Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-sequencing data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ∼69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the present inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames from being regarded as protein-coding.

中文翻译：

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大豆长非编码RNA的分析揭示了小肽编码转录本的子集。

长的非编码RNA（lncRNA）定义为至少200个核苷酸长的非蛋白质转录物。众所周知，它们在调节基因表达中起着关键作用，尤其是在植物的胁迫反应过程中。我们使用了大量在不同条件下处理过的各种大豆组织（大豆组织和大豆组织）的内部转录组数据，来全面鉴定大豆lncRNA。我们还检索了足够质量和测序深度的可公开获得的大豆转录组数据，以丰富我们的分析。总共，将332个样品的RNA测序数据用于该分析。开发了一种基于参考的从头转录本整合体，该组合体鉴定了约69,000个lncRNA基因位点。我们显示，lncRNAs在长度，外显子数量，转座因子组成和整个豆类物种的序列保守水平方面均不同于蛋白质编码转录本和基因组背景噪声。lncRNA基因在某些应激条件下的组织特异性和时间特异性转录反应可能表明它们的生物学相关性。lncRNA基因位点的转录起始位点往往靠近其最接近的蛋白质编码基因，并且它们可能与蛋白质编码基因在转录上相关，特别是对于反义和内含子lncRNA。通过串联质谱从这些lncRNA基因座中鉴定出了以前未报告的小肽编码转录物子集，这为研究其功能作用铺平了道路。