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The genetic structure and recombination analyses of Sweetpotato leaf curl virus (SPLCV) population in China

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Abstract

Sweetpotato leaf curl virus (SPLCV) is a species of virus that causes substantial yield losses in sweetpotato. In this study, twenty-four complete genomic sequences of SPLCV which identified from the sweetpotato samples collected from China, were calculated into four strains. A total of 11.9% isolates were recombinants, and ten recombination patterns were detected. In addition to C3, V1, IR and C1 genes, the both ends of the V2 gene were also identified as recombination hot spots for SPLCV. Negative (purifying) selection was identified among all six SPLCV genes, except for C4 gene was under the variety of choices (positive selection) for adaptive protein evolution. The mismatch distribution of SPLCV in all subgroups and groups was multiple peaked or ragged, indicating SPLCV population has existed for a long time. The gene flows between Shandong, Hebei and Jiangsu Provinces in China were frequent, which was also observed between the groups of China, Brazil, South Korea. Recombination, selection pressure and gene flow promote the evolution of the SPLCV in China.

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References

  • Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ (2016) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses. Adv Virol 161(10):2921–2949

    CAS  Google Scholar 

  • Albuquerque LC, Inoue-Nagata AK, Pinheiro B, Ribeiro SG, Resende RO, Moriones E, Navas-Castillo J (2011) A novel monopartite begomovirus infecting sweetpotato in Brazil. Arch Virol 156:1291–1294

    CAS  PubMed  Google Scholar 

  • Albuquerque LC, Inoue-Nagata AK, Pinheiro B, Resende RO, Moriones E, Nava-Castillo J (2012) Genetic diversity and recombination analysis of sweepoviruses from Brazil. Virol J 9(1):241

    PubMed  PubMed Central  Google Scholar 

  • Bi H, Zhang P (2012) Molecular characterization of two sweepoviruses from china and evaluation of the infectivity of cloned SPLCV-JS in Nicotiana Benthamiana. Adv Virol 157(3):441–454

    CAS  Google Scholar 

  • Briddon RW, Bull SE, Bedford ID (2006) Occurrence of sweetpotato leaf curl virus in sicily. Plant Pathol 55(2):286

    Google Scholar 

  • Clark CA, Valverde RA, Fuentes S, Salazar LF, Moyer JW (2002) Research for improved management of sweetpotato pests and diseases: cultivar decline. Acta Hort 583:103–112

    Google Scholar 

  • Clark CA, Davis JA, Abad JA, Cuellar WJ, Fuentes S, Kreuze JF, Gibson RW, Mukasa SB, Tugume AK, Tairo FD, Valkonen JP (2012) Sweetpotato viruses: 15 years of progress on understanding and managing complex diseases. Plant Dis 96(2):168–185

    CAS  PubMed  Google Scholar 

  • Cuellar WJ, Galvez M, Fuentes S, Tugume J, Kreuze J (2015) Synergistic interactions of begomoviruses with sweetpotato chlorotic stunt virus (genus crinivirus) in sweetpotato (ipomoea batatas l). Mol Plant Pathol 16(5):459–471

    CAS  PubMed  Google Scholar 

  • Fialloolivé E, Katis NI, Navascastillo J (2014) First report of sweetpotato leaf curl virus on blue morning glory in greece. Plant Dis 98(5):700

    Google Scholar 

  • Fuentes S, Salazar LF (2003) First report of sweetpotato leaf curl virus in Peru. Plant Dis 1:98

    Google Scholar 

  • Gao F, Gong Y, Zhang P (2000) Production and deployment of virus-free sweetpotato in china. Crop Protection 19(2):105–111

    Google Scholar 

  • García-Arenal F, McDonald BA (2003) An analysis of the durability of resistance to plant viruses. Phytopathology 93(8):941–952

    PubMed  Google Scholar 

  • Haible D, Kober S, Jeske H (2006) Rolling circle amplication revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135(1):9–16

    CAS  PubMed  Google Scholar 

  • Huang X, Wang Y, Yan Z, Geng C, Tian Y, Li X (2019) Screening and application of attenuated mutants of Papaya ringspot virus-watermelon strain. J Plant Protect 46(4):738–744

