Table 1.
Samples included in the comparison with corresponding results from: HTS (+ virus/viroid detected using pipeline described in section Virus and Viroid Detection Workflow,–virus/viroid not detected using pipeline described in section Virus and Viroid Detection Workflow; NA, not applicable).
| Sample number | Host | Virus/viroid present (Baltimore classification) | Initial detection with HTS sequencing using complete datasets | NCBI GenBank accession number | NCBI SRA accession number (MinION direct RNA sequencing of totRNA / MinION direct RNA sequencing of rRNA-depleted totRNA / MinION cDNA-PCR sequencing of totRNA / MinION cDNA-PCR sequencing of rRNA-depleted totRNA / Illumina rRNA-depleted totRNA sequencing) | ||||
|---|---|---|---|---|---|---|---|---|---|
| MinION direct RNA sequencing of totRNA | MinION direct RNA sequencing of rRNA-depleted totRNA | MinION cDNA-PCR sequencing of totRNA | MinION cDNA-PCR sequencing of rRNA-depleted totRNA | Illumina rRNA-depleted totRNA sequencing | |||||
| I | Solanum lycopersicum | TYLCV (ssDNA) | + | + | + | + | + | KY810789 | SRR17660996/SRR17660995/SRR17660994/SRR17660993/SRR17319908 |
| ToCV (ssRNA+) | + | + | + | + | + | KY810786, KY810787 | |||
| PepMV (ssRNA+) | + | + | + | + | + | KF718832.1 (Pep-MV-EU), JX866666.1 (PepMV-CH) | |||
| ToMV (ssRNA+) | - | + | + | + | + | KY810788 | |||
| STV (dsRNA) | + | + | + | + | + | KY810783 | |||
| CLVd (viroid) | + | + | + | + | + | KY810771 | |||
| II | Brassica oleracea | CaMV (dsDNA-RT) | + | NA | NA | NA | + | KY810770 | SRR17660992/NA/NA/NA/SRR17319907 |
| CCyV1 (ssRNA-) | + | NA | NA | NA | + | KY810772 | |||
| III | Nicotiana tabaccum | TSWV (ssRNA-) | + | NA | NA | NA | + | OM112200, OM112201, OM112202 | SRR17660991/NA/NA/NA/SRR17319906 |
| IV | Solanum lycopersicum | TASVd (viroid) | + | NA | NA | NA | + | KY810784 | SRR17660990/NA/NA/NA/SRR17319905 |
| V | Phaseolus vulgaris | PVeV1 (dsRNA) | + | NA | NA | NA | + | / | SRR17660989/NA/NA/NA/SRR17319904 |
| PVeV2 (dsRNA) | + | NA | NA | NA | + | OM112199 | |||
| PVeV3 (dsRNA) | + | NA | NA | NA | + | / | |||
Virus/viroid names: tomato yellow leaf curl virus (TYLCV, Begomovirus, Geminiviridae), tomato chlorosis virus (ToCV, Crinivirus, Closteroviridae), pepino mosaic virus (PepMV, Potexvirus, Alphaflexiviridae), tomato mosaic virus (ToMV, Tobamovirus, Virgaviridae), southern tomato virus (STV, Amalgavirus, Amalgaviridae), columnea latent viroid (CLVd, Pospiviroid, Pospiviroidae), cauliflower mosaic virus (CaMV, Caulimovirus, Caulimoviridae), cabbage cytorhabdovirus 1 (CCvY1, Cytorhabdovirus, Rhabdoviridae), tomato spotted wilt orthotospovirus (TSWV, Orthotospovirus, Tospoviridae), tomato apical stunt viroid (TASVd, Pospiviroid, Pospiviroidae), and phaseolus vulgaris alphaendornavirus 1, 2, 3 (PVeV1, 2, 3, Alphaendornavirus, Endornaviridae).