's yeastSaccharomyces cerevisiae Genotype:wild type
Tuber melanosporum39416French trufflePerigord truffleTuber melanosporum Genotype:wild type
Uncinocarpus reesii33188  Uncinocarpus reesii Genotype:wild type
Displaying 1-8 of 8 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Aspergillus nidulansRepeat sequenceFASTA1.13 MB2014-10-08
ECMOtherUNKNOWN593.64 MB2014-10-08
ECMAlignmentsBAM2.72 GB2014-10-08
ECMOtherUNKNOWN180.63 MB2014-10-08
ECMOtherWIG11.33 MB2014-10-08
ECMOtherWIG12.01 MB2014-10-08
ECMOtherWIG46.64 MB2014-10-08
FBOtherUNKNOWN1.01 GB2014-10-08
FBAlignmentsBAM13.99 GB2014-10-08
FBOtherUNKNOWN350.56 MB2014-10-08
Displaying 1-10 of 46 File(s).

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