    Google Scholar 

  • Jawad AA, Ayyez HN, Kleaf SF (2018) Sequencing and phylogeny of sulphonamide resistant genes by using MEGA6 software program. Int J Res Pharm Sci 9(SPL1):56

    Google Scholar 

  • Kim J, Kil E, Kim S, Seo H, Byun H, Park J, Chung MN, Kwak HR, Kim MK, Kim CS, Yang JW, Lee KJ, Chol HS, Lee S (2016) Seed transmission of sweetpotato leaf curl virus in sweetpotato (Ipomoea Batatas). Plant Pathol 64(6):1284–1291

    Google Scholar 

  • Latham JR, Saunders K, Pinner MS, Stanley J (1997) Induction of plant cell division by beet curly top virus gene C4. Plant J 11(6):1273–1283

    CAS  Google Scholar 

  • Lefeuvre P, Lett JM, Reynaud B, Martin DP (2007) Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog 3:181

    Google Scholar 

  • Lefeuvre P, Lett JM, Varsani A, Martin DP (2009) Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83:2697–2707

    CAS  PubMed  Google Scholar 

  • Li R, Salih S, Hurtt S (2004) Detection of geminiviruses in sweetpotato by polymerase chain reaction. Plant Dis 88(12):1347–1351

    CAS  PubMed  Google Scholar 

  • Li X, Zhu T, Yin X, Zhang C, Chen J, Tian Y, Liu J (2017) The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China. Virol J 14(1):165–174

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Liu Q, Wang Y, Zhang Z, Lv H, Qiao Q, Qin Y, Zhang D, Tian Y, Wang S (2017) Diversity of sweepoviruses infecting sweetpotato in china. Plant Dis 101(12):2098–2103

    PubMed  Google Scholar 

  • Lotrakul P, Valverde RA, Clark CA, Sim J, De la RT (1998) Detection of a geminivirus infecting sweetpotato in the United States. Plant Dis 82:1253–1257

    CAS  PubMed  Google Scholar 

  • Lozano G, Trenado HP, Valverde RA, Castillo JN (2009) Novel begomovirus species of recombinant nature in sweetpotato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications. J Gen Virol 90:2550–2562

    CAS  PubMed  Google Scholar 

  • Luan YS, Zhang J, An LJ (2006) First report of Sweetpotato leaf curl virus in China. Plant Dis 90:1111

    CAS  PubMed  Google Scholar 

  • Luan YS, Zhang J, Liu DM, Li WL (2007) Molecular characterization of sweetpotato leaf curl virus isolate from China (SPLCV-CN) and its phylogenetic relationship with other members of the Geminiviridae. Virus Genes 35:379–385

    CAS  PubMed  Google Scholar 

  • Maina S, Miano DW, Mbogo E, Amimo JO, Irungu J, Njiruh PN (2017) Occurrence and genetic variability of partial coat protein gene of sweetpotato leaf curl virus (SPLCV) in Kenya. Afr J Biotech 16(45):2112–2120

    CAS  Google Scholar 

  • Martin DP, Murrell B, Khoosal A, Muhire B (2017) Detecting and analyzing genetic recombination using rdp4. Methods Mol Biol 1525:433–460

    CAS  PubMed  Google Scholar 

  • Mohammed HS, Siddig MARE, Hussein AAE, Ibrahim FA, Navas-Castillo J, Fiallo-Olivé E (2017) First report of sweetpotato leaf curl virus infecting sweetpotato in sudan. Plant Dis 101(5):849

    Google Scholar 

  • Muhire MB, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424

    CAS  PubMed  Google Scholar 

  • Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs A (2002) Molecular evolution of Turnip mosaic virus; evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521

    CAS  PubMed  Google Scholar 

  • Paprotka T, Boiteux LS, Fonseca MEN, Resende RO, Jeske H, Faria JC, Ribeiro SG (2010) Genomic diversity of sweetpotato geminiviruses in a Brazilian germplasm bank. Virus Res 149:224–233

    CAS  PubMed  Google Scholar 

  • Pardina PR, Nome C, Colomba EL, Delgado SF, Feo LD (2012) First report of sweetpotato leaf curl virus infecting sweetpotato in Argentina. Australasian Plant Dis Notes 7(1):157–160

