Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.
Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.
复制标题
DOI：
10.1186/s12864-015-2014-2
复制
发表时间：
2015-10-19
期刊：
影响因子：
4.4
通讯作者：
Liu Z
中科院分区：
文献类型：
--
作者：
Kang C;Liu Z
长链非编码RNA（longnon-codingRNAs，lncRNA）是一类新型的调控分子，在多种生物学过程中发挥重要作用。虽然已经投入了大量的努力在已建立的植物模型拟南芥，玉米和水稻的lncRNA的分析，几乎一无所知的lncRNA从水果作物，包括那些在蔷薇科。在这里，我们提出了一个基因组规模的识别和表征lncRNA从二倍体草莓，草莓，基于丰富的RNA-seq数据集从35个不同的花和果实组织。鉴定了来源于3，862个基因座的5，884个Fve-lncRNA。这些lncRNA基于表达水平以及它们是否包含重复序列或产生小RNA而被仔细分类。其中约四分之一被称为高置信度lncRNA（hc-lncRNA），因为它们以高于2的FPKM水平表达，并且既不产生小RNA也不包含重复序列。为了鉴定lncRNA与其潜在的蛋白质编码（PC）基因靶标之间的调控相互作用，基于其表达鉴定具有正相关或负相关表达趋势的lncRNA和PC基因对;这些对可能是顺式或反式作用lncRNA及其靶标的候选者。最后，植物物种内的blast搜索表明lncRNA并不保守。我们的研究鉴定了大量的组织特异性表达的lncRNA在F。vesca，从而强调了它们对草莓花和果实发育的潜在贡献，并为未来的功能研究铺平了道路。本文的在线版本（doi：10.1186/s12864-015-2014-2）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12864-015-2014-2) contains supplementary material, which is available to authorized users.