Identification and characterization of microRNAs in dwarfed citrus trees infected with citrus dwarfing viroid

Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees (Citrus sinensis (L.) Osbeck), propagated on trifoliate orange rootstock (C. trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.). MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA high throughput sequencing was performed in CDVd-infected and non-infected controls using the Illumina TruSeq Small RNA Kit and Illumina HiSeq TM 2500 instrument. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.