Arch Virol (2014) 159:1537–1540 DOI 10.1007/s00705-013-1958-2
ANNOTATED SEQUENCE RECORD
Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China Qili Liu • Zhenchen Zhang • Jianqiang Li • Qi Qiao • Yanhong Qin • Desheng Zhang • Yuting Tian • Shuang Wang • Yongjiang Wang
Received: 14 September 2013 / Accepted: 20 November 2013 / Published online: 1 January 2014 Ó Springer-Verlag Wien 2013
Abstract The complete genome sequence of a novel monopartite begomovirus, isolate G-YU-12-10, was obtained from sweet potato samples exhibiting severe leaf curl symptoms in Xinxiang, Henan Province, China. The genome sequence consisted of 2766 nucleotides and encoded two open reading frames (ORFs) (AV1 and AV2) in the viral-sense strand and four ORFs (AC1-AC4) in the complementary-sense strand. The genome of isolate G-YU-12-10 was closely related to other sweet-potatoinfecting begomoviruses (sweepoviruses) and shared the highest nucleotide sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316). Thus, the G-YU-12-10 isolate represents a novel species according to the demarcation criteria of species in the genus Begomovirus, for which the name Sweet potato leaf curl Henan virus (SPLCHnV) is
Electronic supplementary material The online version of this article (doi:10.1007/s00705-013-1958-2) contains supplementary material, which is available to authorized users. Q. Liu Z. Zhang (&) Q. Qiao Y. Qin D. Zhang Y. Tian S. Wang Y. Wang Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People’s Republic of China e-mail: [email protected] Q. Liu J. Li College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, People’s Republic of China Q. Liu College of Resources and Environment Science, Henan Institute of Science and Technology, Xinxiang 453003, People’s Republic of China
proposed. Interspecific recombination analysis supported the recombination hypothesis, indicating that recombination with other begomoviruses had taken place within AC2 and AC3 ORFs of SPLCHnV and also in the non-coding intergenic region (IR).
Geminiviruses are circular single-stranded DNA plant viruses that cause important diseases in many crop plants worldwide and result in significant crop damage [8]. Based on their host range, genome organization and insect vectors, geminiviruses are classified into seven genera: Mastrevirus, Curtovirus, Topocuvirus, Begomovirus, Becurtovirus, Turncurtovirus and Eragrovirus [1, 9]. The genus Begomovirus is the largest genus in the family Geminiviridae and has been divided into two main groups according to phylogenetic characteristics and genome organization, the Old World and New World begomoviruses [9, 16]. Sweet potato, Ipomoea batatas (L.) Lam. (family Convolvulaceae) is ranked as the seventh most important food crop in global production [15]. China is the largest producer of sweet potato [20]. According to FAO (Food and Agriculture Organization) statistics, the average planting area for sweet potato in China has reached 4.1 million hectares, accounting for 48.3 % of the total world area [12]. Over 30 viruses infecting sweet potato have been identified [5]. Members of ten established begomovirus species and four tentative species are reported to infect sweet potato [7, 9]. Begomoviruses infecting sweet potato are phylogenetically distinct from Old World and New World begomoviruses [10] and are referred to as ‘‘sweepoviruses’’ [2]. Sweepoviruses have been reported to cause sweet potato yield losses and cultivar decline in China [3, 11, 17].
