Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China

doi:10.1016/S2095-3119(16)61533-2

Journal of Integrative Agriculture ›› 2017, Vol. 16 ›› Issue (02): 503-508.DOI: 10.1016/S2095-3119(16)61533-2

• 论文 • 上一篇

收稿日期:2016-07-01 出版日期:2017-02-20 发布日期:2017-01-31

Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China

YU Yun-qi^{1, 2}, WU Qiong^{1, 2}, SU Hua-nan³, WANG Xue-feng², CAO Meng-ji², ZHOU Chang-yong²

¹College of Plant Protection, Southwest University, Chongqing 400715, P.R.China
²National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, P.R.China
³National Navel Orange Engineering and Technology Research Center, Gannan Normal University, Ganzhou 341000, P.R.China

Received:2016-07-01 Online:2017-02-20 Published:2017-01-31
Contact: 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
Supported by:
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).

摘要/Abstract

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.

Key words: citrus, Citrus yellow vein clearing virus (CYVCV), small RNA deep sequencing

YU Yun-qi, WU Qiong, SU Hua-nan, WANG Xue-feng, CAO Meng-ji, ZHOU Chang-yong . [J]. Journal of Integrative Agriculture, 2017, 16(02): 503-508.

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

参考文献

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.

Small RNA deep sequencing reveals full-length genome of Citrus yellow vein clearing virus in Chongqing, China

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