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.
Highlights
Symptoms due to the systemic infection of viruses and virus-like pathogens in vegetatively propagated ornamental plants have been widely described in the past [1,2] even if they could have been largely underestimated in case of latency or mild symptoms of the infection [3,4]
The quick molecular identification and characterization by high-throughput sequencing (HTS) of viruses and viroids has been developed by using all the nucleic acid templates suitable to the scope and libraries run on different platforms
One retro-transcribed dsRNA library and one direct RNA library were prepared for Oxford Nanopore Technology (ONT) sequencing from the J. officinale mixed sample
Summary
Symptoms due to the systemic infection of viruses and virus-like pathogens in vegetatively propagated ornamental plants have been widely described in the past [1,2] even if they could have been largely underestimated in case of latency or mild symptoms of the infection [3,4]. The quick molecular identification and characterization by HTS of viruses and viroids has been developed by using all the nucleic acid templates suitable to the scope (small RNAs, enriched genomic targets of pathogens, total RNA or DNA) and libraries run on different platforms (like Illumina or nanopore sequencing; [6,7,8]) This technique allowed the discovery of new viruses infecting several hosts, including ornamental and cultivated plants, whether the infections were able to express symptoms or not, as well as the detection of already described viruses in new hosts [9,10]. From J. sambac sources, in Taiwan too, a new carlavirus, jasmine virus C (JaVC), was identified in 2012, and its full genome was sequenced [19] This virus was apparently not transmissible on herbaceous test hosts, but always associated in the original jasmine host to pronounced yellow mosaic and not to milder symptoms. In the frame of a Regional Project aimed at surveying and enhancing the phytosanitary quality of some ornamental species during the propagation pipeline, yellow spots and interveinal mosaic symptoms on some clones of J. officinale from a nursery in Apulia (Italy) and our work, based on HTS application through preliminary in-house nanopore fast sequencing, aimed to clarify if and which viral entities could be associated to these symptoms
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