Abstract
The first complete genome sequence of calla lily chlorotic spot virus (CCSV) from Lijiang in northwestern Yunnan Province was obtained using RT-PCR with designed primers. The genome of CCSV isolate LJ-1-Yunnan is tripartite. The small (S) RNA is 3182 nucleotides (nt) in length and encodes a nonstructural protein (NSs, 1383 nt) and a nuclear nucleocapsid (N, 834 nt), separated by an 836-nt intergenic region (IGR). The medium (M) RNA is 4749 nt in length and encodes a nonstructural movement protein (NSm, 930 nt) and a glycoprotein (GnGc, 3,372 nt), also separated by a 349-nt IGR. The large (L) RNA is 8912 nt in length and encodes a predicted RNA-dependent RNA polymerase (RdRp, 8652 nt). The nucleotide sequences of the three viral RNA segments are 92-94 % identical to the published CCSV genome sequence, and the amino acid sequences of the encoded proteins are 96-98 % identical. However, the IGRs of the S and M RNAs are less similar, with 86 and 72 % identity, respectively. Genome sequence comparisons and phylogenetic analysis indicate that the Lijiang CCSV isolate is a unique tospovirus isolate that differs from CCSV isolates in other geographic regions.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.References
Chen C, Chen T, Lin Y, Yeh S, Hsu H (2005) A chlorotic spot disease on calla lilies (Zantedeschia spp.) is caused by a tospovirus serologically but distantly related to Watermelon silver mottle virus. Plant Dis 89:440–445
Chen T, Li J, Lin Y, Yeh Y, Kang Y, Huang L, Yeh S (2012) Genomic characterization of Calla lily chlorotic spot virus and design of broad-spectrum primers for detection of tospoviruses. Plant Pathol 61:183–194
Cheng Y, Zheng Y, Tai C, Yen J, Chen Y, Jan F (2014) Identification, characterisation and detection of a new tospovirus on sweet pepper. Ann Appl Biol 164:107–115
Chu F, Chao C, Peng Y, Lin S, Chen C, Yeh S (2001) Serological and molecular characterization of Peanut chlorotic fan-spot virus, a new species of the genus Tospovirus. Phytopathology 91:856–863
Cortez I, Saaijer J, Wongjkaew K, Pereira A, Goldbach R, Peters D, Kormelink R (2001) Identification and characterization of a novel tospovirus species using a new RT-PCR approach. Arch Virol 146:265–278
De Avila A, De Haan P, Kormelink R, Resende RdO, Goldbach R, Peters D (1993) Classification of tospoviruses based on phylogeny of nucleoprotein gene sequences. J Gen Virol 74:153
De Oliveira AS, Melo FL, Inoue-Nagata AK, Nagata T, Kitajima EW, Resende RO (2012) Characterization of Bean necrotic mosaic virus: a member of a novel evolutionary lineage within the genus Tospovirus. PLoS One 7:e38634
Dong J, Yin Y, Fang Q, McBeath J, Zhang Z (2013) A new tospovirus causing chlorotic ringspot on Hippeastrum sp. in China. Virus Genes 46:567–570
Lin Y, Chen T, Hsu H, Liu F, Chu F, Chen C, Lin Y, Yeh S (2005) Serological comparison and molecular characterization for verification of Calla lily chlorotic spot virus as a new tospovirus species belonging to Watermelon silver mottle virus serogroup. Phytopathology 95:1482–1488
Liu Y, Lu X, Zhi L, Zheng Y, Chen X, Xu Y, Wu F, Li Y (2012) Calla lily chlorotic spot virus from Spider Lily (Hymenocallis litteralis) and Tobacco (Nicotiana tabacum) in the South-west of China. J Phytopathol 160:201–205
Moyer J (1999) Tospoviruses (Bunyaviridae). Encyclopedia of virology. Academic Press, New York, pp 1803–1807
Seepiban C, Gajanandana O, Attathom T, Attathom S (2011) Tomato necrotic ringspot virus, a new tospovirus isolated in Thailand. Arch Virol 156:263–274
Shimomoto Y, Kobayashi K, Okuda M (2014) Identification and characterization of Lisianthus necrotic ringspot virus, a novel distinct tospovirus species causing necrotic disease of lisianthus (Eustoma grandiflorum). J Gen Plant Pathol 80:169–175
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
Torres R, Larenas J, Fribourg C, Romero J (2012) Pepper necrotic spot virus, a new tospovirus infecting solanaceous crops in Peru. Arch Virol 157:609–615
Whitfield AE, Ullman DE, German TL (2005) Tospovirus-thrips interactions. Annu Rev Phytopathol 43:459–489
Xu Y, Lou S, Li X, Zheng Y, Wang W, Liu Y (2013) The complete S RNA and M RNA nucleotide sequences of a hippeastrum chlorotic ringspot virus (HCRV) isolate from Hymenocallis littoralis (Jacq.) Salisb in China. Arch Virol 158:2597–2601
Yin Y, Zheng K, Dong J, Fang Q, Wu S, Wang L, Zhang Z (2014) Identification of a new tospovirus causing necrotic ringspot on tomato in China. Virol J 11:213
Acknowledgments
This work was supported in part by grants from the National Science Foundation of China (Grant No. 31260451, 31471828, 30960224), Key New Product Development Projects in Yunnan Province (2014BB005), Reserve Personnel Fund for Young and Middle-Aged Academic Technical Leaders of Yunnan Province (2013HB071), and Academic Award for Up-and-Coming Doctoral Candidate of Yunnan Province.
Author information
Authors and Affiliations
Corresponding author
Additional information
Y. Xu and S. Wang contributed equally to this work.
The nucleotide sequence data reported in this manuscript have been deposited at the NCBI under accession numbers (KT004452, KT004453, and KT004454).
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Xu, Y., Wang, Sb., Li, Yz. et al. Complete genome sequence of a distinct calla lily chlorotic spot virus isolated in mainland China. Arch Virol 161, 219–222 (2016). https://doi.org/10.1007/s00705-015-2630-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-015-2630-9