ArticlePloS one2017
In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- Virus-InducedPlants (Basel, Switzerland) · 2024Article
- Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation.Plant physiology · 2020Article
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- Article
- Tomato lncRNA23468 functions as a competing endogenous RNA to modulateHorticulture research · 2019Article
- Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato.Frontiers in plant science · 2019Article
- Arabidopsis thaliana ambient temperature responsive lncRNAs.BMC plant biology · 2018Article
- Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Long Noncoding RNAs and mRNA Regulation in Peripheral Blood Mononuclear Cells of Patients with Chronic Obstructive Pulmonary Disease.Mediators of inflammation · 2018Article
- Plant-to-plant communication triggered by systemin primes anti-herbivore resistance in tomato.Scientific reports · 2017Article
- Article
- New technologies accelerate the exploration of non-coding RNAs in horticultural plants.Horticulture research · 2017Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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