RT Journal
A1 Kakrana, Atul
A1 Mathioni, Sandra M.
A1 Huang, Kun
A1 Hammond, Reza
A1 Vandivier, Lee
A1 Patel, Parth
A1 Arikit, Siwaret
A1 Shevchenko, Olga
A1 Harkess, Alex E.
A1 Kingham, Bruce
A1 Gregory, Brian D.
A1 Leebens-Mack, James H.
A1 Meyers, Blake C.
T1 Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots
JF Genome Research 
JO Genome Research 
YR 2018 
FD September 01 
VO 28 
IS 9 
SP 1333 
OP 1344 
DO 10.1101/gr.228163.117 
UL http://genome.cshlp.org/content/28/9/1333.abstract 
AB 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.