LncRNA 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。lncRNA 的表达水平受到压力或发育线索的显着影响。最近的研究表明,lncRNA参与了番茄和草莓的果实发育和成熟过程;然而,在其他肉质水果中,lncRNA 与果实成熟之间的关联在很大程度上仍然难以捉摸。在这里,我们从三种不同的桃(Prunus persica)果实发育阶段,包括第一和第二指数阶段以及果实成熟阶段。根据生物信息学分析,总共获得了来自 887 个位点的 1500 个可信的 lncRNA。与编码蛋白质的 mRNA 相比,桃果实中鉴定的 lncRNA 表现出明显的特征,包括较低的表达水平、较低的选择性剪接复杂性、较短的亚型和较少的外显子数量。表达分析确定了 575 个差异表达的 lncRNAs (DELs),分为 6 个簇,其中簇 1、2、4 和 5 的成员推测与果实发育和成熟过程相关。定量实时 PCR 显示,DEL 确实在桃果实中具有特定阶段的表达模式。GO和KEGG富集分析表明,DELs可能与果实成熟相关的生理和代谢变化有关,如黄酮类生物合成、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lncRNA的相似性分析表明lncRNA的序列保守性较低。我们的研究报告了大量水果表达的lncRNA,并确定了水果发育阶段特异性表达的lncRNA成员,突出了它们在水果发育和成熟过程中的潜在功能,为未来的功能研究奠定了基础。不同植物物种内lncRNA的相似性分析表明lncRNA的序列保守性较低。我们的研究报告了大量水果表达的lncRNA,并确定了水果发育阶段特异性表达的lncRNA成员,突出了它们在水果发育和成熟过程中的潜在功能,为未来的功能研究奠定了基础。不同植物物种内lncRNA的相似性分析表明lncRNA的序列保守性较低。我们的研究报告了大量水果表达的lncRNA,并确定了水果发育阶段特异性表达的lncRNA成员,突出了它们在水果发育和成熟过程中的潜在功能,为未来的功能研究奠定了基础。
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Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening
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.