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Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content

Barbara Montanini1, Pao-Yang Chen23, Marco Morselli15, Artur Jaroszewicz3, David Lopez3, Francis Martin4, Simone Ottonello1* and Matteo Pellegrini3*

Author Affiliations

1 Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma 43124, Italy

2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan

3 Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles 90095, CA, USA

4 Ecogenomics of Interactions’ Lab, UMR “Tree-Microbe Interactions” INRA-Nancy, Champenoux 54180, France

5 Present address: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles 90095, CA, USA

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Genome Biology 2014, 15:411  doi:10.1186/s13059-014-0411-5

Published: 31 July 2014

Additional files

Additional file 1:

Supplementary Tables S1 to S4 and all supplementary figures.

Format: DOCX Size: 2.3MB Download file

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Additional file 2:

Table S5, which lists TE methylation and expression data.

Format: XLSX Size: 2MB Download file

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Additional file 3:

Table S6, which lists gene methylation and expression data.

Format: XLSX Size: 784KB Download file

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Additional file 4:

The source Python and R scripts as well as a brief manual for CRI computation.

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Additional file 5:

The 10 output CRI files used to generate the plots shown in Figure S13A,B in Additional file 1.

Format: ZIP Size: 306KB Download file

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