Abstract
BackgroundLong 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.ResultsHere, 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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12864-015-2014-2) contains supplementary material, which is available to authorized users.
Highlights
Long non-coding RNAs are a new class of regulatory molecules with roles in diverse biological processes
Our analysis provided the first look at the Long non-coding RNAs (lncRNAs) landscape in a fruit crop and laid the foundation for future studies of lncRNA function in strawberry
Identification of F. vesca lncRNAs from flower and fruit RNA-seq datasets To globally identify lncRNAs in the F.vesca genome, we utilized RNA-seq datasets generated from 35 distinct floral and fruit tissues plus two vegetative tissues, which were isolated from a 7th generation inbred line of F. vesca (Yellow Wonder 5AF7 or YW5AF7) (Additional file 2) [41, 42]
Summary
Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While some non-coding RNAs perform housekeeping functions, such as tRNAs, rRNAs and small nuclear RNAs, others such as microRNAs and small interfering RNAs (siRNA) play critical regulatory roles during development or stress responses [3, 4]. The lncRNAs can be grouped into three subclasses: 1) long non-coding natural antisense transcripts (lnc-NATs), 2) intronic lncRNAs, and 3) intergenic lncRNAs. Like protein-coding (PC) genes, a majority of lncRNAs are transcribed by RNA polymerase II with a 5′ cap and a 3′ poly-A tail in animals [5]. LncRNAs can be transcribed by PolII, IV, and V, some may lack poly-A tails [6,7,8,9]
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