Table 4.
Next-generation sequencing of plant viral siRNA, total RNA or dsRNA from virus-infected temperate fruit crop, citrus or fig hosts.
| Host | Study finding/virome | Sample preparation/target | Sequencing platform | Ref. |
|---|---|---|---|---|
| Raspberry | A novel virus isolated from infected raspberry plants was completely sequenced and characterized. It was designated as Raspberry latent virus. The virus is a novel dicot-infecting reovirus in the family Reoviridae, subfamily Spinareovirinae. | dsRNA | Illumina | [55] |
| Citrus | In Citrus tristeza virus (CTV) infected citrus plants It was shown that the citrus homologues of Dicer-like ribonucleases mediate the genesis of the 21 and 22 nt CTV siRNAs and that the ribonucleases act not only on the genomic RNA but also on the 30 co-terminal subgenomic RNAs and, particularly, on their dsRNA forms. A novel citrus miRNAs was also indentified and how CTV influences their accumulation was determined. | CTV sRNAs, gRNA sgRNAs | Illumina | [56] |
| Citrus | Genomic organization and other molecular characterizations were determined for Citrus yellow vein clearing virus. Analyses suggested that the virus is the causal agent of yellow vein clearing disease of lemon trees and represent a new species in the genus Mandarivirus. | siRNAs | Illumina | [57] |
| Citrus | A novel DNA virus species, member of the family Geminiviridae, was identified and associated with citrus chlorotic dwarf disease. A provisional name of Citrus chlorotic dwarf-associated virus was proposed. | siRNAs and total DNA | Illumina HiSeq2000 | [58] |
| Apple, Citrus, Grapevine | Detected ASPV, ACLSV and an unknown mycovirus. Detected two variants of CTV and ASGV. Detected variants of GLRaV-3, GVA and an unknown mycovirus. | siRNAs | Illumina | [59] |
| Apple | Identified agents associated with green crinkle disease of apple trees. The disease is a complex one as the following viruses were identified associated with it: ASGV, ASPV, ACLSV, ApLV, ApPCLSV and PCMV. | siRNAs | Illumina HiSeq2000 | [60] |
| Prunus | Detected and identified known Prunus viruses such as PPV, PNRS, etc. and novel virus agents. | dsRNA | Roche 454 | [61] |
| Fig | Detected Fig mosaic virus and Fig latent virus-1 for their elimination from infected clones. It is the first application of next-generation sequencing technology to detect and identify known and new species of viruses infecting fig trees. | dsRNAs | Illumina | [62] |
| Blackberry | A novel Ampelovirus in the family Closteroviridae was identified as one of the viruses associated with blackberry yellow vein disease complex. | dsRNAs | Illumina | [63] |
| Cherry | Characterization of the genome of the divergent Little cherry virus 1 (LChV1) isolate and establishing that LChV1 isolates could be responsible for Shirofugen stunt disease syndrome. | dsRNAs | Roche 454 Pyrosequencing multiplex approach | [64] |
| Citrus | The complete nucleotide sequence and structure of a novel virus of the genus Cilevirus was determined. The novel virus causes symptoms similar to citrus leprosies and it is suggested to be called Citrus leprosis virus cytoplasmic type 2. | siRNAs | Illumina | [65] |
| Citrus | A novel virus was discovered by analysis of the contigs assembled from the virus siRNAs sequences which showed similarity with luteovirus sequence, particularly with Pea enation mosaic virus, the type member of the genus Enarnovirus. The complete genome of the virus was determined and the new virus was provisionally named Citrus vein enation virus. | siRNAs | Solexa-Illumina | [66] |
Virus abbreviations: ACLSV, Apple chlorotic leaf spot virus; ApLV, Apricot latent virus; ApPCLSV, Apricot pseudo-chlorotic leaf spot virus; ASGV, Apple stem grooving virus; ASPV, Apple stem pitting virus; CTV, Citrus tristeza virus; GLRaV-3, Grapevine leaf roll associated virus 3; GVA, Grapevine virus A; PCMV, Peach chlorotic mottle virus; PNRS, Prunus necrotic ring spot virus; PPV, Plum pox virus.