title: Growth promotion-related miRNAs in Oncidium orchid roots colonized by the endophytic fungus Piriformospora indica.
abstract: Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, we describe miRNAs which are upregulated in Oncidium orchid roots after colonization by the fungus. Growth promotion and vigorous root development were observed in Oncidium hybrid orchid, while seedlings were colonized by P. indica. We performed a genome-wide expression profiling of small RNAs in Oncidium orchid roots either colonized or not-colonized by P. indica. After sequencing, 24,570,250 and 24744,141 clean reads were obtained from two libraries. 13,736 from 17,036,953 unique sequences showed homology to either 86 miRNA families described in 41 plant species, or to 46 potential novel miRNAs, or to 51 corresponding miRNA precursors. The predicted target genes of these miRNAs are mainly involved in auxin signal perception and transduction, transcription, development and plant defense. The expression analysis of miRNAs and target genes demonstrated the regulatory functions they may participate in. This study revealed that growth stimulation of the Oncidium orchid after colonization by P. indica includes an intricate network of miRNAs and their targets. The symbiotic function of P. indica on Oncidium orchid resembles previous findings on Chinese cabbage. This is the first study on growth regulation and development of Oncidium orchid by miRNAs induced by the symbiotic fungus P. indica.
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China ; Sanming Academy of Agricultural Sciences, Sanming, Fujian, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ye
authors.affiliation: Institute of Plant Biology, National Taiwan University, Taipei, Taiwan ; Ecological Materials Technology Department, Green Energy & Eco-technology System Center, ITRI South Campus, Industrial Technology Research Institute, Tainan, Taiwan.
authors.forename: Chin-Hui
authors.initials: CH
authors.lastname: Shen
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
authors.forename: Peng-Jen
authors.initials: PJ
authors.lastname: Chen
authors.affiliation: Sanming Academy of Agricultural Sciences, Sanming, Fujian, China.
authors.forename: Xuming
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of General Botany and Plant Physiology, Friedrich-Schiller University, Jena, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Oelmüller
authors.affiliation: Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
authors.forename: Kai-Wun
authors.initials: KW
authors.lastname: Yeh
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
authors.forename: Zhongxiong
authors.initials: Z
authors.lastname: Lai
mesh_terms: D005658:Fungi / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics*; D029595:Orchidaceae / Q000235:genetics* / Q000254:growth & development / Q000382:microbiology*; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development / Q000382:microbiology*; D019655:Quantitative Trait, Heritable; D034622:RNA Interference; D018749:RNA, Plant
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant