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In plants, however, lncRNAs can be transcribed by PolII, IV, and V, therefore some may lack poly-A tails. 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. The lncRNAs can be grouped into three subclasses: 1) long non-coding natural antisense transcripts (lnc-NATs), 2) intronic lncRNAs, and 3) intergenic lncRNAs. Non-coding RNAs with a length greater than 200bp are defined as long non-coding RNAs (lncRNAs). 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. With the advent of new genomic techniques such as tiling arrays and next generation sequencing, non-coding RNAs are increasingly identified and recognized as an integral and functional component of the genome. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies. Our study identifies a large number of tissue-specifically expressed lncRNAs in F. Finally, blast searches within plant species indicate that lncRNAs are not well conserved.
KIT CAT XLOC PC
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. 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. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. 5,884 Fve-lncRNAs derived from 3,862 loci were identified.
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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. 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.
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Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes.