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. 2022 Jan 24;11(3):309.
doi: 10.3390/plants11030309.

A New Jasmine Virus C Isolate Identified by Nanopore Sequencing Is Associated to Yellow Mosaic Symptoms of Jasminum officinale in Italy

Serafina Serena Amoia  1 , Angelantonio Minafra  1 , Vittorio Nicoloso  1 , Giuliana Loconsole  1 , Michela Chiumenti  1
Affiliations

A New Jasmine Virus C Isolate Identified by Nanopore Sequencing Is Associated to Yellow Mosaic Symptoms of Jasminum officinale in Italy

Serafina Serena Amoia et al. Plants (Basel). .

Abstract

Some plants of Jasminum officinale were selected in a nursery for investigation of sanitary status of candidate mother plants before vegetative propagation. The presence of yellow spots and leaf discoloration symptoms pushed for a generic diagnosis through deep sequencing to discover systemic pathogens. Either dsRNA or total RNA were extracted and used in nanopore and Illumina platform for cDNA-PCR, direct RNA and total RNA rRNA-depleted sequencing. A few single reads obtained by nanopore technology or assembled contigs gave unequivocal annotation for the only presence of a jasmine virus C (JaVC, a putative member of genus Carlavirus) isolate. The full-length genome of this isolate was reconstructed, spanning 8490 nucleotides (nt). This isolate shared 90.9% similarity with coat protein sequences and 84% with the entire ORF1 polyprotein, with the other two available JaVC full genomes, isolated from infections in J. sambac in Taiwan and China. The overall nucleotide identity shared by the newly discovered Italian isolate with the Chinese JaVC full genomes was 76.14% (Taiwan) and 75.60% (Fujian). The application of quick nanopore sequencing for virus discovery was assessed. The identification of the virus in a new ornamental host species, largely used in gardening, creates a concern for the potential virus spread and need of testing for production of clean vegetative material.

Keywords: Carlavirus; high-throughput sequencing; jasmine; virus; virus detection; yellow mosaic.

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Conflict of interest statement

The authors declare no conflict of interests. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Genomic organization of JaVC. Distribution and respective coverage of the reads obtained from the three techniques along the genome of JaVC-Bari isolate.
Figure 2
Figure 2
Heat map graphics of pairwise identity matrix analysis for coat proteins (A) and ORF1 polyprotein (B) of the JaVC isolates compared to other carlaviruses and outgroup flexivirids homolog proteins. GenBank accession numbers are by the virus name (refer also to Supplementary Materials Table S2).
Figure 2
Figure 2
Heat map graphics of pairwise identity matrix analysis for coat proteins (A) and ORF1 polyprotein (B) of the JaVC isolates compared to other carlaviruses and outgroup flexivirids homolog proteins. GenBank accession numbers are by the virus name (refer also to Supplementary Materials Table S2).
Figure 3
Figure 3
Maximum likelihood phylogenetic analysis of coat proteins (A) and ORF1 polyprotein (B) of the JaVC isolates (in red) versus other carlaviruses and outgroup flexivirids homolog proteins. GenBank accession numbers are on the tips (refer also to Supplementary Materials Table S2). Distance bar unit is under the dendrograms.
Figure 4
Figure 4
Leaves of Jasminum officinale showing symptoms of yellow spots and chlorotic variegation (B,C) and leaf of a healthy plant without symptoms (A).
See this image and copyright information in PMC

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