Expression and biogenesis analysis of 21-nt and 24-nt phased small interfering RNAs in maize tissues

Abstract

Abstract Phased secondary small interfering RNAs (phasiRNAs) are generated by double-stranded RNA (dsRNAs), which are cleaved by Dicer as a phase set. So far, hundreds of 21-nt and 24-nt phasiRNAs have been identified in male reproductive organs of rice and maize. Whereas, the expression profile of phasiRNAs among maize tissues is still exclusive. In this study, to identify 21-nt and 24-nt phasiRNAs among tissues, about 600 million signatures from nine tissues were got including root, seedling, embryo, pollen, anther, immature tassel, immature ear, premature ear and silk. As a result, 269 and 135 21-nt and 24-nt PHAS (phasiRNA precursors) loci were identified, respectively. Interestingly, except male tissues, 21-nt and 24-nt phasiRNAs also were identified in immature ear and silk, respectively, which highly overlapped with those characterized in male reproductive organs. But few phasiRNAs were identified in root, seedling and embryo. 93.4% and 81.3% of 21-nt and 24-nt PHAS loci contained 22-nt motif which matched well with miR2118 and miR2275, respectively. The expression levels of miR2118 and miR2275 in tissues accorded well with that of phasiRNAs. Finally, we found that DCL1 might be the direct Dicer nuclease to promote the maturation of 22-nt miR2118 and miR2275 in maize, because the levels of miR2118 and miR2275 were reduced in seedling and tassel primordia of dcl1 mutants. We provided profiling information of 21-nt and 24-nt phasiRNAs among tissues in maize. It could be helpful to understand the biogenesis of phasiRNAs in maize.