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Evolution of rice stripe virus.

Mei He1, Sheng-Yu Guan2, Cheng-Qiang He3

  • 1College of Life Science, Shandong Normal University, Jinan 250014, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.

Molecular Phylogenetics and Evolution
|February 13, 2017
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Rice stripe virus (RSV), a significant insect-borne tenuivirus, shows extensive genetic diversity in China. This study reveals RSV

Keywords:
Codon usage biasCpG dinucleotideDivergenceRSVRecombination

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Area of Science:

  • Virology
  • Molecular Epidemiology
  • Population Genetics

Background:

  • Rice stripe virus (RSV) is an economically important insect-borne tenuivirus prevalent in East Asian rice cultivation.
  • Yunnan Province, China, is a hotspot for RSV genetic diversity, necessitating further investigation into its molecular epidemiology and evolution.

Purpose of the Study:

  • To investigate the molecular epidemiology and evolutionary history of Rice stripe virus (RSV).
  • To detect recombination events and analyze codon usage patterns in RSV.

Main Methods:

  • Recombination analyses were performed on all four RNA segments of RSV.
  • Bayesian coalescent methods were applied to time-stamped coding sequences of the Coat Protein (CP) gene.
  • Nucleotide substitution rates, divergence times, and codon usage variations were estimated.

Main Results:

  • Potential recombination events were detected across all four RNA segments of RSV.
  • Analysis suggests the first RSV diversification event occurred in the early 20th century, with the virus existing in Yunnan long before its official recognition.
  • RSV codon usage is influenced by factors beyond mutational bias, with a dominant influence from its vector, the small brown planthopper, over the host rice.
  • A deficiency in CpG dinucleotides was observed in RSV.

Conclusions:

  • RSV exhibits complex evolutionary dynamics, including recombination and significant host-vector interactions shaping its genetic makeup.
  • The findings provide crucial insights into the long-term persistence and evolution of RSV in Yunnan, China.
  • Understanding RSV's molecular epidemiology is vital for developing effective disease management strategies in rice.