A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data of black truffle, Tuber melanosporum.
Dataset type: Epigenomic, Genomic, Transcriptomic
Data released on November 03, 2014
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.
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 referenced by this study):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|Aspergillus nidulans||162425||Aspergillus nidulans|| Genotype:wild type|
|ECM||39416||French truffle||Perigord truffle||Tuber melanosporum|| Body site:ectomycorrhiza|
|FB||39416||French truffle||Perigord truffle||Tuber melanosporum|| Body site:fruitbody|
|FLM||39416||French truffle||Perigord truffle||Tuber melanosporum|| Body site:mycelium|
|Neurospora crassa||5141||Neurospora crassa|| Genotype:wild type|
|Saccharomyces cerevisiae||4932||brewer's yeast||baker's yeast||Saccharomyces cerevisiae|| Genotype:wild type|
|Tuber melanosporum||39416||French truffle||Perigord truffle||Tuber melanosporum|| Genotype:wild type|
|Uncinocarpus reesii||33188||Uncinocarpus reesii|| Genotype:wild type|