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Genome and phylogenetic analyses of Chinese pepper mottle virus isolates from chili pepper plants

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Abstract

In 2013, a chili pepper (Capsicum annuum cv. ‘Favorite’) sample displaying crinkled and mottled leaves was collected from a field in the Hunan Province, China. Small RNA (sRNA) sequencing identified the putative virus as pepper mottle virus (PepMoV), which was confirmed by RT-PCR analysis. Full length sequence of this virus strain (designated as HN) was obtained and shown to be typical of a potyvirus. Coat protein (CP) genes of nine PepMoV isolates obtained from south China were sequenced and they shared 89 to 99% sequence identity with PepMoV CP sequences retrieved from GenBank. Phylogenetic analysis, and the level of recombination, gene flow and genetic differention revealed that the PepMoV isolates of Chinese lineage clustered within the south-east group. PepMoV has now been detected in three different provinces of southern part of China.

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References

  • Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487

    Article  CAS  PubMed  Google Scholar 

  • Cheng YH, Deng TC, Chen CC, Liao JY, Chang CA, Chiang CH (2011) First report of Pepper mottle virus in bell pepper in Taiwan. Plant Dis 95:617

    Article  CAS  PubMed  Google Scholar 

  • Chung BYW, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han JH, Choi HS, Kim DH, Lee HR, Kim BD (2006) Biological, physical and cytological properties of Pepper mottle virus-SNU1 and its RT-PCR detection. Plant Pathol J 22:155–160

    Article  Google Scholar 

  • Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155: 2011–2014

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  CAS  PubMed  Google Scholar 

  • Lin SW, Chou YY, Shieh HC, Ebert AW, Kumar S, Mavlyanova R, Rouamba A, Tenkouano A, Afari-Sefa V, Gniffke PA (2013) Pepper (Capsicum spp.) germplasm dissemination by AVRDC–the world vegetable center: an overview and introspection. Chron Hortic 53:21–27

    Google Scholar 

  • Liu MY, Liu XN, Li X, Zhang DY, Dai LY, Tang QJ (2016) Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP, and RdRp coding regions. Arch Virol 161:677–683

    Article  CAS  PubMed  Google Scholar 

  • Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16:562–563

    Article  CAS  PubMed  Google Scholar 

  • Melzer MJ, Sugano JS, Cabanas D, Dey KK, Kandouh B, Mauro D, Rushanaedy I, Srivastava S, Watanabe S, Borth WB, Tripathi S, Matsumoto T, Keith L, Gonsalves D, Hu JS (2012) First report of Pepper mottle virus infecting tomato in Hawaii. Plant Dis 96:917

    Article  CAS  PubMed  Google Scholar 

  • Nagy PD (2011) The roles of host factors in tombusvirus RNA recombination. Adv Virus Res 81:63–84

    Article  CAS  PubMed  Google Scholar 

  • Nelson MR, Wheeler RE (1972) A new virus disease of pepper in Arizona. Plant Dis Rep 56:731–735

    Google Scholar 

  • Quiñones M, Arana F, Alfenas-Zerbini P, Soto M, Ribeiro D, Diaz A, González D, Carbonell J, Depestre T, Zerbini FM (2011) First report of Pepper mottle virus in sweet pepper in Cuba. New Dis Rep 24:16

    Article  Google Scholar 

  • Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Cambridge

    Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Liu Z, Niu S, Peng M, Wang D (2006) Natural occurrence of Chilli veinal mottle virus on Capsicum chinense in China. Plant Dis 90:377

    Article  CAS  PubMed  Google Scholar 

  • Warren CE, Murphy JF (2003) The complete nucleotide sequence of Pepper mottle virus-Florida RNA. Arch Virol 148:189–197

    Article  CAS  PubMed  Google Scholar 

  • Wei TY, Yang JG, Liao FR, Liao FL, Gao FL, Lu LM, Zhang XT, Li F, Wu ZJ, Lin QY, Xie LH, Lin HX (2009) Genetic diversity and population structure of Rice stripe virus in China. J Gen Virol 90:1025–1034

    Article  CAS  PubMed  Google Scholar 

  • Wu QF, Luo YJ, Lu R, Lau N, Lai EC, Li WX, Ding SW (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA 107:1606–1611

    Article  PubMed  PubMed Central  Google Scholar 

  • Yin X, Zheng FQ, Tang W, Zhu QQ, Li XD, Zhang GM, Liu HT, Liu BS (2013) Genetic structure of Rice black-streaked dwarf virus populations in China. Arch Virol 158:2505–2515

    Article  CAS  PubMed  Google Scholar 

  • Zitter TA (1972) Naturally occurring pepper virus strains in South Florida. Plant Dis Rep 56:586

    Google Scholar 

Download references

Acknowledgments

This work was partially funded by the National Natural Science Foundation of China (31701765), the Agriculture Research System of China (CARS-25-B-05), the Hunan Talent Project (2016RS2019) and the Science and Technology Project of Hunan Academy of Agricultural Science (2017JC43).

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Author notes

  1. Yu Zhang, and Xiangwen Luo contributed equally to this work.

Authors and Affiliations

  1. Longping Branch, Graduate School of Hunan University, Changsha, 410125, China

    Yu Zhang, Deyong Zhang, Songbai Zhang & Yong Liu

  2. Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Academy of Agricultural Science, Changsha, 410125, China

    Xiangwen Luo, Deyong Zhang, Xian OuYang, Zhanhong Zhang, Chengjia Zhang, Songbai Zhang & Yong Liu

  3. Key Laboratory of Agricultural Biodiversity for Pest Management of China Education Ministry, Yunnan Agricultural University, Kunming, 650201, China

    Fan Li

  4. Ipro Chemistry Co., Ltd, Shenzhen, 518001, China

    Jianxin Chen

  5. Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA

    Xuguo Zhou

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  1. Yu Zhang
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  2. Xiangwen Luo
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  3. Deyong Zhang
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  4. Xian OuYang
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  5. Zhanhong Zhang
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  6. Fan Li
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  8. Jianxin Chen
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  9. Xuguo Zhou
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  10. Songbai Zhang
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  11. Yong Liu
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Correspondence to Songbai Zhang or Yong Liu.

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Zhang, Y., Luo, X., Zhang, D. et al. Genome and phylogenetic analyses of Chinese pepper mottle virus isolates from chili pepper plants. J Plant Pathol 101, 559–564 (2019). https://doi.org/10.1007/s42161-018-00235-w

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  • DOI: https://doi.org/10.1007/s42161-018-00235-w

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