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Fig. 1 Foliar symptoms of viral infection observed in sweet potato sample G-YU-12-10 analyzed in this work
A sweet potato sample (G-YU-12-10) showing severe leaf curl symptoms was collected from a farm in Xinxiang, Henan Province, China (Fig. 1). Total DNA was extracted from leaves using a Universal Genomic DNA Extraction Kit (TaKaRa, Dalian, China). The viral genome was amplified by the rolling-circle amplification (RCA) method [6] using a TempliPhiTM kit (GE Healthcare) following the manufacturer’s protocol. The amplified product was digested with BamHI endonuclease and separated by electrophoresis on a 1.0 % agarose gel. A DNA fragment of the expected size (2.8 kb) was purified and ligated into the pUC118 vector (TaKaRa) digested with corresponding restriction enzyme. The recombinant plasmid was used to transform competent cells of Escherichia coli strain JM109, and the insert was sequenced at TaKaRa (China). Nucleotide similarity searches were initially performed by BLAST in the NCBI database (www.ncbi.nlm.nih.gov). Nucleotide identity percentages of the complete genome and the predicted open reading frames (ORFs) were compared with those of the most closely related begomoviruses using the SDT program [14]. A neighbor-joining phylogenetic tree was generated using the MEGA5 software [21]. Recombination analysis was carried out using the RDP, GENECOV, Bootscan, Max Chi, Chimaera, SiScan and 3Seq methods in the RDP3.44 software [13]. The G-YU-12-10 sequence consisted of 2766 nt (GenBank accession number KC907406), encoding six open reading frames (ORFs). Two ORFs, AV1 (nt 257-1021) and AV2 (nt 91-465), were located in the viral-sense
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strand, and four ORFs, namely AC1 (nt 1524-2618), AC2 (nt 1169-1615), AC3 (nt 1018-1452) and AC4 (nt 2204-2461), were located in the complementary-sense strand. A non-coding intergenic region (IR) consisting of 404 nt was located between AC1and AV1. This IR contained the conserved nonanucleotide sequence TAATATTAC, which functions in the initiation of rolling-circle replication of begomoviruses [19]. BLAST analysis showed that the genome of G-YU-12-10 was closely related to those of other sweepoviruses. Sequence identity analysis showed that the G-YU-12-10 genome had the highest sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316) and shared nucleotide sequence identity (85.7 %) with sweet potato leaf curl Georgia virus (SPLCGoV; AF326775). The nucleotide sequence identities of AV1, AV2, AC1, AC2, AC3, AC4 between G-YU-12-10 and SPLCCSV were 92.4 %, 93.0 %, 90.9 %, 77.3 %, 79.3 %, 99.2 %, respectively (Supplemental Table 1). Phylogenetic analysis confirmed the relationships between the G-YU-1210 isolate and other sweepoviruses (Fig. 2). DNA-B or satellite molecules were not detected in the DNA or RCA products of the sweet potato sample (G-YU12-10) using primers specific for DNA-B or DNAb of begomoviruses [4, 18]. These results suggest that isolate G-YU-12-10 is a monopartite begomovirus. G-YU-12-10 represents a novel species according to the species demarcation criteria for begomoviruses proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) [7]. We propose the name Sweet potato leaf curl Henan virus (SPLCHnV) for this species. Interspecific recombination analysis provided evidence for recombination events in the SPLCHnV sequence. It was predicted that the AC2 and AC3 regions of SPLCHnV were generated by recombination between the AC2 and AC3 genes of sweet potato leaf curl China virus (SPLCCNV[CN:05], DQ512731) and sweet potato leaf curl virusCE[BR:For1] (SPLCV-CE[BR:For1], FJ969832). In the IR region, the recombination was between sweet potato leaf curl Bengal virus (SPLCBeV, FN432356) and SPLCCNVZJ (JF736657) (Supplemental Table 2). Many viral diseases of sweet potato severely limit sustainable production of this crop in China [22]. Henan is the major sweet-potato-producing province in China, and the occurrence of SPLCHnV may lead to increasing yield losses of sweet potato in the future. Further studies are in progress to confirm the potential harmfulness and the geographical distribution of SPLCHnV in China.
