Please wait a minute...
Journal of Integrative Agriculture  2017, Vol. 16 Issue (02): 503-508    DOI: 10.1016/S2095-3119(16)61533-2
Short Communication Advanced Online Publication | Current Issue | Archive | Adv Search |
Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China
YU Yun-qi1, 2, WU Qiong1, 2, SU Hua-nan3, WANG Xue-feng2, CAO Meng-ji2, ZHOU Chang-yong2

1 College of Plant Protection, Southwest University, Chongqing 400715, P.R.China

2 National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, P.R.China

3 National Navel Orange Engineering and Technology Research Center, Gannan Normal University, Ganzhou 341000, P.R.China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  To identity the potential pathogen associated with the yellow vein clearing symptom on lemon trees, the profiles of virus-derived small interfering RNAs from citrus samples were obtained and analyzed by deep sequencing method in this study.  Twenty-seven contigs almost cover the full length genome of Citrus yellow vein clearing virus (CYVCV) isolate YN were obtained using the small RNA deep sequencing technology.  Analysis showed that this isolate CQ shared the highest nucleotide identity with isolate Y1 (JX040635) and YN (KP313242), both of which belong to the genus Mandarivirus in the family Alphaflexiviridae.  Mapping analysis of viral-derived siRNA (vsiRNA) profiles revealed an uneven distribution pattern of their generations along both positive and negative genome strands, and 22- and 21-nt vsiRNAs ranked the majority.  BLAST against viroids and other viral databases confirmed that this sample was single-infected only by CYVCV, which indicated that CYVCV was the exact causal agent for the yellow clearing symptom occurring on lemon.  This is the first CYVCV isolate detected in Chongqing and the second in China.  This result could provide a molecular basis for the investigation of citrus viral diseases to protect citrus health in this region. 
Keywords:  citrus      Citrus yellow vein clearing virus (CYVCV)      small RNA deep sequencing  
Received: 01 July 2016   Accepted:
Fund: 

This work was partially supported by the National Natural Science Foundation of China (31501611), the Special Fund for Agro-scientific Research in the Public Interest, China (201203076) and the Fundamental Research Funds for the Central Universities, China (XDJK2016B021, SWU116012, XDJK2014A001 and XDJK2015A009).

Corresponding Authors:  Cao Meng-ji, Tel: +86-23-68349002, E-mail: caomengji@cric.cn; Zhou Chang-yong, Tel: +86-23-68349601, E-mail: zhoucy@cric.cn    
About author:  Yu Yun-qi, E-mail: yyqsniper@163.com

Cite this article: 

YU Yun-qi, WU Qiong, SU Hua-nan, WANG Xue-feng, CAO Meng-ji, ZHOU Chang-yong . 2017. Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China. Journal of Integrative Agriculture, 16(02): 503-508.

