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Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

BACKGROUND: Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit c...

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Autores principales: Kang, Chunying, Liu, Zhongchi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617481/
https://www.ncbi.nlm.nih.gov/pubmed/26481460
http://dx.doi.org/10.1186/s12864-015-2014-2
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author Kang, Chunying
Liu, Zhongchi
author_facet Kang, Chunying
Liu, Zhongchi
author_sort Kang, Chunying
collection PubMed
description BACKGROUND: Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those in the Rosaceae family. RESULTS: Here, we present a genome-scale identification and characterization of lncRNAs from a diploid strawberry, Fragaria vesca, based on rich RNA-seq datasets from 35 different flower and fruit tissues. 5,884 Fve-lncRNAs derived from 3,862 loci were identified. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. About one fourth of them are termed high-confidence lncRNAs (hc-lncRNAs) because they are expressed at a level of FPKM higher than 2 and produce neither small RNAs nor contain repetitive sequence. To identify regulatory interactions between lncRNAs and their potential protein-coding (PC) gene targets, pairs of lncRNAs and PC genes with positively or negatively correlated expression trends were identified based on their expression; these pairs may be candidates of cis- or trans-acting lncRNAs and their targets. Finally, blast searches within plant species indicate that lncRNAs are not well conserved. CONCLUSIONS: Our study identifies a large number of tissue-specifically expressed lncRNAs in F. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2014-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-46174812015-10-24 Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development Kang, Chunying Liu, Zhongchi BMC Genomics Research Article BACKGROUND: Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those in the Rosaceae family. RESULTS: Here, we present a genome-scale identification and characterization of lncRNAs from a diploid strawberry, Fragaria vesca, based on rich RNA-seq datasets from 35 different flower and fruit tissues. 5,884 Fve-lncRNAs derived from 3,862 loci were identified. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. About one fourth of them are termed high-confidence lncRNAs (hc-lncRNAs) because they are expressed at a level of FPKM higher than 2 and produce neither small RNAs nor contain repetitive sequence. To identify regulatory interactions between lncRNAs and their potential protein-coding (PC) gene targets, pairs of lncRNAs and PC genes with positively or negatively correlated expression trends were identified based on their expression; these pairs may be candidates of cis- or trans-acting lncRNAs and their targets. Finally, blast searches within plant species indicate that lncRNAs are not well conserved. CONCLUSIONS: Our study identifies a large number of tissue-specifically expressed lncRNAs in F. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2014-2) contains supplementary material, which is available to authorized users. BioMed Central 2015-10-19 /pmc/articles/PMC4617481/ /pubmed/26481460 http://dx.doi.org/10.1186/s12864-015-2014-2 Text en © Kang and Liu. 2015 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
Kang, Chunying
Liu, Zhongchi
Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title_full Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title_fullStr Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title_full_unstemmed Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title_short Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development
title_sort global identification and analysis of long non-coding rnas in diploid strawberry fragaria vesca during flower and fruit development
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617481/
https://www.ncbi.nlm.nih.gov/pubmed/26481460
http://dx.doi.org/10.1186/s12864-015-2014-2
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