title: Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome.
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.
authors.affiliation: INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France.
authors.forename: E
authors.initials: E
authors.lastname: Tisserant
authors.affiliation: CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France.
authors.forename: C
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France.
authors.forename: A
authors.initials: A
authors.lastname: Kohler
authors.affiliation: INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France.
authors.forename: E
authors.initials: E
authors.lastname: Morin
authors.affiliation: CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France.
authors.forename: P
authors.initials: P
authors.lastname: Wincker
authors.affiliation: INRA, UMR INRA/Nancy Université'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France.
authors.forename: F
authors.initials: F
authors.lastname: Martin
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D001483:Base Sequence; D018387:Codon, Initiator; D005091:Exons; D048690:Fruiting Bodies, Fungal; D015723:Gene Library; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D025282:Mycelium; D038821:Mycorrhizae; D016366:Open Reading Frames; D012331:RNA, Fungal / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods*; D020506:Untranslated Regions
chemical_list: D018387:Codon, Initiator; D012331:RNA, Fungal; D020506:Untranslated Regions