title: In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits.
abstract: The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. We report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, we investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Our strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, our work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.
authors.affiliation: Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, Portici (NA), Italy.
authors.forename: Daria
authors.initials: D
authors.lastname: Scarano
authors.affiliation: Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, Portici (NA), Italy.
authors.forename: Rosa
authors.initials: R
authors.lastname: Rao
authors.affiliation: Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, Portici (NA), Italy.
authors.forename: Giandomenico
authors.initials: G
authors.lastname: Corrado
mesh_terms: D017398:Alternative Splicing; D020451:Contig Mapping; D005638:Fruit / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics*; D058977:Molecular Sequence Annotation; D011110:Polymorphism, Genetic; D018749:RNA, Plant / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D059467:Transcriptome
chemical_list: D018749:RNA, Plant; D022661:RNA, Untranslated