Table 1.

Utilization of NGS in various studies of plant virus small RNAs.

Virus small RNAs (vsRNAs)	Reference
vsRNAs of nine different viruses in four different hosts extended the knowledge of distribution and composition of these RNAs in virus-infected plants and contributed to better understanding of vsRNAs biogenesis	Donaire et al., 2009
Identification of two novel badnaviruses (dsDNA) and one novel mastrevirus (ssDNA) in sweet potato plants and detection of the often symptomless sweet potato feathery mottle virus and the phloem-limited sweet potato chlorotic stunt virus in the same plants	Kreuze et al., 2009
vsRNA of tobacco mosaic virus mediate virus-host interactions which may contribute to viral pathogenicity and host specificity	Qi et al., 2009
vsRNAs profiles of cymbidium ringspot virus were obtained. These RNAs primarily derived from the positive strand of the virus, accumulated with different frequency, had a 5′monophosphate, and were not perfect duplexes	Szittya et al., 2010
Characterization of vsRNAs from the four genome RNAs of rice stripe virus in infected rice plants	Yan et al., 2010
Profiling vsRNAs of bamboo mosaic virus and its associated satellite RNAs	Lin et al., 2010
vsRNAs of four virus genera (Foveavirus, Maculavirus, Marafivirus and Nepovirus) originate from both genomic and antigenomic strands. In addition, most vsRNAs of members of the genus Tymovirus are derived from the antigenomic virus strand	Pantaleo et al., 2010
Extending the host range of cereal yellow dwarf virus (genus Luteovirus) to wild cocksfoot grass	Pallett et al., 2010
Characterization of vsRNAs from tomato yellow leaf curl virus and its associated beta satellite DNA in infected tomato and Nicotiana benthamiana plants	Yang et al., 2011
Characterization of vsRNAs of cotton leafroll dwarf virus in infected cotton plants	Silva et al., 2011
Identification of a novel badnavirus in grapevine. It is the first DNA virus discovered in this host	Zhang et al., 2011
Detection of tomato spotted wilt virus in tomato before symptoms appeared at levels too low for conventional detection methods. Analysis of the virus quasispecies; identification of a tospovirus and a squash-infecting geminivirus	Hagen et al., 2011
vsRNAs sequencing reconstructed the full genome of the T318A Spanish citrus tristeza virus isolate that infects sweet and sour orange as well as Mexican lime. vsRNAs map preferentially at the 3′-terminal region of the genomic RNA. Virus infection affect the host sRNA profiles	Ruiz-Ruiz et al., 2011
Characterization of vsRNAs and transcriptome profiling of Arabidopsis plants infected by oil seed rape mosaic virus (genus Tobamovirus).	Hu et al., 2011
vsRNAs of both sense and antisense polarities without gaps densely cover the circular genome of DNA viruses, thus enabling de novo reconstruction of the complete DNA virus from vsRNAs	Blevins et al., 2011; Aregger et al., 2012; Rajeswaran et al., 2012
vsRNAs of rice stripe virus were shown to be generated preferentially in different plant hosts and they were identified in the viruleferous vector small brown leafhopper	Xu et al., 2012
Identification and differentiation of two strains of pepino mosaic virus and complete genome sequences of a novel potyvirus named tomato necrotic stunt virus in tomato. Identification of gene expression changes associated with disease	Li et al., 2012
Detection of sweet potato members of different genera (Potyvirus, Crinivirus, Begomovirus) in sweet potato. vsRNAs NGS analysis is a reliable and sensitive method for virus detection in infected crops	Kashif et al., 2012
Identification of a novel member of the genus Mandarivirus in citrus	Loconsole et al., 2012a
Identification of a novel DNA virus member of the family Geminiviridae in citrus	Loconsole et al., 2012b
Detection of four apple viruses and two apricot viruses associated with apple green crinkle, a disease of undermined etiology	Yoshikawa et al., 2012
Identification of a novel members of the genus Tricovirus, grapevine pinot gris virus, in grapevine cv. Pinot gris. Detection of grapevine rupestris stem-pitting associated virus, grapevine rupestris vein feathering virus and grapevine Syrah virus 1	Giampetruzzi et al., 2012
Characterization of vsRNA associated with grapevine leafroll disease	Alabi et al., 2012
vsRNAs sequencing reconstructed the full genome of the Mexican tomato mottle mosaic virus, genus Tobamovirus, that infects tomato	Li et al., 2013
Identification of a novel member of the genus Enarnovirus, citrus vein enation virus, in Etrog citron plants	Vives et al., 2013
Identification of a novel member of the genus Cilevirus, citrus leprosies virus cytoplasmic type 2, in citrus	Roy et al., 2013
vsRNAs of tomato spotted wilt virus accumulate at different amounts in different hosts such as tomato and Nicotiana benthamiana	Mitter et al., 2013
vsRNAs profiles of potato virus Y strains O, N, and NTN were different in the same host which indicated they interact differently. vsRNAs were derived from every position in the genome and certain hot spots were identified for each strain	Naveed et al., 2014
vsiRNAs of potato virus X were successfully differentiated according to their strains	Kutnjak et al., 2014
vsRNAs and vd-sRNAs allowed de novo reconstruction of DNA and RNA viruses or viroids and their variants. vsiRNAs could be used for diagnosis of known and emerging virus or viroid diseases and for assessing rapid generation of biologically active clones	Seguin et al., 2014
vsRNAs profiles of apple stem grooving virus latent infection in apple seedlings showed an increase toward the 3′end of the virus genome. The involvement of tRNA-derived sRNAs in plant–virus interaction was demonstrated	Visser et al., 2014
vsRNAs of zucchini mosaic virus were used to study the systemic movement of the virus within the inoculated leaf of Cucurbita pepo. The number of virus variants increases with the distance from the inoculation site and the variant mutations resulted in significant conformation in the cylindrical inclusion protein	Dunham et al., 2014
Identification of a novel geminivirus, genus Mastrevirus, named sugarcane white streak virus in post quarantine sugarcane plant material. The accumulating vsRNAs are strongly influenced by secondary structures within both the viral genomic single-stranded DNA and its mRNA transcripts	Candresse et al., 2014
Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease	Ma et al., 2015
Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees	Liang et al., 2015
Identification of a new genotype of squash mosaic virus in squash grown in Spain	Li et al., 2015
Extending the host range of tomato mottle mosaic virus, genus Tobamovirus, to chickpea (Cicer arietinum) with red seeds and its geographical distribution to Europe	Pirovano et al., 2015
First comparative analysis among the vsRNAs of source, sink and conductive (phloem) tissues in two different plant–virus pathosystems. Melon and cucumber plants were infected with melon necrotic spot virus and prunus necrotic ringspot, respectively, two viruses differing in genome organization and replication strategy. The vsRNA profile remains constant in phloem but not in the other tissues. vsRNAs share the same size distribution in all analyzed tissues. Both viruses were able to modulate the host sRNA profile.	Herranz et al., 2015
Identification and molecular characterization of a novel closterovirus named rose leaf rosette-associated virus	He et al., 2015