Abstract
BackgroundHop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time. Severe hop stunt disease caused by the recently discovered Citrus bark cracking viroid (CBCVd) is one of the most devastating diseases among other viroid infections in hop. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in gene expression regulation. To identify miRNAs in hop and their response to CBCVd-infection, two small RNA (sRNA) libraries were prepared from healthy and CBCVd-infected hop plants and were investigated by high throughput sequencing.ResultsA total of 67 conserved and 49 novel miRNAs were identified. Among them, 36 conserved and 37 novel miRNAs were found to be differentially recovered in response to CBCVd-infection. A total of 311 potential targets was predicted for conserved and novel miRNAs based on a sequence homology search using hop transcriptome data. The majority of predicted targets significantly belonged to transcriptional factors that may regulate hop leaf, root and cone growth and development. In addition, the identified miRNAs might also play an important roles in other cellular and metabolic processes, such as signal transduction, stress response and other physiological processes, including prenylflavonoid biosynthesis pathways. Quantitative real time PCR analysis of selected targets revealed their negative correlation with their corresponding CBCVd-responsive miRNAs.ConclusionsBased on the results, we concluded that CBCVd-responsive miRNAs modulate several hormone pathways and transcriptional factors that play important roles in the regulation of metabolism, growth and development. These results provide a framework for further analysis of regulatory roles of sRNAs in plant defense mechanism including other hop infecting viroids in particular.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3271-4) contains supplementary material, which is available to authorized users.
Highlights
Hop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time
The initial step includes the formation of complex with the aid of the the double-stranded RNA (dsRNA)-binding protein HYPONASTIC LEAVES 1 (HYL1), C2H2 zinc-finger protein SERRATE (SE), DCL and the nuclear cap-binding protein complex that cleaves the pri-miRNA near the base of the stem to yield a double-stranded intermediate miRNA: passenger strand duplex known as pre-miRNA [8]
After removing adaptor sequences, filtering out low-quality tags and eliminating contamination produced by the adaptor-adaptor ligation, 7,253,175 and 15,907,779 clean reads were obtained from Hop healthy plant (HP) and CBCVd-infected plants (CIP) libraries, respectively (Table 1)
Summary
Hop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time. The endogenous small interfering RNAs (siRNAs) can be classified into several classes based on their biogenesis pathways, genomic loci origin and biological function, such as transacting siRNAs (tasiRNAs), chromatin-associated siRNAs, repeat-associated siRNAs (rasiRNAs) and natural antisense transcript-associated siRNAs (nat-siRNAs) [2]. All these siRNAs are usually processed by the action of DICER-like enzymes from double-stranded RNA (dsRNA) precursors, derived from transgenes, endogenous repeat sequences or transposons through various mechanisms [3]. MiRNAs are involved in the regulation of various biological processes, such as leaf, root, stem and floral organ morphogenesis and development, biosynthesis, metabolism and homeostasis, vegetative to reproductive growth phase transition, senescence, signal transduction and response to biotic/abiotic stresses [3, 9, 11], including drought [12], salinity [13], oxidative [14], hypoxia [15], nutrient stresses [16] and micronutrient deficiency or toxicity [17]
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