A dynamic
evolutionary and functional landscape of plant phased small interfering RNAs
- *Corresponding
authors: Biao Ding ding.35@osu.edu -
Zhangjun Fei zf25@cornell.edu
- †
Equal contributors
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BMC Biology 2015, 13:32 doi:10.1186/s12915-015-0142-4
Yi Zheng and Ying Wang contributed equally to this work.
Published: 16 May 2015
Background Secondary, phased small interfering RNAs
(phasiRNAs) derived from protein-coding or noncoding loci (PHAS) are emerging
as a new type of regulators of gene expression in plants. However, the
evolution and function of these novel siRNAs in plant species remain largely
unexplored. Results We systematically analyzed PHAS loci in 23 plant species
covering major phylogenetic groups spanning alga, moss, gymnosperm, basal
angiosperm, monocot and dicot. We identified over 3,300 PHAS loci, among which
~1,600 were protein-coding genes. Most of these PHAS loci were novel and clade-
or species-specific and showed distinct expression patterns in association with
particular development stages, viral infection or abiotic stresses.
Unexpectedly, numerous PHAS loci produced phasiRNAs from introns or exon-intron
junction regions. Our comprehensive analysis suggests that phasiRNAs
predominantly regulate protein-coding genes from which they are derived and
genes from the same families of the phasiRNA-deriving genes, in contrast to the
dominant trans-regulatory mode of miRNAs. The stochastic occurrence of many
PHAS loci in the plant kingdom suggests their young evolutionary origins.
Conclusions Our study discovered an unprecedented diversity of protein-coding
genes that produced phasiRNAs in a wide variety of plants, and set a
kingdom-wide foundation for investigating the novel roles of phasiRNAs in
shaping phenotype diversities of plants.
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