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Genome Res. 2018 Sep;28(9):1333-1344. doi: 10.1101/gr.228163.117. Epub 2018 Jul 12.

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

Author information

1
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714, USA.
2
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
3
Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
4
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
5
Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand.
6
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
7
Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA.

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.

PMID:
30002159
PMCID:
PMC6120631
DOI:
10.1101/gr.228163.117
[Indexed for MEDLINE]
Free PMC Article

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