title: Genome-wide discovery and analysis of phased small interfering RNAs in Chinese sacred lotus.
abstract: Phased small interfering RNA (phasiRNA) generating loci (briefly as PHAS) in plants are a novel class of genes that are normally regulated by microRNAs (miRNAs). Similar to miRNAs, phasiRNAs encoded by PHAS play important regulatory roles by targeting protein coding transcripts in plant species. We performed a genome-wide discovery of PHAS loci in Chinese sacred lotus and identified a total of 106 PHAS loci. Of these, 47 loci generate 21 nucleotide (nt) phasiRNAs and 59 loci generate 24 nt phasiRNAs, respectively. We have also identified a new putative TAS3 and a putative TAS4 loci in the lotus genome. Our results show that some of the nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance proteins and MYB transcription factors potentially generate phasiRNAs. Furthermore, our results suggest that some large subunit (LSU) rRNAs can derive putative phasiRNAs, which is potentially resulted from crosstalk between small RNA biogenesis pathways that are employed to process rRNAs and PHAS loci, respectively. Some of the identified phasiRNAs have putative trans-targets with less than 4 mismatches, suggesting that the identified PHAS are involved in many different pathways. Finally, the discovery of 24 nt PHAS in lotus suggests that there are 24 nt PHAS in dicots.
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China.
authors.forename: Shengpeng
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America.
authors.forename: Ramanjulu
authors.initials: R
authors.lastname: Sunkar
mesh_terms: D001483:Base Sequence; D035264:Flowers / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D031653:Nelumbo / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000145:classification / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D034741:RNA, Small Interfering / Q000145:classification / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D015398:Signal Transduction / Q000235:genetics
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D012335:RNA, Ribosomal; D034741:RNA, Small Interfering