Abstract
Contigs with sequence identities to turnip mosaic virus (TuMV) were detected by deep sequencing of the small RNAs extracted from a passion fruit (Passiflora edulis) plant showing virus-like symptoms in Fujian Province, China. The complete genome of the TuMV, designated TuMV-FJ here, was determined based on the sequences of these contigs and Sanger sequencing of RT-PCR and 5′/3’ RACE amplicons. The TuMV-FJ genome consists of 9,833 nucleotides excluding the poly(A) tail. It contains an open reading frame encoding a polypeptide with 3164 amino acid residues. The polypeptide was predicted to be cleaved into ten functional proteins by viral proteases. Phylogenetic analysis indicated that TuMV-FJ is a member of a world-B phylogenetic group of TuMV. TuMV-FJ shared more than 94% nucleotide and amino acid sequence identities with its closest relative, namely BJ-B01, a TuMV isolate from Brassica oleracea. A RT-LAMP assay was developed to facilitate the molecular detection of TuMV-FJ. As far as we know, this is the first report of the complete genome sequence of TuMV infecting P. edulis. In addition, the RT-LAMP assay provides a rapid, robust and highly sensitive approach for the detection of TuMV in passion fruit.
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Data availability
Sequence data obtained in this study has been deposited in GenBank under the accession number MK340758.
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Funding
This work was financially supported by the National Key R&D Program of China (No. 2016YFF0203200), Special Project of Fundamental Research Funds for Public Welfare Research Institutes of Fujian Province (No. 2020R1028005), Guided Scientific and Technological Innovation Project of Fujian Academy of Agricultural Sciences (No. YDXM202202), Program of Technology Center of Fuzhou Customs District of China (No. FK2020-10) and the Agricultural Guidance (Key) Project of Fujian Province, China (No. 2020N0024).
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42161_2023_1425_MOESM4_ESM.pdf
Supplementary file 4 Fig. S2 Specificity of RT-LAMP for the detection of TuMV. (A) Graph of turbidity over time for the RT-LAMP assay. (B) Visual inspection of the RT-LAMP assay. A1, turnip mosaic virus (TuMV); A2, cucumber mosaic virus (CMV); A3, telosma mosaic virus (TeMV); A4, east Asian Passiflora virus (EAPV); A5, soybean mosaic virus (SMV); A6, passiflora latent virus (PLV); A7, hibiscus latent Fort Pierce virus (HLFPV); A8, Negative control (healthy plant) (PDF 743 KB)
42161_2023_1425_MOESM5_ESM.pdf
Supplementary file 5 Fig. S3 Sensitivity of RT-LAMP for the detection of TuMV. (A) Graph of turbidity over time for the RT-LAMP assay. (B) Visual inspection of the RT-LAMP assay. (C) Agarose gel electrophoresis of RT-PCR product. M, DNA Marker (100 bp); A1-A7, the cDNA dilution of TuMV for 100-106 times; A8, Negative control (healthy plant) (PDF 857 KB)
42161_2023_1425_MOESM6_ESM.pdf
Supplementary file 6 Fig. S4 The results for RT-LAMP assay that applied to detect TuMV. 1-80, passion fruit leaf samples; 81-82, negative control 1 (healthy plant) and negative control 2 (water), respectively (PDF 833 KB)
42161_2023_1425_MOESM7_ESM.pdf
Supplementary file 7 Fig. S5 The results for RT-PCR assay that applied to detect TuMV. M. DNA marker; lane 1-80: passion fruit leaf samples; lane 81-82, negative control 1 (healthy plant) and negative control 2 (water), respectively (PDF 105 KB)
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Li, X., Xie, L., Chen, X. et al. Complete genomic sequence of turnip mosaic virus infecting passionfruit in Fujian province of China. J Plant Pathol 105, 1123–1127 (2023). https://doi.org/10.1007/s42161-023-01425-x
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DOI: https://doi.org/10.1007/s42161-023-01425-x