A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.
BACKGROUND
Tuber melanosporum, also known in the gastronomic community as "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. Thus, it was of interest to examine if and how T. melanosporum exploits DNA methylation to maintain genome integrity.


RESULTS
We performed whole-genome DNA bisulfite sequencing and mRNA sequencing 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 uncovered multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs, almost exclusively in free-living mycelium propagated in vitro. 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.


CONCLUSIONS
The datasets presented here 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 subphylum, Pezizomycotina. Evidence derived from comparative methylome and transcriptome analyses indicates that a non-exhaustive and partly reversible methylation process operates in truffles.
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan ; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Pao-Yang
PY
Chen
Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma 43124, Italy.
Barbara
B
Montanini
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
Wen-Wei
WW
Liao
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA ; Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma 43124, Italy.
Marco
M
Morselli
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Artur
A
Jaroszewicz
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
David
D
Lopez
Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma 43124, Italy.
Simone
S
Ottonello
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Matteo
M
Pellegrini
5-azacytidine; Ascomycete truffle; Copy number variation; DNA methylation; Genome plasticity; Methylome; Pezizomycetes; Transposable elements; Transposon expression; Tuber melanosporum; Whole-genome bisulfite sequencing