Genetic diversity analysis of the coat protein gene revealed strong evolutionary constraints on Ornithogalum mosaic virus

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1 Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
2 Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, Fujian, China
3 Inspection and Quarantine Technology Center, Xiamen Exit-Entry Inspection and Quarantine Bureau, Xiamen, Fujian, China
DOI
10.7287/peerj.preprints.3463v1
Published
Accepted
Subject Areas
Agricultural Science, Evolutionary Studies, Microbiology, Virology, Population Biology
Keywords
phylogenetic analysis, host-driven adaptation, evolutionary constraint, Ornithogalum mosaic virus
Copyright
© 2017 Gao et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Gao F, Du Z, Shen J, Yang H, Liao F. 2017. Genetic diversity analysis of the coat protein gene revealed strong evolutionary constraints on Ornithogalum mosaic virus . PeerJ Preprints 5:e3463v1

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.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Table S1

OrMV isolates used in this study

DOI: 10.7287/peerj.preprints.3463v1/supp-1

Table S2

Recombination events detected in OrMV CP gene by RDP4 Suites

DOI: 10.7287/peerj.preprints.3463v1/supp-2

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

DOI: 10.7287/peerj.preprints.3463v1/supp-3

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.

DOI: 10.7287/peerj.preprints.3463v1/supp-4