Abstract
Isolates of Turnip mosaic virus (TuMV) are divided into four molecular lineages based on host range and geographical origins. Basal-BR is one of the four lineages and represented a new emergent lineage in East Asia. In one previous paper, we report the occurrence of basal-BR isolates in China. Here, we presented the first two complete genomic sequences of Chinese TuMV basal-BR isolates, WFLB06 and TANX2. The genomes of both isolates were 9833 nucleotides excluding the poly(A) tail, and had identical genomic structure. Most of their genes shared the highest identities with Japanese isolates. Recombination analysis showed that WFLB06 was an interlineage recombinant of basal-BR and Asian-BR parents, while TANX2 was an intralineage recombinant of basal-BR parents, and these two isolates represented two novel recombination patterns of TuMV. The ratio of nonsynonymous and synonymous substitution for the P1 gene of Chinese TuMV population was the highest and amounted to 12 times higher than that for the NIa-Pro gene, which implies that the selection pressure on the P1 gene was the highest among the genes present in the genome.
Similar content being viewed by others
References
C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball, Virus Taxonomy. Eighth report of the International Committee on Taxonomy of Viruses (Elsevier Academic Press, San Diego, USA, 2005)
D.D. Shukla, C.W. Ward, A.A. Brunt, The Potyviridae (CAB International, Wallingford, UK, 1994), pp. 385–389
A.A. Brunt, K. Crabtree, M.J. Dallwitz, A.J. Gibbs, L. Watson, Viruses of Plants- Descriptions and lists from the VIDE database. (CAB International, 1996)
J.A. Tomlinson, Ann. Appl. Biol. 110, 661–681 (1987). doi:https://doi.org/10.1111/j.1744-7348.1987.tb04187.x
J.A. Walsh, C.E. Jenner, Mol. Plant Pathol. 3, 289–300 (2002). doi:https://doi.org/10.1046/j.1364-3703.2002.00132.x
J.L. Riechmann, S. Lain, J.A. Garcia, J. Gen. Virol. 73, 1–16 (1992). doi:https://doi.org/10.1099/0022-1317-73-1-1
B.Y.W. Chung, W.A. Miller, J.F. Atkins, A.E. Firth, Proc. Natl. Acad. Sci. USA 105, 5897–5902 (2008). doi:https://doi.org/10.1073/pnas.0800468105
S.K. Green, T.C. Deng, Plant Dis. 69, 28–31 (1985). doi:https://doi.org/10.1094/PD-69-28
C.E. Jenner, G.J. Keane, J.A. Walsh, Plant Pathol. 48, 101–108 (1999). doi:https://doi.org/10.1046/j.1365-3059.1999.00309.x
C.E. Jenner, J.A. Walsh, Plant Pathol. 45, 848–856 (1996). doi:https://doi.org/10.1111/j.1365-3059.1996.tb02895.x
K. Ohshima, Y. Yamaguchi, R. Hirota, T. Hamamoto, K. Tomimura, Z. Tan, T. Sano, F. Azuhata, J.A. Walsh, J. Fletcher, J. Chen, A. Gera, A. Gibbs, J. Gen. Virol. 83, 1511–1521 (2002)
K. Tomimura, A.J. Gibbs, C.E. Jenner, J.A. Walsh, K. Ohshima, Mol. Ecol. 12, 2099–2111 (2003). doi:https://doi.org/10.1046/j.1365-294X.2003.01881.x
Z.Y. Tan, A.J. Gibbs, Y. Tomitaka, F. Sánchez, F. Ponz, K. Ohshima, J. Gen. Virol. 86, 501–510 (2005). doi:https://doi.org/10.1099/vir.0.80540-0
