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. 2011 Feb;189(3):883-891.
doi: 10.1111/j.1469-8137.2010.03597.x.

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

E Tisserant  1 , C Da Silva  2 , A Kohler  1 , E Morin  1 , P Wincker  2 , F Martin  1
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Free article

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

E Tisserant et al. New Phytol. 2011 Feb.
Free article

Abstract

• The functional complexity of the Tuber melanosporum transcriptome has not yet been fully elucidated. Here, we applied high-throughput Illumina RNA-sequencing (RNA-Seq) to the transcriptome of T. melanosporum at different major developmental stages, that is free-living mycelium, fruiting body and ectomycorrhiza. • Sequencing of cDNA libraries generated a total of c. 24 million sequence reads representing > 882 Mb of sequence data. To construct a coverage signal profile across the genome, all reads were then aligned to the reference genome assembly of T. melanosporum Mel28. • We were able to identify a substantial number of novel transcripts, antisense transcripts, new exons, untranslated regions (UTRs), alternative upstream initiation codons and upstream open reading frames. • This RNA-Seq analysis allowed us to improve the genome annotation. It also provided us with a genome-wide view of the transcriptional and post-transcriptional mechanisms generating an increased number of transcript isoforms during major developmental transitions in T. melanosporum.

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