    Google Scholar 

  • Park J, Hwang HS, Buckley KJ, Park JB, Auh CK, Kim DG, Lee S, Davis KR (2010a) C4 protein of beet severe curly top virus is a pathomorphogenetic factor in arabidopsis. Plant Cell Rep 29:1377–1389

    CAS  PubMed  Google Scholar 

  • Park J, Hwang HS, Buckley KJ, Park JB, Auh CK, Kim DG, Lee S, Davis KR (2010b) C4 protein of Beet severe curly top virus is a pathomorphogenetic factor in Arabidopsis. Plant Cell Rep 29(12):1377–1389

    CAS  PubMed  Google Scholar 

  • Park J, Kim S, Choi E, Kwak HR, Kim MK, Lee KY, Choi HS, Lee S (2011) Molecular characterization of sweetpotato leaf curl virus (SPLCV) isolates from Korea: phylogenetic relationship and recombination analysis. Acta Virol 55(4):327–335

    CAS  PubMed  Google Scholar 

  • Prasanna HC, Rai M (2007) Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia. Virol J 4:111

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rubio L, Angeles M, Ayllón A, Kong P, Fernándes A, Polek M, Guerri J, Moreno P, Falk BW (2001) Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol 75:8054–8062

    CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Google Scholar 

  • Tian YP, Liu JL, Zhang CL, Liu YY, Wang B, Li XD, Guo ZK, Valkonen JP (2011) Genetic diversity of Potato virus Y Infecting tobacco crops in China. Phytopathology 101:377–387

    CAS  PubMed  Google Scholar 

  • Tomitaka Y, Ohshima K (2006) A phylogeographic study of the Turnip mosaic virus population in east Asia reveals an ‘emergent’ lineage in Japan. Mol Ecol 15:4437–4457

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tomitaka Y, Yamashita T, Ohshima K (2007) The genetic structure of populations of turnip mosaic virus in kyushu and central honshu, Japan. J Gen Plant Pathol 73(3):197–208

    CAS  Google Scholar 

  • Xie YP, Xing JY, Li XY, Wang X, Sun HJ, Zhao YQ, Zhang CL, Ma DF (2013) Survey of sweetpotato viruses in China. Acta Virol 57(1):81–84

    PubMed  Google Scholar 

  • Yang CX, Wu ZJ, Xie LH (2009) First report of the occurrence of sweetpotato leaf curl virus in tall morning glory (Ipomoea purpurea) in china. Plant Dis 93(7):764

    CAS  PubMed  Google Scholar 

  • Zerbini FM, Briddon RW, Idris A, Martin DP, Moriones E, Navas-Castillo J, Rivera-Bustamante R, Roumagnac P, Varsani A (2017) ICTV virus taxonomy profile: geminiviridae. J Gen Virol 98(2):131

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang SC, Ling KS (2011) Genetic diversity of sweetpotato begomoviruses in the United States and identification of a natural recombinant between sweetpotato leaf curl virus and sweetpotato leaf curl Georgia virus. Adv Virol 156(6):955–968

    CAS  Google Scholar 

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Acknowledgements

Chengling Zhang and Houjun Sun had full access to all the data in the study, and they take the full responsibility for the integrity of the data and the accuracy of the data analyses; Chengling Zhang helped in study conception and design; Dongjing Yang, Mei Zhang and Yiping Xie contributed to acquisition of data ; Chengling Zhang and Jukui Ma analyzed and interpreted the data. All authors read and approved the final manuscript. This work was supported by the National Key R&D Program of China (Grant Number 2018YFD1000703, 2018YFD1000700), the Jiangsu Provincial Natural Science Foundation, China (grant number BK20140230) and the Earmarked Fund for China Agriculture Research System (Grant Number CARS-10-B15).

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  1. Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, 221131, Jiangsu, China

    Chengling Zhang, Houjun Sun, Yiping Xie, Dongjing Yang, Mei Zhang & Jukui Ma

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  1. Chengling Zhang
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Correspondence to Chengling Zhang.

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Zhang, C., Sun, H., Xie, Y. et al. The genetic structure and recombination analyses of Sweetpotato leaf curl virus (SPLCV) population in China. J Plant Dis Prot 127, 741–751 (2020). https://doi.org/10.1007/s41348-020-00348-4

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