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

GigaScience

Matteo Pellegrini²  Simone Ottonello¹  David Lopez²  Artur Jaroszewicz²  Marco Morselli¹  Wen-Wei Liao³  Barbara Montanini¹  Pao-Yang Chen² 

[1] Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma 43124, Italy;Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA;Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan

关键词: Genome plasticity;    5-azacytidine;    Transposon expression;    Copy number variation;    Methylome;    Whole-genome bisulfite sequencing;    Transposable elements;    Pezizomycetes;    Ascomycete truffle;    Tuber melanosporum;    DNA methylation;   

Others  :  1118578
DOI  :  10.1186/2047-217X-3-25

 received in 2014-07-30, accepted in 2014-10-16,  发布年份 2014

【 摘 要 】

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.

Findings

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.

【 授权许可】

   
2014 Chen et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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