Monopartite begomovirus infecting sweet potato in China
Fig. 2 Phylogenetic tree illustrating the relationships among SPLCHnV (marked with a dot) and other 30 begomovirus isolates obtained from GenBank. The tree was constructed by the neighborjoining method with 1,000 bootstrap replicates using MEGA5 software. Acronyms and accession numbers of these begomoviruses are as follows: SPLCCaV-[ES:CI:BG21:02] (sweet potato leaf curl Canary virus), EU856365; SPLCCNV-[CN:05] (sweet potato leaf curl China virus), DQ512731; SPLCGoV-[US:Geo16] (sweet potato leaf curl Georgia virus), AF326775; SPLCLaV-[ ES:CI:BG27:02] (sweet potato leaf curl Lanzarote virus), EF456746; SPLCESV[ES:CI:BG1:02] (sweet potato leaf curl Spain virus), EF456741; SPLCBeV (sweet potato leaf curl Bengal virus), FN432356; SPLCITV (sweet potato leaf curl Italy virus), AJ586885; SPLCJV (sweet potato leaf curl Japan virus), AB433787; SPLCShV (sweet potato leaf
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curl Shanghai virus), EU309693; SPLCV-CN-[CN:Yn:RL31:07] (sweet potato leaf curl virus), EU253456; SPLCV-[US:SC:377-23], HQ333135; SPLCV-CE[BR:For1], FJ969832; SPLCV-JS, FJ176701; SPLCV-F-p1, FJ515896; SPLCV-F-p2, FJ515897; SPLCV-F-p3, FJ515898; SPLCV-RL7, EU267799; SPLCV-GZ01, JX286653; SPLCV-GZ02, JX286654; SPLCV-XN01, JX286655; SPLCCNVZJ, JF736657; SPLCV-MG, JF768740; SPLCV-Y338, FN806776; SPLCV-Merremia N4, DQ644563; SPLCV-J-508, FJ560719; sweet potato leaf curl South Carolina virus (SPLCSCV), HQ333144; sweet potato leaf curl Sao Paulo virus (SPLCSPV), HQ393477; sweet potato mosaic virus (SPMoV), FJ969831; sweet potato leaf curl Uganda virus (SPLCUV), FR751068; sweet potato leaf curl China Sichuan virus (SPLCCSV), KC488316
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1540 Acknowledgments This work was supported by a grant from the Earmarked Fund for China Agriculture Research System (CARS-11B-07)
References 1. Adams MJ, King AMQ, Carstens EB (2013) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses. Arch Virol 158:2023–2030 2. Albuquerque LC, Inoue-Nagata AK, Pinheiro B, Resende RO, Moriones E, Navas-Castillo J (2012) Genetic diversity and recombination analysis of sweepoviruses from Brazil. Virol J 9:241 3. Bi HP, Zhang P (2012) Molecular characterization of two sweepoviruses from China and evaluation of the infectivity of cloned SPLCV-JS in Nicotiana benthamiana. Arch Virol 157:441–454 4. Briddon RW, Bull SE, Mansoor S, Amin I, Markham PG (2002) Universal primers for the PCR-mediated amplification of DNA b: a molecule associated with some monopartite begomoviruses. Mol Biotechnol 20:315–318 5. Clark CA, Davis JA, Abad JA, Cuellar W, Fuentes S, Kreuze J, Gibson R, Mukasa SB, Tugume AK, Tairo F, Valkonen JPT (2012) Sweet potato viruses: 15 years of progress on understanding and managing complex diseases. Plant Dis 96:168–185 6. Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9–16 7. ICTV Geminiviridae Study Group (2013) New species and revised taxonomy proposal for the genus Begomovirus (Geminiviridae): phylogenetic and pairwise distance analysis using the same approach as implemented for the genera Mastrevirus and Curtovirus in the same family. http://talk.ictvonline.org/files/pro posals/taxonomy_proposals_plant1/m/plant04/4720.aspx 8. Jeske H (2009) Geminiviruses. In: Zur Hausen H, de Villiers E-M (eds) Torque Teno Virus: the still elusive human pathogens, vol 331. Springer, Berlin, pp 185–226 9. King AMQ, Adams MJ, Carstcns EB, Lefkowitz EJ (2012) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier/Academic Press, San Diego, pp 351–372 10. Lozano G, Trenado HP, Valverde RA, Navas-Castillo J (2009) Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications. J Gen Virol 90:2550–2562
