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In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits
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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302821/ https://www.ncbi.nlm.nih.gov/pubmed/28187155 http://dx.doi.org/10.1371/journal.pone.0171504 |
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author | Scarano, Daria Rao, Rosa Corrado, Giandomenico |
author_facet | Scarano, Daria Rao, Rosa Corrado, Giandomenico |
author_sort | Scarano, Daria |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5302821 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-53028212017-02-28 In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits Scarano, Daria Rao, Rosa Corrado, Giandomenico PLoS One Research Article 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. Public Library of Science 2017-02-10 /pmc/articles/PMC5302821/ /pubmed/28187155 http://dx.doi.org/10.1371/journal.pone.0171504 Text en © 2017 Scarano et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Scarano, Daria Rao, Rosa Corrado, Giandomenico In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title | In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title_full | In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title_fullStr | In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title_full_unstemmed | In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title_short | In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits |
title_sort | in silico identification and annotation of non-coding rnas by rna-seq and de novo assembly of the transcriptome of tomato fruits |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302821/ https://www.ncbi.nlm.nih.gov/pubmed/28187155 http://dx.doi.org/10.1371/journal.pone.0171504 |
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