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

Virology Journal

Xueping Zhou¹  Yi Xu²  Yajuan Qian²  Shuai Fu²  Xiu Su² 

[1] Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing 100193, People’s Republic of China;Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310029, People’s Republic of China

关键词: RNA interference;    Small RNA;    Viroid;    Citrus limon;   

Others  :  1224906
DOI  :  10.1186/s12985-015-0332-2

 received in 2015-04-13, accepted in 2015-06-26,  发布年份 2015

【 摘 要 】

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 cultivarHop 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.

【 授权许可】

   
2015 Su et al.

【 图 表 】

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【 参考文献 】

• [1]Flores R, Gago-Zachert S, Serra P, Sanjuan R, Elena SF. Viroids: survivors from the RNA world? Annu Rev Microbiol. 2014; 68:395-414.
• [2]Ding SW, Li H, Lu R, Li F, Li WX. RNA silencing: a conserved antiviral immunity of plants and animals. Virus Res. 2004; 102:109-15.
• [3]Sano T, Barba M, Li SF, Hadidi A. Viroids and RNA silencing: mechanism, role in viroid pathogenicity and development of viroid-resistant plants. GM crops. 2010; 1:80-6.
• [4]Minoia S, Carbonell A, Di Serio F, Gisel A, Carrington JC, Navarro B. Specific argonautes selectively bind small RNAs derived from potato spindle tuber viroid and attenuate viroid accumulation in vivo. J Virol. 2014; 88:11933-45.
• [5]Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX et al.. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A. 2010; 107:1606-11.
• [6]Xu Y, Huang L, Wang Z, Fu S, Che J, Qian Y et al.. Identification of Himetobi P virus in the small brown planthopper by deep sequencing and assembly of virus-derived small interfering RNAs. Virus Res. 2014; 179:235-40.
• [7]Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-9.
• [8]Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10:R25. BioMed Central Full Text
• [9]Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G et al.. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. Plos One. 2009; 4: Article ID e7686
• [10]Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P et al.. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 2012; 163:262-8.
• [11]Mi SJ, Cai T, Hu YG, Chen Y, Hodges E, Ni FR et al.. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell. 2008; 133:116-27.
• [12]Xu Y, Huang LZ, Fu S, Wu JX, Zhou XP. Population diversity of Rice stripe virus-derived siRNAs in three different hosts and RNAi-based antiviral immunity in Laodelphgax striatellus. Plos One. 2012;7.
• [13]Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology. 2009; 392:203-14.
• [14]Hammann C, Steger G. Viroid-specific small RNA in plant disease. RNA Biol. 2012; 9:809-19.
• [15]Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. Plant J. 2012; 70:991-1003.
• [16]Gomez G, Martinez G, Pallas V. Viroid-induced symptoms in Nicotiana benthamiana plants are dependent on RDR6 activity. Plant Physiol. 2008; 148:414-23.
• [17]Reanwarakorn K, Semancik JS. Regulation of pathogenicity in hop stunt viroid-related group II citrus viroids. J Gen Virol. 1998; 79(Pt 12):3163-71.
• [18]Serra P, Gago S, Duran-Vila N. A single nucleotide change in Hop stunt viroid modulates citrus cachexia symptoms. Virus Res. 2008; 138:130-4.
• [19]Yue D, Liu H, Huang Y. Survey of computational algorithms for microRNA target prediction. Curr Genomics. 2009; 10:478-92.
• [20]Dai X, Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011; 39:W155-9.
• [21]Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM et al.. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell. 2006; 126:1203-17.
• [22]Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res. 2005; 33:W701-4.