Table 3 Assembled viruses with their genome lineage and summary of virus-associated contigs in mRNA, sRNA and whole transcriptome (WT) library
From: Virome analysis of field-collected chilli samples reveals diverse viruses
Reconstructed virus | Species new name | Segment | Genome | No. of contigs associated with virus | Reference genome | Size (nt) | Genome recovered (nt) | Percentage of genome recovery | FPKM values | Virus copy number (%) | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
mRNA | sRNA | WT | ||||||||||
ChiLCV | Begomovirus chillicapsici | DNA-A | Circular, ssDNA | 4 | 25 | 2 | NC_004628.1 | 2754 | 2510 | 91.14 | 166623.14 | 45.36 |
CMV | Cucumovirus CMV | RNA1 | Linear, (+) ssRNA | 6 | 11 | 18 | NC_002034.1 | 3357 | 3313 | 98.69 | 66337.55 | 18.06 |
RNA2 | 3 | 13 | 7 | NC_002035.1 | 3050 | 3016 | 98.89 | 30678.99 | 8.35 | |||
RNA3 | 5 | 11 | 24 | NC_001440.1 | 2216 | 2175 | 98.15 | 96986.43 | 26.4 | |||
GBNV | Orthotospovirus arachinecrosis | L segment | Linear, (-) ssRNA | 9 | 0 | 6 | NC_003614.1 | 8911 | 859 | 9.64 | - | - |
M segment | 3 | 0 | 5 | NC_003620.1 | 4801 | 972 | 20.25 | - | - | |||
S segment | 0 | 0 | 2 | NC_003619.1 | 3057 | 667 | 21.82 | - | - | |||
PCV-2 | Deltapartitivirus duocapsici | RNA1 | Linear, dsRNA | 1 | 3 | 1 | NC_034159.1 | 1609 | 1585 | 98.51 | 1527.73 | 0.42 |
RNA2 | 1 | 0 | 1 | NC_034167.1 | 1525 | 1490 | 97.7 | 763.38 | 0.21 | |||
PeVYV | Polerovirus PeVYV2 | Â | Linear, (+) ssRNA | 6 | 2 | 8 | NC_055129.1 | 6028 | 5998 | 99.5 | 1230.51 | 0.33 |
BPEV | Alphaendornavirus capsici | Â | Linear, dsRNA | 1 | 7 | 1 | NC_039216.1 | 14,714 | 14,702 | 99.92 | 3234.88 | 0.88 |