The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China
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RESEARCH
Open Access
The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China Xiangdong Li1†, Tiansheng Zhu2†, Xiao Yin1†, Chengling Zhang4, Jia Chen1, Yanping Tian1* and Jinliang Liu3*
Abstract Background: Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. Results: To understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent. Conclusions: The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China. Keywords: Turnip mosaic virus, Potyvirus, Genetic structure, Population, China
Background Due to the error-prone nature of their RNA-dependent RNA polymerases, populations of plant RNA viruses are genetically heterogeneous and the genetic structure may change with time and environment [1, 2]. Studies of the genetic structure of viruses will provide information about the mechanisms and factors driving their evolution and help us to understand the molecular evolutionary history of viruses in relation to their dispersion and emergence of new epidemics [3]. Turnip mosaic virus (TuMV) is a species of the largest plant virus genus Potyvirus (family Potyviridae). TuMV * Correspondence: [email protected]; [email protected] † Equal contributors 1 Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China 3 College of Plant Sciences, Jilin University, Changchun 130062, China Full list of author information is available at the end of the article
has flexuous filamental particles of 700–750 nm long and can be transmitted by 40–50 species of aphids in a non-persistent manner [4, 5]. The TuMV genome consists of one single-stranded positive sense RNA molecule of approximately 9830 nucleotides (nt) and contains a large open reading frame (ORF) [6]. The genomic RNA is translated into a large polyprotein and a frame-shift protein. The large polyprotein are subsequently processed by the action of three viral-encoded proteinases (Pl, HC-Pro and NIa-Pro) i
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