Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots

Abstract

In grasses, two pathways that generate diverse and numerous 21-nt (premeiotic) and 24-nt (meiotic) phased siRNAs are highly enriched in anthers, the male reproductive organs. These "phasiRNAs" are analogous to mammalian piRNAs, yet their functions and evolutionary origins remain largely unknown. The 24-nt meiotic phasiRNAs have only been described in grasses, wherein their biogenesis is dependent on a specialized Dicer (DCL5). To assess how evolution gave rise to this pathway, we examined reproductive phasiRNA pathways in nongrass monocots: garden asparagus, daylily, and lily. The common ancestors of these species diverged approximately 115-117 million years ago (MYA). We found that premeiotic 21-nt and meiotic 24-nt phasiRNAs were abundant in all three species and displayed spatial localization and temporal dynamics similar to grasses. The miR2275-triggered pathway was also present, yielding 24-nt reproductive phasiRNAs, and thus originated more than 117 MYA. In asparagus, unlike in grasses, these siRNAs are largely derived from inverted repeats (IRs); analyses in lily identified thousands of precursor loci, and many were also predicted to form foldback substrates for Dicer processing. Additionally, reproductive phasiRNAs were present in female reproductive organs and thus may function in both male and female germinal development. These data describe several distinct mechanisms of production for 24-nt meiotic phasiRNAs and provide new insights into the evolution of reproductive phasiRNA pathways in monocots.

Intercellular delivery of small RNAs in plant gametes

“…Besides heterochromatic siRNAs, phasiRNAs, generated from noncoding TAS transcripts (Allen et al ., ) in a miRNA‐triggered phase manner, have been widely detected in plants. Recently, a class of phasiRNAs, analogous to mammalian piRNAs, has been shown to play an essential role in the proper progression of meiosis in monocots (Zhai et al ., ; Fei et al ., ; Kakrana et al ., ).…”

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA‐dominated PHAS loci

“…The discovery of 24 nt‐dominated PHAS loci in maize (Zhai, Bischof, et al., ; Zhai, Zhang, et al., ), rice (Song et al., ), asparagus, daylily, and lily (Kakrana et al., ) opened up the possibility that these loci exist in other species, even distantly related eudicots. However, 24 nt‐dominated hc‐siRNA loci are widespread in land plant genomes (Ghildiyal & Zamore, ).…”

“…The targets of these 24 nt phasiRNAs are unknown, but they are apparently necessary for proper male gametogenesis (Ono et al., ). 24 nt‐dominated PHAS loci were also described in the non‐grass monocots asparagus, lily, and daylily (Kakrana et al., ). These phasiRNAs are produced from processing of inverted repeat (IR) RNAs, instead of the double‐stranded RNA precursors observed in rice and maize (Kakrana et al., ).…”

“…21–22 nt phasiRNA‐producing loci ( PHAS ) are clearly represented in all land plants that have been sequenced thus far (Fei et al., ; Zheng, Wang, Wu, Ding, & Fei, ). However, 24 nt‐dominated PHAS loci are only currently described in rice (Song et al., ), maize (Zhai, Bischof, et al., ; Zhai, Zhang, et al., ), and other non‐grass monocots (Kakrana et al., ). Much like 21 nt‐dominated PHAS , the biogenesis of these 24 nt‐dominated PHAS loci begins with the Pol II‐dependent transcription of a single‐stranded RNA precursor which is then targeted by miR2275 and hydrolyzed.…”

“…These phasiRNAs are produced from processing of inverted repeat (IR) RNAs, instead of the double‐stranded RNA precursors observed in rice and maize (Kakrana et al., ). Although the 24 nt‐dominated PHAS loci from non‐grass monocots are still expressed most greatly in male reproductive tissue, in asparagus they are also expressed in female reproductive tissue (Kakrana et al., ).…”