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Q. Liu et al. 11. Luan YS, Zhang J, Liu DM, Wen LL (2007) Molecular characterization of sweet potato leaf curl virus isolate from China (SPLCV-CN) and its phylogenetic relationship with other members of the Geminiviridae. Virus Genes 35:379–385 12. Ma D, Li H, Tang J, Xie Y, Li Q, Cao Q, Zhang Y, Zhang A (2010) Current status and future prospects of development of sweet potato industry in China. Sweet potato in food and energy security: In: Proceedings of China Xuzhou 4th international sweet potato symposium and 4th China–Japan–Korea sweet potato workshop. Xuzhou, China, pp 3–10 13. Martin DP, Lemey P, Lott M, Vincent M, Posada D, Lefeuvre P (2010) RDP3: A flexible and fast computer program for analyzing recombination. Bioinformatics 26(19):2462–2463 14. Muhire B, 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 15. O’ Brien PJ (1972) The sweet potato: its origin and dispersal. Am Anthropol 74:342–365 16. Paximadis M, Idris AM, Torres-Jerez I, Villarreal A, Rey ME, Brown JK (1999) Characterization of tobacco geminiviruses in the Old and New World. Arch Virol 144:703–717 17. Qiao Q, Zhang ZC, Zhang DS, Qin YH, Tian YT, Wang YJ (2012) Serological and molecular detection of viruses infecting sweet potato in China (in Chinese). Acta Phytopathol Sin 42(1):10–16 18. Rojas MR, Gilbertson RL, Russell DR, Maxwell DP (1993) Use of degenerate primers in the polymerase chain-reaction to detect whitefly-transmitted geminiviruses. Plant Dis 77:340–347 19. Stenger DC, Revington GN, Stevenson MC, Bisaro DM (1991) Replicational release of geminivirus genomes from tandemly repeated copies: evidence for rolling-circle replication of a plant viral DNA. Proc Natl Acad Sci 88:8029–8803 20. Tairo F, Mukasa SB, Jones RAC, Kullaya A, Rubaihayo PR, Valkonen JPT (2005) Unravelling the genetic diversity of the three main viruses involved in sweet potato virus disease (SPVD), and its practical implications. Mol Plant Pathol 6:199–211 21. 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 22. Wang QM, Zhang LM, Wang B, Yin ZF, Feng CH, Wang QC (2010) Sweetpotato viruses in China. Crop Prot 29:110–114
ANNOTATED SEQUENCE RECORD
Complete genome sequence of a novel monopartite begomovirus infecting sweet potato in China Qili Liu • Zhenchen Zhang • Jianqiang Li • Qi Qiao • Yanhong Qin • Desheng Zhang • Yuting Tian • Shuang Wang • Yongjiang Wang
Received: 14 September 2013 / Accepted: 20 November 2013 / Published online: 1 January 2014 Ó Springer-Verlag Wien 2013
Abstract The complete genome sequence of a novel monopartite begomovirus, isolate G-YU-12-10, was obtained from sweet potato samples exhibiting severe leaf curl symptoms in Xinxiang, Henan Province, China. The genome sequence consisted of 2766 nucleotides and encoded two open reading frames (ORFs) (AV1 and AV2) in the viral-sense strand and four ORFs (AC1-AC4) in the complementary-sense strand. The genome of isolate G-YU-12-10 was closely related to other sweet-potatoinfecting begomoviruses (sweepoviruses) and shared the highest nucleotide sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316). Thus, the G-YU-12-10 isolate represents a novel species according to the demarcation criteria of species in the genus Begomovirus, for which the name Sweet potato leaf curl Henan virus (SPLCHnV) is
Electronic supplementary material The online version of this article (doi:10.1007/s00705-013-1958-2) contains supplementary material, which is available to authorized users. Q. Liu Z. Zhang (&) Q. Qiao Y. Qin D. Zhang Y. Tian S. Wang Y. Wang Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, People’s Republic of China e-mail: [email protected] Q. Liu J. Li College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, People’s Republic of China Q. Liu College of Resources and Environment Science, Henan Institute of Science and Technology, Xinxiang 453003, People’s Republic of China
proposed. Interspecific recombination analysis supported the recombination hypothesis, indicating that recombination with other begomoviruses had taken place within AC2 and AC3 ORFs of SPLCHnV and also in the non-coding intergenic region (IR).