E.R. Chare, E.C. Holmes, Arch. Virol. 151, 933–946 (2006). doi:https://doi.org/10.1007/s00705-005-0675-x
Z. Tan, Y. Wada, J. Chen, K. Ohshima, J. Gen. Virol. 85, 2683–2696 (2004). doi:https://doi.org/10.1099/vir.0.80124-0
K. Ohshima, Y. Tomitaka, J.T. Wood, Y. Minematsu, H. Kajiyama, K. Tomimura, A.J. Gibbs, J. Gen. Virol. 88, 298–315 (2007). doi:https://doi.org/10.1099/vir.0.82335-0
Y. Tomitaka, K. Ohshima, Mol. Ecol. 15, 4437–4457 (2006). doi:https://doi.org/10.1111/j.1365-294X.2006.03094.x
Y. Tomitaka, T. Yamashita, K. Ohshima, J. Gen. Plant Pathol. 73, 197–208 (2007). doi:https://doi.org/10.1007/s10327-007-0003-2
M.L. Shi, Acta Phytopathologica Sin. 37, 383–389 (2007)
Y.Z. Song, L.L. Li, C.X. Zhu, F.J. Wen, F.K. Wen, Sci. Agric. Sin. 38, 504–510 (2005)
Y.P. Tian, X.P. Zhu, J.L. Liu, X.Q. Yu, J. Du, J. Kreuze, X.D. Li, J. Phytopathol. 155, 333–341 (2007). doi:https://doi.org/10.1111/j.1439-0434.2007.01236.x
K.S. Ling, H.Y. Zhu, N. Petrovic, D. Gonsalves, J. Phytopathol. 155, 65–69 (2007). doi:https://doi.org/10.1111/j.1439-0434.2007.01179.x
X.Q. Yu, Y.F. Lan, H.Y. Wang, J.L. Liu, X.P. Zhu, J.P.T. Valkonen, X.D. Li, Virus Genes 35, 801–806 (2007). doi:https://doi.org/10.1007/s11262-007-0135-7
J.D. Thompson, D.G. Higgins, T.J. Gibson, Nucleic Acids Res. 22, 4673–4680 (1994). doi:https://doi.org/10.1093/nar/22.22.4673
S. Kumar, K. Tamura, M. Nei, Brief. Bioinform. 5, 150–163 (2004). doi:https://doi.org/10.1093/bib/5.2.150
S.A. Sawyer, GENECONV: A Computer Package for the Statistical Detection of Gene Conversion. (Department of Mathematics, Washington University in St. Louis, available at http://www.math.wustl.edu/~sawyer, 1999)
M.O. Salminen, J.K. Carr, D.S. Burke, F.E. McCutchan, AIDS Res. Hum. Retroviruses 11, 1423–1425 (1995)
J. Maynard Smith, J. Mol. Evol. 34, 126–129 (1992)
D. Posada, K.A. Crandall, Proc. Natl. Acad. Sci. USA 98, 13757–13762 (2001). doi:https://doi.org/10.1073/pnas.241370698
M.J. Gibbs, J.S. Armstrong, A.J. Gibbs, Bioinformatics 16, 573–582 (2000). doi:https://doi.org/10.1093/bioinformatics/16.7.573
D. Martin, C. Williamson, D. Posada, Bioinformatics 21, 260–262 (2005). doi:https://doi.org/10.1093/bioinformatics/bth490
G.F. Weiller, Mol. Biol. Evol. 15, 326–335 (1998)
P. Pamilo, N.O. Bianchi, Mol. Biol. Evol. 10, 271–281 (1993)
W.H. Li, J. Mol. Evol. 36, 96–99 (1993). doi:https://doi.org/10.1007/BF02407308
J. Verchot, E.V. Koonin, J.C. Carrington, Virology 185, 527–535 (1991). doi:https://doi.org/10.1016/0042-6822(91)90522-D
C. Robaglia, M. Durand-Tardif, M. Tronchet, G. Boudazin, S. Astier-Manifacier, F. Casse-Delbart, J. Gen. Virol. 70, 935–947 (1989). doi:https://doi.org/10.1099/0022-1317-70-4-935
A. Gal-On, Phytopathology 90, 467–473 (2000). doi:https://doi.org/10.1094/PHYTO.2000.90.5.467
A. Gal-On, Mol. Plant Pathol. 8, 139–150 (2007). doi:https://doi.org/10.1111/j.1364-3703.2007.00381.x
