Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.

中文翻译：

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集成注释和来自47种不同植物的小RNA产生基因座的分析。

植物内源小RNA（sRNA）是基因表达的重要调节剂。植物sRNA分为两大类：microRNA（miRNA）和内源性短干扰RNA（siRNA）。MicroRNA基因座的注释相对较好，但仅占总sRNA库的一小部分。siRNA基因座注释已远远落后。在这里，我们使用了已发布和新生成的sRNA测序数据的大数据集（1333 sRNA-seq库包含200亿个读数）和统一的生物信息流水线来生成47种不同植物的全面sRNA基因座注释，产量超过270万sRNA基因座。两种最大量的siRNA基因座分别主要产生24和21核苷酸（nt）siRNA。大多数情况下，以24nt为主的siRNA基因座发生在基因间区域，特别是在蛋白质编码基因的5'侧翼区域。相比之下，21-nt为主的siRNA基因座最常来自剪接的mRNA复制的双链RNA前体。遗传21-nt为主的基因座尤其是从疾病抗性基因（包括大量单子叶植物）中获得。所有类型的单个siRNA序列在物种间的保守性都非常低，而成熟的miRNA更有可能被保守。我们开发了一个Web服务器，可以免费访问我们的数据以及一些搜索和分析工具。所有类型的单个siRNA序列在物种间的保守性都很小，而成熟的miRNA更有可能被保守。我们开发了一个Web服务器，可以免费访问我们的数据以及一些搜索和分析工具。所有类型的单个siRNA序列在物种间的保守性都非常低，而成熟的miRNA更有可能被保守。我们开发了一个Web服务器，可以免费访问我们的数据以及一些搜索和分析工具。