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Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype

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Abstract

Sugarcane yellow leaf virus (SCYLV; genus Polerovirus, family Luteoviridae) is a recombinant virus associated with yellow leaf disease, a serious threat to sugarcane in China and worldwide. Among the nine known SCYLV genotypes existing worldwide, COL, HAW, REU, IND, CHN1, CHN2, BRA, CUB and PER, the last five have been reported in China. In this study, the complete genome sequences (5,880 nt) of GZ-GZ18 and HN-CP502 isolates from the Chinese provinces of Guizhou and Hainan, respectively, were cloned, sequenced and characterized. Phylogenetic analysis showed that, among 29 SCYLV isolates described worldwide, the two Chinese isolates clustered together into an independent clade based on the near-complete genome nucleotide (ORF0-ORF5) or amino acid sequences of individual genes, except for the MP protein (ORF4). We propose that the two isolates represent a novel genotype, CHN3, diverging from other genotypes by 1.7-13.6 % nucleotide differences in ORF0-ORF5, and 2.7-28.1 %, 1.8-20.4 %, 0.5-5.1 % and 2.7-15.9 % amino acid differences in P0 (ORF0), RdRp (RNA-dependent RNA polymerase) (ORF1+2), CP (coat protein) (ORF3) and RT (readthrough protein) (ORF3+5), respectively. CHN3 was closely related to the BRA, HAW and PER genotypes, differing by 1.7-3.8 % in the near-complete genome nucleotide sequence. Recombination analysis further identified CHN3 as a new recombinant strain, arising from the major parent CHN-HN1 and the minor parent CHN-GD-WY19. Recombination breakpoints were distributed mostly within the RdRp region in CHN3 and the four significant recombinant genotypes, IND, REU, CUB and BRA. Recombination is considered to contribute significantly to the evolution and emergence of such new SCYLV variants.

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Acknowledgments

This research was supported by an Earmark Fund from the China Agriculture Research System (CARS-20-2-4) and a grant from the National Natural Science Foundation of China (31170345). We are grateful to Dr. Jia-Ju Lu (Guizhou Subtropical Crop Institute, Xingyi, China) and Mr. Zhong-xing Huang (Guangzhou Sugarcane Industry Research Institute, Guangzhou, China) for supplying the sugarcane leaf samples.

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Authors and Affiliations

  1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Yi-Hua Lin, San-Ji Gao, Hua-Ying Fu & Ru-Kai Chen

  2. Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research, Weslaco, TX, 78596, USA

    Mona B. Damaj & T. Erik Mirkov

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  1. Yi-Hua Lin
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  2. San-Ji Gao
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  3. Mona B. Damaj
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  4. Hua-Ying Fu
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  5. Ru-Kai Chen
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  6. T. Erik Mirkov
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Correspondence to San-Ji Gao.

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Lin, YH., Gao, SJ., Damaj, M.B. et al. Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype. Arch Virol 159, 1421–1429 (2014). https://doi.org/10.1007/s00705-013-1957-3

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  • DOI: https://doi.org/10.1007/s00705-013-1957-3

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