Coupling of microRNA-directed phasiRNA generation with alternative splicing in small RNA-mediated gene silencing

Purpose:We aimed to characterize genome-widely the miRNA population and phasiRNA-generating genes/loci in litchi (Litchi chinensis). Multiple high throughput sequencing strategies, including sRNA sequencing, parallel analysis of RNA ends (PARE) sequencing, and strand-specific RNA-seq, were applied in combination with thorough bioinformatics analyses using a variety of computational methods. 6 tissues sRNA libraries were builtin lithi, including: fruit pedicel, fruitlet, leaf, root, stem shoot and flower; 4 parallel analysis of RNA ends (PARE) libraries were built, including mixed (equal amounts of RNA from all tissues), pedicel, flower and fruitlet;Two strand-specific RNA-seq (ssRNA-seq) libraries were generated for the flower tissues