High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.
高通量RNA测序技术大大加快了发现未知RNA的过程。近年来小RNA的种类在不断扩增，除了已知的一些小RNA，例如microRNA（miRNA），Piwi-interacting RNA（piRNA）和小核仁RNA（snoRNA）外，最近一系列研究集中在两种全新的小RNA： tRNA来源的小RNA（tsRNA）以及rRNA来源的小RNA（rsRNA）。由于现有的小RNA注释工具主要集中用于分析miRNA或者piRNA，对其他新型小RNA的支持并不完善。为了同时注释多种小RNA，特别是针对tsRNA和rsRNA，本文开发了SPORTS1.0（small RNA annotation pipeline optimized for rRNA- and tRNA- derived small RNAs）作为优化的小RNA注释工具。此外，SPORTS1.0还能通过RNA序列错配预测潜在的RNA修饰位点。为了方便用户使用，SPORTS1.0提供了广达68个物种（横跨动、植物及微生物）的预编译注释数据库，同时用户也可以自定义注释所用的数据库。作为举例，本文利用SPORTS1.0分析发现，tsRNA和rsRNA存在于不同小鼠细胞类型中并各自具有独特的分布模式。此外，本文还发现相较于其他小RNA，tsRNA具有更高的错配率，这与tRNA中具有更高的RNA修饰比率相符。SPORTS1.0是一款开源软件并可下载自https://github.com/junchaoshi/sports1.0。





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