Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Sci Rep. 2022 Jun 30;12(1):11044. doi: 10.1038/s41598-022-15330-3.
LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.
长链非编码 RNA 代表一类长度超过 200 个核苷酸（nt）的 RNA 转录本，没有明显的蛋白质编码潜力。lncRNAs 的表达水平受应激或发育线索的显著影响。最近的研究表明，lncRNAs 参与了番茄和草莓的果实发育和成熟过程；然而，在其他肉质果实中，lncRNAs 与果实成熟之间的关联在很大程度上仍未被揭示。在这里，我们从三个不同的桃（Prunus persica）果实发育阶段构建了 9 个 ssRNA-Seq 文库，包括第一和第二指数阶段和果实成熟阶段。总共根据生物信息学分析获得了 887 个位点的 1500 个置信 lncRNAs。与蛋白质编码 mRNA 相比，在桃果实中鉴定出的 lncRNAs 具有明显的特征，包括表达水平较低、选择性剪接的复杂性较低、同工型较短和外显子数量较少。表达分析鉴定出 575 个差异表达的 lncRNA（DEL）分为 6 个簇，其中簇 1、2、4 和 5 的成员被推测与果实发育和成熟过程有关。实时定量 PCR 显示，DEL 在桃果实中确实具有阶段特异性的表达模式。GO 和 KEGG 富集分析表明，DEL 可能与果实成熟相关的生理和代谢变化有关，如类黄酮生物合成、果实质地软化、叶绿素分解和香气化合物积累。最后，不同植物物种内 lncRNAs 的相似性分析表明 lncRNAs 的序列保守性较低。我们的研究报告了大量的果实表达 lncRNAs，并鉴定了果实发育阶段特异性表达的 lncRNA 成员，这突出了它们在果实发育和成熟过程中的潜在功能，并为未来的功能研究奠定了基础。
