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

Author:
Tisserant, E., Da Silva, C., Kohler, A., Morin, E., Wincker, P., Martin, F.
Source:
The new phytologist 2011 v.189 no.3 pp. 883-891
ISSN:
0028-646X
Subject:
ectomycorrhizae, DNA libraries, complementary DNA, open reading frames, developmental stages, Tuber melanosporum, mycelium, codons, transcriptome, exons, fruiting bodies
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.
Agid:
506421