Geminiviruses are circular single-stranded DNA plant viruses that cause important diseases in many crop plants worldwide and result in significant crop damage [8]. Based on their host range, genome organization and insect vectors, geminiviruses are classified into seven genera: Mastrevirus, Curtovirus, Topocuvirus, Begomovirus, Becurtovirus, Turncurtovirus and Eragrovirus [1, 9]. The genus Begomovirus is the largest genus in the family Geminiviridae and has been divided into two main groups according to phylogenetic characteristics and genome organization, the Old World and New World begomoviruses [9, 16]. Sweet potato, Ipomoea batatas (L.) Lam. (family Convolvulaceae) is ranked as the seventh most important food crop in global production [15]. China is the largest producer of sweet potato [20]. According to FAO (Food and Agriculture Organization) statistics, the average planting area for sweet potato in China has reached 4.1 million hectares, accounting for 48.3 % of the total world area [12]. Over 30 viruses infecting sweet potato have been identified [5]. Members of ten established begomovirus species and four tentative species are reported to infect sweet potato [7, 9]. Begomoviruses infecting sweet potato are phylogenetically distinct from Old World and New World begomoviruses [10] and are referred to as ‘‘sweepoviruses’’ [2]. Sweepoviruses have been reported to cause sweet potato yield losses and cultivar decline in China [3, 11, 17].
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Fig. 1 Foliar symptoms of viral infection observed in sweet potato sample G-YU-12-10 analyzed in this work
A sweet potato sample (G-YU-12-10) showing severe leaf curl symptoms was collected from a farm in Xinxiang, Henan Province, China (Fig. 1). Total DNA was extracted from leaves using a Universal Genomic DNA Extraction Kit (TaKaRa, Dalian, China). The viral genome was amplified by the rolling-circle amplification (RCA) method [6] using a TempliPhiTM kit (GE Healthcare) following the manufacturer’s protocol. The amplified product was digested with BamHI endonuclease and separated by electrophoresis on a 1.0 % agarose gel. A DNA fragment of the expected size (2.8 kb) was purified and ligated into the pUC118 vector (TaKaRa) digested with corresponding restriction enzyme. The recombinant plasmid was used to transform competent cells of Escherichia coli strain JM109, and the insert was sequenced at TaKaRa (China). Nucleotide similarity searches were initially performed by BLAST in the NCBI database (www.ncbi.nlm.nih.gov). Nucleotide identity percentages of the complete genome and the predicted open reading frames (ORFs) were compared with those of the most closely related begomoviruses using the SDT program [14]. A neighbor-joining phylogenetic tree was generated using the MEGA5 software [21]. Recombination analysis was carried out using the RDP, GENECOV, Bootscan, Max Chi, Chimaera, SiScan and 3Seq methods in the RDP3.44 software [13]. The G-YU-12-10 sequence consisted of 2766 nt (GenBank accession number KC907406), encoding six open reading frames (ORFs). Two ORFs, AV1 (nt 257-1021) and AV2 (nt 91-465), were located in the viral-sense
