mobileRNA：基于多基因组比对的移动 RNA 自动识别工具
mobileRNA : an integrative, automated tool for accurate identification of mobile RNA molecules based on multiple genome mapping
研究团队发布自动化流程 mobileRNA，通过将 RNA 测序数据同时比对到合并参考基因组，识别嫁接植物中跨细胞移动的 mRNA 和小 RNA。作者用模拟嫁接组合验证该方法并与其他方法比较；应用于真实数据时，结果与已有移动 mRNA 注释重叠很少，这与近期质疑既往移动 mRNA 可靠性的研究一致。团队还引入基因组可映射性指数作为检测成功可能性的判据，发现基于 SNP 或两步比对的方法受错误和可映射性差的限制，而进化距离较大的跨物种嫁接更具优势。
来源：Nucleic Acids Research · doi.org
RNA molecules can act as intercellular signals, with evidence of transport for both messenger RNA (mRNA) and small RNA over long distances. Such molecules that move from the cell in which they originated are termed mobile RNA. In grafted plants, when different genotypes are joined together, the movement of RNAs between tissues can be revealed by approaches that exploit natural polymorphisms between the genomes involved. However, current methods suffer from a high level of technological noise, and the lack of standardized approaches makes it challenging for researchers to robustly identify mobile RNA molecules. Here, we introduce an automated pipeline, mobileRNA, which uses a multi-genome approach based on simultaneous alignment of RNA sequencing data to merged reference genomes. We validated our approach using simulated grafting combinations and compared to other methods. When applying mobileRNA to real data, we find poor overlap to existing mobile mRNA annotations, consistent with recent studies that question the reliability of previously reported mobile mRNAs. Introducing a genome mappability index as a criterion for the likely success of detecting mobile RNAs, we find that SNP-based or two-step mapping approaches are inherently limited due to errors and poor mappability compared to cross-species grafting with large evolutionary distances.