Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.

中文翻译：

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植物中由长链非编码 RNA 编码的大量谱系特异性微生物蛋白

真核生物基因组的普遍转录导致长链非编码 RNA (lncRNA) 的表达，其中大部分在进化中保守性差，似乎没有功能。然而，一些 lncRNA 已被证明具有特定的功能，特别是转录调节。位于 lncRNA 上的数千个小的开放阅读框（smORF，<100 个密码子）可能被翻译成肽或微生物蛋白。我们报告了对来自苔藓 Physcommitrium patens 的 lncRNAs-smORFs 在 479 个植物物种的转录组中的保护和进化轨迹的综合分析。尽管数以千计的 smORF 受到大量纯化选择，但大多数 smORF 似乎是进化的年轻基因，可能代表功能创新的主要库。使用纳米孔 RNA 测序，我们表明，平均而言，保守 smORF 的转录水平高于非保守 smORF。蛋白质组学分析证实了 82 种新的物种特异性 smORF 的翻译。鉴定了许多包含低复杂性区域 (LCR) 或跨膜结构域的保守 smORF，并通过实验证明了所选 LCR-smORF 的生物学功能。因此，由 smORFs 编码的微生物蛋白是植物蛋白质组中一个主要的、功能多样的成分。实验证明了选定的 LCR-smORF 的生物学功能。因此，由 smORFs 编码的微生物蛋白是植物蛋白质组中一个主要的、功能多样的成分。实验证明了选定的 LCR-smORF 的生物学功能。因此，由 smORFs 编码的微生物蛋白是植物蛋白质组中一个主要的、功能多样的成分。