123
Q. Liu et al.
strand, and four ORFs, namely AC1 (nt 1524-2618), AC2 (nt 1169-1615), AC3 (nt 1018-1452) and AC4 (nt 2204-2461), were located in the complementary-sense strand. A non-coding intergenic region (IR) consisting of 404 nt was located between AC1and AV1. This IR contained the conserved nonanucleotide sequence TAATATTAC, which functions in the initiation of rolling-circle replication of begomoviruses [19]. BLAST analysis showed that the genome of G-YU-12-10 was closely related to those of other sweepoviruses. Sequence identity analysis showed that the G-YU-12-10 genome had the highest sequence identity (89.0 %) with sweet potato leaf curl China Sichuan virus (SPLCCSV, KC488316) and shared nucleotide sequence identity (85.7 %) with sweet potato leaf curl Georgia virus (SPLCGoV; AF326775). The nucleotide sequence identities of AV1, AV2, AC1, AC2, AC3, AC4 between G-YU-12-10 and SPLCCSV were 92.4 %, 93.0 %, 90.9 %, 77.3 %, 79.3 %, 99.2 %, respectively (Supplemental Table 1). Phylogenetic analysis confirmed the relationships between the G-YU-1210 isolate and other sweepoviruses (Fig. 2). DNA-B or satellite molecules were not detected in the DNA or RCA products of the sweet potato sample (G-YU12-10) using primers specific for DNA-B or DNAb of begomoviruses [4, 18]. These results suggest that isolate G-YU-12-10 is a monopartite begomovirus. G-YU-12-10 represents a novel species according to the species demarcation criteria for begomoviruses proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) [7]. We propose the name Sweet potato leaf curl Henan virus (SPLCHnV) for this species. Interspecific recombination analysis provided evidence for recombination events in the SPLCHnV sequence. It was predicted that the AC2 and AC3 regions of SPLCHnV were generated by recombination between the AC2 and AC3 genes of sweet potato leaf curl China virus (SPLCCNV[CN:05], DQ512731) and sweet potato leaf curl virusCE[BR:For1] (SPLCV-CE[BR:For1], FJ969832). In the IR region, the recombination was between sweet potato leaf curl Bengal virus (SPLCBeV, FN432356) and SPLCCNVZJ (JF736657) (Supplemental Table 2). Many viral diseases of sweet potato severely limit sustainable production of this crop in China [22]. Henan is the major sweet-potato-producing province in China, and the occurrence of SPLCHnV may lead to increasing yield losses of sweet potato in the future. Further studies are in progress to confirm the potential harmfulness and the geographical distribution of SPLCHnV in China.
Monopartite begomovirus infecting sweet potato in China
Fig. 2 Phylogenetic tree illustrating the relationships among SPLCHnV (marked with a dot) and other 30 begomovirus isolates obtained from GenBank. The tree was constructed by the neighborjoining method with 1,000 bootstrap replicates using MEGA5 software. Acronyms and accession numbers of these begomoviruses are as follows: SPLCCaV-[ES:CI:BG21:02] (sweet potato leaf curl Canary virus), EU856365; SPLCCNV-[CN:05] (sweet potato leaf curl China virus), DQ512731; SPLCGoV-[US:Geo16] (sweet potato leaf curl Georgia virus), AF326775; SPLCLaV-[ ES:CI:BG27:02] (sweet potato leaf curl Lanzarote virus), EF456746; SPLCESV[ES:CI:BG1:02] (sweet potato leaf curl Spain virus), EF456741; SPLCBeV (sweet potato leaf curl Bengal virus), FN432356; SPLCITV (sweet potato leaf curl Italy virus), AJ586885; SPLCJV (sweet potato leaf curl Japan virus), AB433787; SPLCShV (sweet potato leaf
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curl Shanghai virus), EU309693; SPLCV-CN-[CN:Yn:RL31:07] (sweet potato leaf curl virus), EU253456; SPLCV-[US:SC:377-23], HQ333135; SPLCV-CE[BR:For1], FJ969832; SPLCV-JS, FJ176701; SPLCV-F-p1, FJ515896; SPLCV-F-p2, FJ515897; SPLCV-F-p3, FJ515898; SPLCV-RL7, EU267799; SPLCV-GZ01, JX286653; SPLCV-GZ02, JX286654; SPLCV-XN01, JX286655; SPLCCNVZJ, JF736657; SPLCV-MG, JF768740; SPLCV-Y338, FN806776; SPLCV-Merremia N4, DQ644563; SPLCV-J-508, FJ560719; sweet potato leaf curl South Carolina virus (SPLCSCV), HQ333144; sweet potato leaf curl Sao Paulo virus (SPLCSPV), HQ393477; sweet potato mosaic virus (SPMoV), FJ969831; sweet potato leaf curl Uganda virus (SPLCUV), FR751068; sweet potato leaf curl China Sichuan virus (SPLCCSV), KC488316
