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

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.

Nanovirseq: dsRNA sequencing for plant virus and viroid detection by Nanopore sequencing

“…While there wasn't any difficulty choosing a pipeline for analyzing MiSeq data, there were some challenges in analyzing nanopore sequencing data. Similar to the situation described by Amoia et al 2022 (45), our dsRNAcD libraries provided relatively low quality, and low quantities of viral reads to meet the requirements of long read based de novo assembler software. Thus, these software was not able to assemble long and numerous viral contigs.…”

“…The aim of this study was to develop and evaluate two nanopore sequencing strategies for detecting viruses and viroids in mixed-infected grapevine samples: direct-RNA sequencing and direct-cDNA sequencing. We tried to answer two main questions relative to grapevine virus and Until now nanopore dsRNA sequencing has been used to identify or characterize viruses in single virus infections (45,46). In fact, when it comes to identify and characterize the virome using nanopore sequencing technology, total RNA extraction is the common method used in the published literature.…”

“…Until now nanopore dsRNA sequencing has been used to identify or characterize viruses in single virus infections (45, 46). In fact, when it comes to identify and characterize the virome using nanopore sequencing technology, total RNA extraction is the common method used in the published literature.…”

“…Despite the fact that different nucleic acid types (DNA or RNA) and various library preparation strategies have been used for plant virus detection by nanopore sequencing (31,(36)(37)(38)(39)(40)(41)(42)(43)(44), there is only two reports of plant virus detection through double-stranded RNA (dsRNA) nanopore sequencing and there were related to single virus infections by new isolates of Jasmine Virus C (45) and cucumber Bulgarian latent virus (46). Plant virus detection is usually accomplished using total RNA (31,47) but using total RNA has a number of limitations.…”

Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses

“…In recent years, ONT has demonstrated success across a wide variety of plant viruses by generating long-read single-molecule sequence data in real time with an innovation in third-generation sequencing technology ( Jain et al, 2015 ; Lewandowski et al, 2019 ; Zhu et al, 2020 ). ONT has been used to detect plant viruses in a variety of plants, including peaches ( Bronzato Badial et al, 2018 ), tomatoes ( Chalupowicz et al, 2019 ), yams ( Filloux et al, 2018 ), potatoes ( Della Bartola et al, 2020 ), wheat ( Fellers et al, 2019 ), cowpea ( Naito et al, 2019 ), cassava ( Boykin et al, 2019 ), Medicago arborea ( Ben Chehida et al, 2021 ), Jasminum officinale ( Amoia et al, 2022 ), grapevine ( Javaran et al, 2021 ), roses ( Vazquez-Iglesias et al, 2022 ), and lamon bean ( Tarquini et al, 2022 ).…”