Open Access

ARTICLE

Incidence, genomic diversity, and evolution of strawberry mottle virus in China

LINGJIAO FAN, CHENGYONG HE, MENGMENG WU, DEHANG GAO, ZHENFEI DONG, SHENGFAN HOU, ZEKUN FENG, HONGQING WANG^*

College of Horticulture, China Agricultural University, Beijing, 100193, China

* Address correspondence to: Hongqing Wang,

BIOCELL 2021, 45(4), 1137-1151. https://doi.org/10.32604/biocell.2021.015396

Received 16 December 2020; Accepted 18 February 2021; Issue published 22 April 2021

Abstract

Strawberry mottle virus (SMoV) is one of the most common viruses infecting strawberries, causing losses to fruit yield and quality. In this study, 165 strawberry leaf samples were collected from six provinces of China, 46 of which tested positive for SMoV. The complete genome sequences of 11 SMoV isolates were obtained from Liaoning (DGHY3, DGHY16-2, DGHY17, DGHY20-2, DGHY21, DGHY26-2), Shandong (SDHY1, SDHY5, SDHY31-2, SDHY33-2), and Beijing (BJMX7). The RNA1 and RNA2 nucleotide identities between the 11 Chinese isolates were 95.4–99.3% and 96.3–99.6%, respectively, and they shared 78.4–96.6% and 84.8–93.5% identities with the available SMoV isolates in GenBank. Recombination analysis revealed that Chinese isolate SDHY33-2 and Canadian isolates Ontario and Simcoe were recombinants, and recombination events frequently occurred in the 3’ UTR of SMoV. Phylogenetic analysis showed that in an RNA1 tree, most Chinese isolates clustered into the same group while isolate DGHY17 clustered into another group together with Czech isolate C and three Canadian isolates. In an RNA2 tree, all Chinese isolates clustered into a single group. The phylogenetic analysis based on nucleotide sequences was consistent with the results based on coat protein (CP) and RNA-dependent RNA polymerase (RdRp). Further evolutionary analysis indicated that negative selection drives SMoV evolution, and gene flow plays a major role in genetic differentiation. Additionally, reassortment and recombination also influence the evolution of SMoV. To our knowledge, this is the first report of the complete genome of SMoV isolates from China and a detailed analysis of the SMoV population structure.

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