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1540 Acknowledgments This work was supported by a grant from the Earmarked Fund for China Agriculture Research System (CARS-11B-07)
References 1. Adams MJ, King AMQ, Carstens EB (2013) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses. Arch Virol 158:2023–2030 2. Albuquerque LC, Inoue-Nagata AK, Pinheiro B, Resende RO, Moriones E, Navas-Castillo J (2012) Genetic diversity and recombination analysis of sweepoviruses from Brazil. Virol J 9:241 3. Bi HP, Zhang P (2012) Molecular characterization of two sweepoviruses from China and evaluation of the infectivity of cloned SPLCV-JS in Nicotiana benthamiana. Arch Virol 157:441–454 4. Briddon RW, Bull SE, Mansoor S, Amin I, Markham PG (2002) Universal primers for the PCR-mediated amplification of DNA b: a molecule associated with some monopartite begomoviruses. Mol Biotechnol 20:315–318 5. Clark CA, Davis JA, Abad JA, Cuellar W, Fuentes S, Kreuze J, Gibson R, Mukasa SB, Tugume AK, Tairo F, Valkonen JPT (2012) Sweet potato viruses: 15 years of progress on understanding and managing complex diseases. Plant Dis 96:168–185 6. Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9–16 7. ICTV Geminiviridae Study Group (2013) New species and revised taxonomy proposal for the genus Begomovirus (Geminiviridae): phylogenetic and pairwise distance analysis using the same approach as implemented for the genera Mastrevirus and Curtovirus in the same family. http://talk.ictvonline.org/files/pro posals/taxonomy_proposals_plant1/m/plant04/4720.aspx 8. Jeske H (2009) Geminiviruses. In: Zur Hausen H, de Villiers E-M (eds) Torque Teno Virus: the still elusive human pathogens, vol 331. Springer, Berlin, pp 185–226 9. King AMQ, Adams MJ, Carstcns EB, Lefkowitz EJ (2012) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier/Academic Press, San Diego, pp 351–372 10. Lozano G, Trenado HP, Valverde RA, Navas-Castillo J (2009) Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications. J Gen Virol 90:2550–2562
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Q. Liu et al. 11. Luan YS, Zhang J, Liu DM, Wen LL (2007) Molecular characterization of sweet potato leaf curl virus isolate from China (SPLCV-CN) and its phylogenetic relationship with other members of the Geminiviridae. Virus Genes 35:379–385 12. Ma D, Li H, Tang J, Xie Y, Li Q, Cao Q, Zhang Y, Zhang A (2010) Current status and future prospects of development of sweet potato industry in China. Sweet potato in food and energy security: In: Proceedings of China Xuzhou 4th international sweet potato symposium and 4th China–Japan–Korea sweet potato workshop. Xuzhou, China, pp 3–10 13. Martin DP, Lemey P, Lott M, Vincent M, Posada D, Lefeuvre P (2010) RDP3: A flexible and fast computer program for analyzing recombination. Bioinformatics 26(19):2462–2463 14. Muhire B, 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 15. O’ Brien PJ (1972) The sweet potato: its origin and dispersal. Am Anthropol 74:342–365 16. Paximadis M, Idris AM, Torres-Jerez I, Villarreal A, Rey ME, Brown JK (1999) Characterization of tobacco geminiviruses in the Old and New World. Arch Virol 144:703–717 17. Qiao Q, Zhang ZC, Zhang DS, Qin YH, Tian YT, Wang YJ (2012) Serological and molecular detection of viruses infecting sweet potato in China (in Chinese). Acta Phytopathol Sin 42(1):10–16 18. Rojas MR, Gilbertson RL, Russell DR, Maxwell DP (1993) Use of degenerate primers in the polymerase chain-reaction to detect whitefly-transmitted geminiviruses. Plant Dis 77:340–347 19. Stenger DC, Revington GN, Stevenson MC, Bisaro DM (1991) Replicational release of geminivirus genomes from tandemly repeated copies: evidence for rolling-circle replication of a plant viral DNA. Proc Natl Acad Sci 88:8029–8803 20. Tairo F, Mukasa SB, Jones RAC, Kullaya A, Rubaihayo PR, Valkonen JPT (2005) Unravelling the genetic diversity of the three main viruses involved in sweet potato virus disease (SPVD), and its practical implications. Mol Plant Pathol 6:199–211 21. 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 22. Wang QM, Zhang LM, Wang B, Yin ZF, Feng CH, Wang QC (2010) Sweetpotato viruses in China. Crop Prot 29:110–114
