title: Identification of miRNAs and Their Targets in the Liverwort Marchantia polymorpha by Integrating RNA-Seq and Degradome Analyses.
abstract: Bryophytes (liverworts, hornworts and mosses) comprise the three earliest diverging lineages of land plants (embryophytes). Marchantia polymorpha, a complex thalloid Marchantiopsida liverwort that has been developed into a model genetic system, occupies a key phylogenetic position. Therefore, M. polymorpha is useful in studies aiming to elucidate the evolution of gene regulation mechanisms in plants. In this study, we used computational, transcriptomic, small RNA and degradome analyses to characterize microRNA (miRNA)-mediated pathways of gene regulation in M. polymorpha. The data have been integrated into the open access ContigViews-miRNA platform for further reference. In addition to core components of the miRNA pathway, 129 unique miRNA sequences, 11 of which could be classified into seven miRNA families that are conserved in embryophytes (miR166a, miR390, miR529c, miR171-3p, miR408a, miR160 and miR319a), were identified. A combination of computational and degradome analyses allowed us to identify and experimentally validate 249 targets. In some cases, the target genes are orthologous to those of other embryophytes, but in other cases, the conserved miRNAs target either paralogs or members of different gene families. In addition, the newly discovered Mpo-miR11707.1 and Mpo-miR11707.2 are generated from a common precursor and target MpARGONAUTE1 (LW1759). Two other newly discovered miRNAs, Mpo-miR11687.1 and Mpo-miR11681.1, target the MADS-box transcription factors MpMADS1 and MpMADS2, respectively. Interestingly, one of the pentatricopeptide repeat (PPR) gene family members, MpPPR_66 (LW9825), the protein products of which are generally involved in various steps of RNA metabolism, has a long stem-loop transcript that can generate Mpo-miR11692.1 to autoregulate MpPPR_66 (LW9825) mRNA. This study provides a foundation for further investigations of the RNA-mediated silencing mechanism in M. polymorpha as well as of the evolution of this gene silencing pathway in embryophytes.
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 These authors contributed equally to this work.
authors: Pin-Chun
authors: PC
authors: Lin
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 These authors contributed equally to this work.
authors: Chia-Wei
authors: CW
authors: Lu
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Bing-Nan
authors: BN
authors: Shen
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Guan-Zong
authors: GZ
authors: Lee
authors: School of Biological Sciences, Monash University, Melbourne, Australia.
authors: John L
authors: JL
authors: Bowman
authors: Instituto de Biotecnologia y Ecologia Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa Veracruz, Mexico.
authors: Mario A
authors: MA
authors: Arteaga-Vazquez
authors: Department of Agronomy, National Taiwan University, 1 Sec. 4, Roosevelt Rd. Taipei, Taiwan 106.
authors: Li-Yu Daisy
authors: LY
authors: Liu
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Syuan-Fei
authors: SF
authors: Hong
authors: Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Taiwan 701.
authors: Chu-Fang
authors: CF
authors: Lo
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Gong-Min
authors: GM
authors: Su
authors: Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan.
authors: Takayuki
authors: T
authors: Kohchi
authors: Graduate School of Science, Kobe University, Kobe 657-8501 Japan.
authors: Kimitsune
authors: K
authors: Ishizaki
authors: University of Osnabrück, Botany Department, D-49076 Osnabrück, Germany.
authors: Sabine
authors: S
authors: Zachgo
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Felix
authors: F
authors: Althoff
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106.
authors: Mizuki
authors: M
authors: Takenaka
authors: Faculty of Biology-Oriented Science and Technology, Kinki University, Nishimitani, Kinokawa, Wakayama, 649-6493 Japan.
authors: Katsuyuki T
authors: KT
authors: Yamato
authors: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan 106 Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 115 Center of Biotechnology, National Taiwan University, Taipei, Taiwan 106 linss01@ntu.edu.tw.
authors: Shih-Shun
authors: SS
authors: Lin
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D020868:Gene Silencing; D017343:Genes, Plant; D017930:Genes, Reporter; D047008:Marchantia / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D020871:RNA Stability / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs
keywords: ARGONAUTE; Class III homeodomain leucine zipper; Degradome; MADS-box; Marchantia polymorpha; Transcriptome; miRNA prediction