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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 .

Growth Promotion-Related miRNAs in Oncidium Orchid Roots Colonized by the Endophytic Fungus Piriformospora indica