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. 2018 Mar 27:6:e4550.
doi: 10.7717/peerj.4550. eCollection 2018.

Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

Fangluan Gao  1 , Zhenguo Du  1 , Jianguo Shen  2 , Hongkai Yang  1 , Furong Liao  3
Affiliations

Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

Fangluan Gao et al. PeerJ. .

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 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 dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA) indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

Keywords: Host-driven adaptation; Ornithogalum mosaic virus; Phylogenetic analysis; Selective constraints.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Phylogenetic networks of the CP gene from 36 OrMV isolates from different countries (A) and hosts (B).
Hippeastrum mosaic virus (NC_017967) served as an outgroup. OrMV isolates from different countries or hosts are indicated by a unique color. Branch lengths are proportional to the genetic distances.
Figure 2
Figure 2. Evolutionary relationship of the CP gene from the 35 recombination-free OrMV isolates and comparison of dN/dS values between the two clades.
(A) ML phylogenetic tree showing genetic relationship among OrMV isolates. OrMV isolates from different regions (solid circle) and host species (diamond) are indicated by a unique color. Bootstrap percentage (BP ≥ 50%) are indicated above major branches. The distance unit is substitutions/site; (B) boxplots showing the dN/dS ratio of clade A (pink) and clade B (light blue) for the CP gene of OrMV.
See this image and copyright information in PMC

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