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RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’
BACKGROUND: The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifer...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712117/ https://www.ncbi.nlm.nih.gov/pubmed/29197332 http://dx.doi.org/10.1186/s12864-017-4346-6 |
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author | Harris, Zachary N. Kovacs, Laszlo G. Londo, Jason P. |
author_facet | Harris, Zachary N. Kovacs, Laszlo G. Londo, Jason P. |
author_sort | Harris, Zachary N. |
collection | PubMed |
description | BACKGROUND: The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar ‘Riesling’ to improve annotation of the grapevine reference genome sequence. RESULTS: Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS: In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4346-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5712117 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57121172017-12-06 RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ Harris, Zachary N. Kovacs, Laszlo G. Londo, Jason P. BMC Genomics Research Article BACKGROUND: The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar ‘Riesling’ to improve annotation of the grapevine reference genome sequence. RESULTS: Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS: In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4346-6) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-02 /pmc/articles/PMC5712117/ /pubmed/29197332 http://dx.doi.org/10.1186/s12864-017-4346-6 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Harris, Zachary N. Kovacs, Laszlo G. Londo, Jason P. RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title_full | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title_fullStr | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title_full_unstemmed | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title_short | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
title_sort | rna-seq-based genome annotation and identification of long-noncoding rnas in the grapevine cultivar ‘riesling’ |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712117/ https://www.ncbi.nlm.nih.gov/pubmed/29197332 http://dx.doi.org/10.1186/s12864-017-4346-6 |
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