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Identification of a novel dicistro-like virus associated with the roots of tomato plants

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Abstract

Viruses belonging to the family Dicistroviridae have a monopartite positive-sense single-stranded RNA genome and infect a variety of arthropods. Using high-throughput sequencing, we detected a novel dicistro-like virus, tentatively named "tomato root-associated dicistro-like virus" (TRaDLV), in the roots of tomato plants showing yellow mosaic symptoms on the leaves. The diseased tomato plants were coinfected with multiple plant viruses, and TRaDLV was present in the roots but not in the leaves. The genome of TRaDLV is 8726 nucleotides in length, excluding the poly(A) tail, and contains two open reading frames (ORFs) separated by an intergenic region (IGR). The TRaDLV genome showed characteristics similar to those of dicistroviruses, including the presence of a 3C-like protease domain, repeated amino acid sequences representing multiple copies of viral genome-linked protein (VPg)-like sequences in the ORF1 polyprotein, and a series of stem-loop structures resembling an internal ribosome entry site in the IGR. Phylogenetic analysis revealed that TRaDLV clustered with unclassified dicistro-like viruses from invertebrates or identified in samples of plant-derived material. These findings indicate the existence of a novel dicistro-like virus that may associate with plant roots or a root-inhabiting organism.

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Data availability

The complete genomic nucleotide sequence of TRaDLV has been deposited in the NCBI GenBank database under accession number OQ983468.

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Acknowledgements

The authors thank Shenli Sui for assistance during the collection of plant samples.

Funding

This research was supported by the National Natural Science Foundation of China (31970159, 32001867) and the Natural Science Foundation of Shandong Province of China (ZR2020QC129).

Author information

Author notes

  1. Xinran Cao and Ziqi Wang contributed equally.

Authors and Affiliations

  1. College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China

    Xinran Cao, Ziqi Wang & Ida Bagus Andika

  2. Shandong Agricultural University, 271018, Tai’an, China

    Xinran Cao

  3. Shouguang International vegetable Sci-tech Fair Management Service Center, 262700, Shouguang, China

    Xinran Cao

  4. University Library, Northwest A&F University, 712100, Xianyang, China

    Jianguo Pang

  5. State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 712100, Xianyang, China

    Liying Sun

  6. Institute of Plant Science and Resources, Okayama University, 710-0046, Kurashiki, Japan

    Hideki Kondo

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  1. Xinran Cao
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  2. Ziqi Wang
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Correspondence to Ida Bagus Andika.

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Cao, X., Wang, Z., Pang, J. et al. Identification of a novel dicistro-like virus associated with the roots of tomato plants. Arch Virol 168, 214 (2023). https://doi.org/10.1007/s00705-023-05843-1

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