Adams I P, Glover R H, Monger W A, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N. 2009. Next-generation sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Molecular Plant Pathology, 10, 537–545.
Alshami A A A, Ahlawat Y S, Pant R P. 2003. A hitherto unreported yellow vein clearing disease of citrus in India and its viral aetiology. Indian Phytopathology, 56, 422–427.
Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses, 6, 106–136.
Cao M J, Du P, Wang X B, Yu Y Q, Qiu Y H, Li, W X, Gal-On A, Zhou C Y, Li Y, Ding S W. 2014. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 111, 14613–14618.
Cao M J, Wu Q, Atta S, Su H N, Yu Y Q, Chen H M, Zhou C Y. 2016. First molecular evidence of Citrus yellow vein clearing virus from citrus in Punjab, Pakistan. Plant Disease, 100, 540.
Catara A, Azzaro A, Davino M, Polizzi G. 1993. Yellow vein clearing of lemon in Pakistan. In: Proceedings of 12th Conference of IOCV, Riverside, CA. pp. 364–367.
Chen H M, Li Z A, Wang X F, Zhou Y, Tang K Z, Zhou C Y, Yue J Q. 2014. First Report of Citrus yellow vein clearing virus on lemon in Yunnan, China. Plant Disease, 98, 1747–1747.
Cowan G H, Lioliopoulou F, Ziegler A, Torrance L. 2002. Subcellular localisation, protein interactions, and RNA binding of Potato mop-top virus triple gene block proteins. Virology, 298, 106–115.
Deleris A, Gallego-Bartolome J, Bao J, Kasschau K D, Carrington J C, Voinnet O. 2006. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science, 313, 68–71.
Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, De Stradis A, Savino V, Yokomi R K, Saponari M. 2012a. Identification and characterization of Citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology, 102, 1168–1175.
Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli G P, Saponari M. 2012b. Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology, 432, 162–172.
Önelge N. 2003. First report of yellow vein clearing of lemons in Turkey. The Journal of Turkish Phytopathology, 32, 53–55.
Önelge N, Satar S, Elibüyük Ö, Bozan O. 2011a. Citrus yellow vein clearing virus: A new aphid-transmitted citrus virus. Citrograph, January/February, 22–24.
Önelge N, Satar S, Elibüyük Ö, Bozan O, Kambero?lu M. 2011b. Transmission studies on Citrus yellow vein clearing virus. In: Proceedings of 18th Conference IOCV. Riverside, CA.
Song C N, Wang C, Zhang C Q, Korir N K, Yu H P, Ma Z Q, Fang J G. 2010. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics, 11, 431.
Song Z, Kurth E G, Peremyslov V V, Zhou C Y, Dolja V V. 2015. Molecular characterization of a Citrus yellow vein clearing virus strain from China. Archives of Virology, 160, 1811–1813.
Verchot-Lubicz J, Torrance L, Solovyev A G, Morozov S Y, Jackson A O, Gilmer D. 2010. Varied movement strategies employed by triple gene block-encoding viruses. Molecular Plant-Microbe Interactions, 23, 1231–1247.
Vives M C, Velazquez K, Pina J A, Moreno P, Guerri J, Navarro L. 2013. Identification of a new enamovirus associated with citrus vein enation disease by deep sequencing of small RNAs. Phytopathology, 103, 1077–1086.
Wu Q F, Ding S W, Zhang Y J, Zhu S F. 2015. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. Annual Review of Phytopathology, 53, 425–444.
Wu Q F, Luo Y J, Lu R, Lau N, Lai E C, Li W X, Ding S W. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proceedings of the National Academy of Sciences of the United States of America, 107, 1606–1611.
Wu Q F, Wang Y, Cao M J, Pantaleo V, Burgyan J, Li W X, Ding S W. 2012. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proceedings of the National Academy of Sciences of the United States of America, 109, 3938–3943.
Xie Q, Bao F S, Xie Z. 2009. Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE, 4, e4971.
Zerbino D R, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821–829.
Zhou C, Li Z A. 2010. Current occurrence and research status of graft-transmissible citrus diseases in P.R.China. In: Proceedings of 18th Conference IOCV. Riverside, CA.
[1] Ping Liao, Ting Zeng, Mengyang Huangfu, Cairong Zheng, Jiequn Ren, Changyong Zhou, Yan Zhou.

Eureka lemon zinc finger protein ClDOF3.4 interacts with citrus yellow vein clearing virus coat protein to inhibit viral infection [J]. >Journal of Integrative Agriculture, 2024, 23(6): 1979-1993.

[2] Jia Fu, Jie Fan, Chenxi Zhang, Yongyao Fu, Baohang Xian, Qiyuan Yu, Xin Huang, Wen Yang, Shanchun Chen, Yongrui He, Qiang Li.

High-throughput screening system of citrus bacterial canker-associated transcription factors and its application to the regulation of citrus canker resistance [J]. >Journal of Integrative Agriculture, 2024, 23(1): 155-165.

