title: A dynamic evolutionary and functional landscape of plant phased small interfering RNAs.
abstract: 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 produce 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.
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. yz357@cornell.edu.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. wang.974@buckeyemail.osu.edu.|The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. wang.974@buckeyemail.osu.edu.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. wu.1495@buckeyemail.osu.edu.|Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA. wu.1495@buckeyemail.osu.edu.
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA. ding.35@osu.edu.|The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. ding.35@osu.edu.|Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43210, USA. ding.35@osu.edu.
authors.forename: Biao
authors.initials: B
authors.lastname: Ding
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. zf25@cornell.edu.|USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY, 14853, USA. zf25@cornell.edu.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
mesh_terms: D005075:Biological Evolution; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D018749:RNA, Plant; D034741:RNA, Small Interfering