BRC Bioinformatics Facility Cornell University, Ithaca, 14850, USA.
Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
BMC Plant Biol. 2018 May 4;18(1):75. doi: 10.1186/s12870-018-1300-y.
Long non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. There is growing evidence that they are associated with development; but their expression and regulation during fruit ripening in the model plant tomato (Solanum lycopersicum) has yet to be described.
Following integration of 134 RNA-seq data sets, we identified 79,322 putative lncRNAs, consisting of 70,635 lincRNAs, 8085 antisense non-coding RNAs (ancRNAs) and 602 sense lncRNAs (slncRNAs). lncRNAs had specific features that are distinct from mRNAs, including tissue-specificity, and shorter and fewer exons. Notably, more than 5000 of the novel lincRNAs were found to be expressed across the mature green (MG), breaker (BR) and breaker plus 7 days (BR + 7) developmental stages. The differently expressed lincRNAs had different DNA methylation profiles from the mRNAs.
Integrating transcriptome datasets and genome-wide screening enabled the identification of a comprehensive set of tomato lncRNAs. Here, we found that the lncRNAs DNA methylation profiles were different from those of mRNAs. This will help future investigation of lncRNA function, especially for the dissection of the molecular mechanisms involved in the regulation of fruit development.
长非编码 RNA（lncRNA）参与哺乳动物和植物的多种生物学过程。越来越多的证据表明，它们与发育有关；但它们在模式植物番茄（Solanum lycopersicum）果实成熟过程中的表达和调控尚未被描述。
整合了 134 个 RNA-seq 数据集后，我们鉴定了 79322 个推定的 lncRNA，包括 70635 个 lincRNA、8085 个反义非编码 RNA（ancRNA）和 602 个正义 lncRNA（slncRNA）。lncRNA 具有与 mRNAs 不同的特定特征，包括组织特异性、较短的外显子和较少的外显子。值得注意的是，超过 5000 个新的 lincRNA 在成熟绿（MG）、破裂（BR）和破裂加 7 天（BR+7）发育阶段表达。差异表达的 lincRNA 的 DNA 甲基化模式与 mRNAs 不同。
整合转录组数据集和全基因组筛选，使我们能够鉴定出一套全面的番茄 lncRNA。在这里，我们发现 lncRNA 的 DNA 甲基化模式与 mRNAs 不同。这将有助于对 lncRNA 功能的未来研究，特别是对涉及果实发育调控的分子机制的剖析。
