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Background  The advent of next generation sequencing technology has allowed for significant advances in plant virus discovery, particularly for identification of covert viruses and previously undescribed viruses. The  Citrus limon Burm. f.  ( C. limon ) is a small evergreen tree native to Asia, and . China is the world’s top lemon-producing nation.    Findings  In this work, lemon samples were collected from southwestern of China, where an unknown disease outbreak had caused huge losses in the lemon production industry. Using high-throughput pyrosequencing and the assembly of small RNAs, we showed that the  Hop stunt viroid  (HSVd) was present in  C. limon  leaf sample. The majority of it is a main lemon producing agricultural cultivar Hop stunt viroid  derived siRNAs (HSVd-siRNAs) in  C. limon  were 21 nucleotides in length, and nearly equal amount of HSVd-siRNAs originated from the plus-genomic RNA strand as from the complementary strand. A bias of HSVd-siRNAs toward sequences beginning with a 5′-Guanine was observed. Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome.    Conclusions  Our results suggest that  C. limon  could set up a small RNA-mediated gene silencing response to  Hop stunt viroid , Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development .

Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach