Coupling of micro RNA ‐directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA ‐mediated gene silencing

Summary Micro RNA s (mi RNA s) and phased small interfering RNA s (phasi RNA s) play vital regulatory roles in plant growth and development. Little is known about these small RNA s in litchi ( Litchi chinensis ), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep‐sequencing techniques and in‐depth bioinformatic analyses. The genome‐wide identification of mi RNA s, their target genes, and phasi RNA ‐generating ( PHAS ) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, mi RNA ‐mediated phasi RNA production was coupled with alternative splicing (AS) and alternative polyadenylation ( APA ). Most of these loci encoded long noncoding RNA s. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS / APA , and diverse phasi RNA s generated from these isoforms appeared to target long terminal repeat ( LTR ) retrotransposons and other unrelated genes. This coupling enables phasi RNA production from different exons of noncoding PHAS genes and yields diverse phasi RNA populations, both broadening and altering the range of downstream phasi RNA ‐regulated genes. Our results reveal the diversity of mi RNA and phasi RNA in litchi, and demonstrate AS / APA as a new layer of regulation in small RNA ‐mediated gene silencing.