Abstract
Cymbidium mosaic virus (CymMV) is one of the most important viruses causing economic losses in orchids. The complete genomic sequences of three CymMV isolates collected from Guangdong Province, namely, CymMV-GDFS1, CymMV-GDFS2 and CymMV-GDFS3, were obtained via cloning, sequencing and assembling to clarify the variation and recombination of CymMVs. The mutation analyses of CymMV isolates demonstrated that the gene variation in CymMV followed the order of RdRp >TGBp1 > TGBp2 > TGBp3 > CP. Amongst them, RdRp had the most mutation sites, whereas TGBp3 had the least one. Moreover, the gene mutation of CymMV showed an obvious preference, the main type of mutation was the base transition of T→C or C→T. Notably, a recombinant event was detected in the RdRp gene of CymMV-GDFS1. The complete sequences of the three CymMV isolates shared more than 97% identities at nucleotide levels, phylogenetic relationship analyses revealed that the three CymMV Guangdong isolates belonged to subgroup A. This study provides a theoretical basis for the study of the evolution and pathogenicity of CymMV.
Data availability
The datasets analyzed during the current study are available in the GenBank (https://www.ncbi.nlm.nih.gov/).
References
Chen TY, Pai H, Hou LY, Lee SC, Lin TT, Chang CH, Hsu FC, Hsu YH, Lin NS (2019) Dual resistance of transgenic plants against cymbidium mosaic virus and odontoglossum ringspot virus. Scientific Reports 9:10230
Duffy S, Holmes EC (2009) Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. Journal of General Virology 90:1539–1547
Elena SF, Rodrigo G (2012) Towards an integrated molecular model of plant–virus interactions. Current Opinion in Virology 2:719–724
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:c1979–c2000
He Z, Jiang D, Liu A, Sang L, Li W, Li S (2011) The complete sequence of cymbidium mosaic virus from Vanilla fragrans in Hainan, China. Virus Genes 42:440–443
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772–780
Kim SM, Choi SH (2015) Simultaneous detection of cymbidium mosaic virus and odontoglossum ringspot virus in orchids using multiplex RT-PCR. Virus Genes 51:417–22
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452
Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution 1:1–5
Mathioudakis MM, Khechmar S, Owen CA, Medina V, Ben Mansour K, Tomaszewska W, Spanos T, Sarris PF, Livieratos IC (2018) A thioredoxin domain-containing protein interacts with pepino mosaic virus triple gene block protein 1. International Journal of Molecular Sciences 19:3747–3763
Pai H, Jean WH, Lee YS, Chang YA, Lin NS (2020) Genome-wide analysis of small RNAs from odontoglossum ringspot virus and cymbidium mosaic virus synergistically infecting Phalaenopsis. Molecular Plant Pathology 21:188–205
Rantalainen KI, Eskelin K, Tompa P, Mäkinen K (2011) Structural flexibility allows the functional diversity of potyvirus genome-linked protein VPg. Journal of Virology 85:2449–2457
Rao X, Li Y, Sun J, Li X, Li M, Xiang M (2015) Genetic diversities of cymbidium mosaic virus and odontoglossum ringspot virus isolates based on the coat protein genes from orchids in Guangdong Province, China. Journal of Phytopathology 163:324–329
Srivastava A, Pandey V, Sahu AK, Yadav D, Al-Sadi AM, Shahid MS, Gaur RK (2022) Evolutionary dynamics of begomoviruses and its satellites infecting papaya in India. Frontiers in Microbiology 13:879413
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30:2725–2729
Vaughan SP, Grisoni M, Kumagai MH, Kuehnle AR (2008) Characterization of Hawaiian isolates of cymbidium mosaic virus (CymMV) co-infecting Dendrobium orchid. Archives of Virology 153:1185–1189
Yoon JY, Chung BN, Choi GS, Choi SK (2012) Genetic variability in the coat protein genes of Cymbidium mosaic virus isolates from orchids. Virus Genes 44:323–328
Yusop MSM, Mohamed-Hussein ZA, Ramzi AB, Bunawan H (2022) Cymbidium mosaic virus infecting orchids: What, how, and what next? Iran Journal of Biotechnology 20:e3020
Funding
Our research was supported by the project of modern agricultural technology system innovation team of Guangdong province (2060302).
Author information
Authors and Affiliations
Contributions
All authors contributed to the study conception and design. Conceptualization: Xueqin Rao; Methodology: Xia Li, Ruonan Song, Huazhou Chen; Formal analysis: Xia Li, Ruonan Song, Huazhou Chen; Writing original draft preparation: Xia Li, Xueqin Rao; Writing – review and editing: Xueqin Rao; Funding acquisition: Xueqin Rao; Supervision: Xueqin Rao.
Corresponding author
Ethics declarations
Declarations
The materials in the article have not been submitted elsewhere for publication. This article does not involve any studies with human participants or animals. Informed consent was obtained from all individual participants included in the study.
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Li, X., Song, R., Chen, H. et al. Analyses of the genetic variation and recombination of CymMV Guangdong isolates. Trop. plant pathol. 49, 317–321 (2024). https://doi.org/10.1007/s40858-023-00625-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s40858-023-00625-1