Y.M. Shiboleth, E. Haronsky, D. Leibman, T. Arazi, M. Wassenegger, S.A. Whitham, V. Gaba, A. Gal-On, J. Virol. 82, 13135–13148 (2007). doi:https://doi.org/10.1128/JVI.01031-07
H. Huet, A. Gal-On, E. Meir, H. Lecoq, B. Raccah, J. Gen. Virol. 75, 1407–1414 (1994)
C. Plisson, M. Drucker, S. Blanc, S. German-Retana, O. Le Gall, D. Thomas, P. Bron, J. Biol. Chem. 278, 23753–23761 (2003). doi:https://doi.org/10.1074/jbc.M302512200
G. Kadare, A.L. Haenni, Virus-encoded RNA helicases. J. Virol. 71, 2583–2590 (1997)
W.X. Liang, L.M. Song, G.Z. Tian, H.F. LI, Z.F. Fan, Arch. Virol. 151, 2311–2319 (2006). doi:https://doi.org/10.1007/s00705-006-0780-5
J.F. Murphy, P.G. Klein, A.G. Hunt, J.G. Shaw, Virology 220, 535–538 (1996). doi:https://doi.org/10.1006/viro.1996.0344
W.G. Dougherty, T.D. Parks, S.M. Cary, J.F. Bazan, R.J. Fletterrick, Virology 172, 302–310 (1989). doi:https://doi.org/10.1016/0042-6822(89)90132-3
G. Dujovny, T. Sasaya, H. Koganesawa, T. Usugi, K. Shohara, S.L. Lenardon, Arch. Virol. 145, 2249–2258 (2000). doi:https://doi.org/10.1007/s007050070018
C.D. Atreya, B. Raccah, T.P. Pirone, Virology 178, 161–165 (1990). doi:https://doi.org/10.1016/0042-6822(90)90389-9
A. Valli, G. Dujovny, J.A. García, J. Virol. 82, 974–986 (2008). doi:https://doi.org/10.1128/JVI.01664-07
K. Ohshima, M. Tanaka, N. Sako, Arch. Virol. 141, 1991–1997 (1996)
E. Kozubek, W. Irzykowski, P. J. Lehmann, J. Appl. Genet. 48, 295–306 (2007)
C.E. Jenner, X. Wang, K. Tomimura, K. Ohshima, F. Ponz, J.A. Walsh, Mol. Plant Microbe Interact. 16, 777–784 (2003)
C.E. Jenner, K. Tomimura, K. Ohshima, S.L. Hughes, J.A. Walsh, Virology 300, 50–59 (2002)
O. Nicolas, J.F. Laliberte, J. Gen. Virol. 73, 2785–2793 (1992)
C.C. Chen, C.H. Chao, C.C. Chen, S.D. Yeh, H.T. Tsai, C.A. Chang, Plant Dis. 87, 901–905 (2003)
N. Suehiro, T. Natsuaki, T. Watanabe, S. Okuda, J. Gen. Virol. 85, 2087–2098 (2004)
C.E. Jenner, F. Sánchez, S.B. Nettleship, G.D. Foster, F. Ponz, J.A. Walsh. Mol. Plant Microbe Interact. 13, 1102–1108 (2000)
Acknowledgments
We thank the anonymous reviewers and Dr. Shien Lu in Department of Entomology and Plant Pathology, Mississippi State University for their valuable suggestions on revising the manuscript. This study was supported partially by Program for New Century Excellent Talents in Universities (NCET-07-0520), Natural Scientific Foundation of China (NSFC, 30471138) and Shandong Province (Z2007D04), and Special Research Fund for the Doctoral Program of Higher Education (SRFDP, 20050434003, 20080434006).
Author information
Authors and Affiliations
Corresponding author
Additional information
Hong-Yan Wang and Jin-Liang Liu contributed equally.
Rights and permissions
About this article
Cite this article
Wang, HY., Liu, JL., Gao, R. et al. Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China. Virus Genes 38, 421–428 (2009). https://doi.org/10.1007/s11262-009-0335-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11262-009-0335-4