mobileRNA: a tool for efficient analysis of mobile RNA molecules in multiple genomes.

In plants, mobile RNA molecules play a significant role in long distance signalling, with evidence of transport mechanisms and functional roles for both mobile messenger RNA (mRNA) and small RNA (sRNA) molecules. The movement of RNAs between distant tissues can be revealed in plant grafting experiments involving different genotypes (hetero-grafting) associated to genomic analysis, using the natural polymorphisms between the genotypes to discriminate between RNAs produced in the sampled tissue from those which have travelled from distant organs. However, the hight level of noise in the analyses of RNA sequencing datasets involving two different genotypes, and the lack of a standardised pipeline for the analysis of grafted plants, make the identification of natural mobile RNA molecules a challenge. Here, we introduce a pipeline integrated into an R package, mobileRNA, which performs simultaneous alignment of RNA sequencing samples on a merged reference genome. Using simulated datasets, we show that mobileRNA can identify putative mobile RNAs with unprecedented efficiency in absence of post-processing steps.