Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

中文翻译：

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发现，鉴定和功能特征的花生中长非编码RNA。

长度通常大于200 nt的长非编码RNA（lncRNA）参与了许多生物学过程。在栽培花生（花生）中对lncRNAs的研究在很大程度上仍然未知。花生（Arachis hypogaea L.）转录组的全基因组扫描确定了1442个lncRNA，它们由分布在每个染色体上的基因座编码。长的基因间非编码RNA占这些lncRNA的85.58％。另外，在根，叶或种子中有189个lncRNA差异丰富。通常，lncRNA与mRNA相比，表达水平较低，组织特异性表达更紧密，剪接较少。具有外显子/内含子结构的lncRNA约有44.17％被剪接；该速率略低于mRNA的剪接速率。起始位点事件的转录是花生lncRNA中发生频率最高的替代剪接（AS）事件（28.05％），而内含子保留事件的发生率（30.19％）在mRNA中最高。AS改变了lncRNA的靶基因谱并增加了lncRNA的多样性和灵活性，这对于lncRNA执行其功能可能是重要的。另外，从蛋白质编码基因产生的大量花生AS同工型似乎是非编码的，因为它们是截短的转录本。此类同工型可合法地视为一类lncRNA。lncRNA的预测靶基因参与了广泛的生物学过程。此外，在盐胁迫下检查了几种选定的lncRNA及其靶基因的表达模式，结果表明，它们都能以不同方式应对盐胁迫。这项研究提供了候选lncRNA及其在整个组织中的表达模式的资源，这些lncRNA是否具有功能将在我们随后的实验中进一步研究。