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Genetic variability of rice stripe virus after its pandemic in Jiangsu

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Abstract

Background

Rice stripe virus (RSV) caused a serious disease pandemic in rice in East China between 2001 and 2010. The continuous integrated managements reduced virus epidemic year by year until it was non-epidemic. As an RNA virus, its genetic variability after undergoing a long-term non-epidemic period was meaningful to study. While in 2019, the sudden occurrence of RSV in Jiangsu provided an opportunity for the study.

Methods and results

The complete genome of JY2019, an RSV isolate from Jiangyan, was determined. A genotype profile of 22 isolates from China, Japan and Korea indicated that the isolates from Yunnan formed the subtype II, and other isolates clustered the subtype I. RNA 1–3 of JY2019 isolate well-clustered in the subtype I clade, and RNA 4 was also in subtype I, but it had a slight separation from other intra-group isolates. After phylogenetic analyses, it was considered NSvc4 gene contributed to the tendency, because it exhibited an obvious trend towards the subtype II (Yunnan) group. High sequence identity (100%) of NSvc4 between JY2019 and barnyardgrass isolate from different regions demonstrated genetic variation of NSvc4 was consistent in RSV natural populations in Jiangsu in the non-epidemic period. In the phylogenetic tree of all 74 NSvc4 genes, JY2019 belonged to a minor subtype Ib, suggesting the subtype Ib isolates might have existed in natural populations before the non-epidemic period, but not a dominant population.

Conclusions

Our results suggested that NSvc4 gene was susceptible to selection pressure, and the subtype Ib might be more adaptable for the interaction between RSV and hosts in the non-epidemic ecological conditions.

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Data availability

All data generated or analysed during this study are included in this published article and its supplementary information files.

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Funding

This work was financially supported by the Jiangsu Agricultural Science and Technology Independent Innovation Fund (grant No. CX[21]1011).

Author information

Author notes

  1. Chengye Lu and Qian Miu contributed equally to this work.

Authors and Affiliations

  1. Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Chengye Lu, Qian Miu, Daoran Jin, Zhaobang Cheng, Yijun Zhou & Shuo Li

  2. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China

    Chengye Lu & Yunyue Wang

  3. Plant Protection and Quarantine Station, Agricultural Technology Extension Center of Jiangyan, Taizhou, 225500, China

    Aiguo Li

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  1. Chengye Lu
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Correspondence to Shuo Li.

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Supplementary Information

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Fig. S1.

Schematic diagram ofRSV genome (DOCX 77.4 kb)

Fig. S2.

Phylogeneticanalyses of RSV genomic intergenic regions (DOCX 318.9 kb)

Table S1.

Primers used in thisstudy (DOC 62.5 kb)

Table S2.

GenBank numbers of NSvc4 genes from all 74 RSV isolates (DOCX 23.4 kb)

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Lu, C., Miu, Q., Jin, D. et al. Genetic variability of rice stripe virus after its pandemic in Jiangsu. Mol Biol Rep 50, 7263–7274 (2023). https://doi.org/10.1007/s11033-023-08652-6

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