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

Tisserant, E., Da Silva, C., Kohler, A., Morin, E., Wincker, P., Martin, F.
The new phytologist 2011 v.189 no.3 pp. 883-891
ectomycorrhizae, DNA libraries, complementary DNA, open reading frames, developmental stages, Tuber melanosporum, mycelium, codons, transcriptome, exons, fruiting bodies
• 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.