Genetic diversity analysis of the coat protein gene revealed strong evolutionary constraints on Ornithogalum mosaic virus
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Abstract
Ornithogalum mosaic virus (OrMV) has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP) gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have a significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with ω-values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from molecular variance of analysis (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. In BaTS analysis, OrMV isolates from the genera Ornithogalum, Lachenalia, Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation. Furthermore, age calculations suggested that the first divergence event of the OrMV isolates analyzed might take place around 1068 BC.
Cite this as
2017. Genetic diversity analysis of the coat protein gene revealed strong evolutionary constraints on Ornithogalum mosaic virus . PeerJ Preprints 5:e3463v1 https://doi.org/10.7287/peerj.preprints.3463v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
Table S2
Recombination events detected in OrMV CP gene by RDP4 Suites
Table S3
Selection analyses in OrMV CP gene (a) Results of CODEML analyses of selective constraint for CP gene of OrMV. (b) Codon positions under positive selection
Figure S1 Bayesian Maximum clade credibility (MCC) chronogram inferred from the CP gene of the recombination-free isolates of OrMV
The tree is scaled to time generated under the relaxed clock and constant demographic models. Posterior probabilities are shown at major nodes.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Fangluan Gao conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Zhenguo Du reviewed drafts of the paper.
Jianguo Shen conceived and designed the experiments, reviewed drafts of the paper.
Hongkai Yang prepared figures and/or tables.
Furong Liao conceived and designed the experiments, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
The OrMV isolates used in this study is provided as Table S1.
Funding
This work was supported by grants from Fujian Natural Science Funds for Distinguished Young Scholar (Grant No. 2014J06008) and the Training Program of Fujian Excellent Talents in University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