[3] XUAN Zhi-you, ZHANG Song, LI Ping, YANG Fang-yun, CHEN Hong-ming, LIU Ke-hong, ZHOU Yan, LI Zhong-an, ZHOU Chang-yong, CAO Meng-ji. Apple stem grooving virus is associated with leaf yellow mottle mosaic disease on Citrus grandis cv. Huangjinmiyou in China[J]. >Journal of Integrative Agriculture, 2022, 21(7): 2031-2041.
[4] LEI Tian-gang, HE Yong-rui, ZOU Xiu-ping, WANG Xue-feng, FU Shi-min, PENG Ai-hong, XU Lan-zhen, YAO Li-xiao, CHEN Shan-chun, ZHOU Chang-yong. A rapid multiplication system for 'Candidatus Liberibacter asiaticus' through regeneration of axillary buds in vitro[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1683-1693.
[5] LI Zheng-gang, NONG Yuan, Tahir FAROOQ, TANG Ya-fei, SHE Xiao-man, YU Lin, LAN Guo-bing, ZHOU Xue-ping, HE Zi-fu. Small RNA deep sequencing reveals the presence of multiple viral infections in cucurbit crops in Guangdong, China[J]. >Journal of Integrative Agriculture, 2022, 21(5): 1389-1400.
[6] LIU Cong, LI De-xiong, HUANG Xian-biao, Zhang Fu-qiong, Xie Zong-zhou, Zhang Hong-yan, Liu Ji-hong. Manual thinning increases fruit size and sugar content of Citrus reticulata Blanco and affects hormone synthesis and sugar transporter activity[J]. >Journal of Integrative Agriculture, 2022, 21(3): 725-735.
[7] YANG Zhen, ZHANG Lan, ZHAO Jin-fa, ZHANG Xing-kai, WANG Ying, LI Tai-sheng, ZHANG Wei, ZHOU Yan. New geographic distribution and molecular diversity of Citrus chlorotic dwarf-associated virus in China[J]. >Journal of Integrative Agriculture, 2022, 21(1): 293-298.
[8] CHEN Wei-yu, YU Jia, XU Heng, LU Xin-yu, DAI Ting-ting, TIAN Yue-e, SHEN Dan-yu, DOU Dao-long. Combining simplified DNA extraction technology and recombinase polymerase amplification assay for rapid and equipment-free detection of citrus pathogen Phytophthora parasitica[J]. >Journal of Integrative Agriculture, 2021, 20(10): 2696-2705.
[9] JING Jia-yi, ZHANG Hong-yan, XUE Yao-bi, ZENG Kai-fang.
Effects of INA on postharvest blue and green molds and anthracnose decay in citrus fruit
[J]. >Journal of Integrative Agriculture, 2020, 19(5): 1396-1406.
[10] ZHONG Xi, LIU Xue-lu, LOU Bing-hai, ZHOU Chang-yong, WANG Xue-feng . Development of a sensitive and reliable droplet digital PCR assay for the detection of ‘Candidatus Liberibacter asiaticus’[J]. >Journal of Integrative Agriculture, 2018, 17(2): 483-487.
[11] LI Ping, LI Min, ZHANG Song, WANG Jun, YANG Fang-yun, CAO Meng-ji, LI Zhong-an. Complete genome sequences of four isolates of Citrus leaf blotch virus from citrus in China[J]. >Journal of Integrative Agriculture, 2018, 17(03): 712-715.
[12] ZHANG Hua, YANG Yi-fei, ZHOU Zhi-qin. Phenolic and flavonoid contents of mandarin (Citrus reticulata Blanco) fruit tissues and their antioxidant capacity as evaluated by DPPH and ABTS methods[J]. >Journal of Integrative Agriculture, 2018, 17(01): 256-263.
[13] Dirceu Mattos Jr, Franz W R Hippler, Rodrigo M Boaretto, Eduardo S Stuchi, José A Quaggio . Soil boron fertilization: The role of nutrient sources and rootstocks in citrus production[J]. >Journal of Integrative Agriculture, 2017, 16(07): 1609-1616.
[14] P Panigrahi, A K Srivastava. Water and nutrient management effects on water use and yield of drip irrigated citrus in vertisol under a sub-humid region[J]. >Journal of Integrative Agriculture, 2017, 16(05): 1184-1194.
[15] GUAN Xin, TAN Si, Günther Buchholz, Peter Nick, ZHOU Zhi-qin. A method to evaluate the bioactive function of fruit extracts of Chinese wild Citrus with microtubular activity[J]. >Journal of Integrative Agriculture, 2017, 16(04): 867-873.
No Suggested Reading articles found!