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Complete genome sequence analysis of a novel citlodavirus isolated from the leaves of Myrica rubra in Yunnan

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Abstract

Through high-throughput sequencing, a novel citlodavirus, tentatively named “Myrica rubra citlodavirus 1” (MRV1, accession no. OP374189), was isolated from the leaves of Myrica rubra in Yunnan exhibiting narrow deformity of leaf tips, shrinkage, and chlorosis along the veins. The complete genome sequence was determined and analyzed using cloning and Sanger sequencing. MRV1 is a single-stranded circular non-enveloped DNA virus with a genome size of 3775 nucleotides and contains six open reading frames (ORFs). The virion-sense genome strand encodes a coat protein (CP, nt 750-1,493, 247 aa), two hypothetical movement proteins (V3, nt 382–666, 94 aa; and V2, nt 461–895, 144 aa), and one movement protein (MP, nt 1,527-2,438, 303 aa). The complementary strand of the genome encodes two replication proteins (RepA, nt 3,712-2,834, 292 aa; Rep, nt 2,867-2,553, 104 aa). The MRV1 genome contains the stem-loop motif 5′-TAATATTAC-3′, which is a highly conserved nonanucleotide motif found in the origin of virion-strand replication in geminiviruses. Genome sequence alignment analysis showed that citrus chlorotic dwarf associated virus (CCDaV, accession no. JQ920490) shared the highest nucleotide sequence similarity (66.10% identity) with MRV1. Phylogenetic analysis showed that CCDaV is the closest known relative of MRV1, and that these viruses clustered in a single branch within a clade consisting of citlodaviruses. These results indicate that MRV1 should be regarded as a new species of the genus Citlodavirus in the family Geminiviridae.

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Data availability

The dataset generated during the current study is available in the GenBank database (accession no. OP374189).

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Authors and Affiliations

  1. Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China

    Like Gao, Zeli Chen, Yueqiu He, Shangyun Li, Shaomei Zi, Zefen Yang, Bifan Chu, Guosong Wen & Mingfu Zhao

  2. Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, 650201, Yunnan, China

    Like Gao, Zeli Chen, Shangyun Li, Shaomei Zi, Zefen Yang, Bifan Chu, Guosong Wen & Mingfu Zhao

  3. Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, 23 Innovation Walk, Clayton, VIC, 3800, Australia

    Rex Frimpong Anane

  4. College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China

    Zeli Chen, Shangyun Li, Zefen Yang & Guosong Wen

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  1. Like Gao
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Correspondence to Guosong Wen or Mingfu Zhao.

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Communicated by Elvira Fiallo-Olivé

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First author: Like Gao

First co-author: Rex Frimpong Anane

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Gao, L., Anane, R.F., Chen, Z. et al. Complete genome sequence analysis of a novel citlodavirus isolated from the leaves of Myrica rubra in Yunnan. Arch Virol 168, 139 (2023). https://doi.org/10.1007/s00705-023-05762-1

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