Table 2.
Sanitary status.
| GFLV consensus | Viroids | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| RNA1 | RNA2 | RNA3 | GRSPaV | HSVd | GYSVd1 | GaTLV | Contigs related to | ||||
| Sample name | Total clean reads | Size (nt) | 7,341 | 3,750 | 1,114 | 8,725 | 298 | 366 | 6,033 | Insect | Fungi |
| EVC53 | 13,147,378 | reads # | 22 | 50 | 0 | 7,853 | 564 | 396 | 627 | ||
| healthy grapevine | RPKM | 0 | 1 | 0 | 68 | 144 | 82 | 8 | 10 | 144 | |
| Genome | 0 | 0 | 0 | 2 | 2 | 2 | 1 | ||||
| EVC42 | 12,258,388 | reads # | 77,887 | 92,619 | 13 | 6,341 | 1,214 | 747 | 3,247 | ||
| GFLV-infected | RPKM | 701 | 1,630 | 1 | 48 | 269 | 135 | 44 | 7 | 174 | |
| Genome | 1 | 2 | 0 | 3 | 2 | 1 | 1 | ||||
| EVC60 | 14,210,779 | reads # | 48,433 | 53,089 | 15 | 9,209 | 1,098 | 504 | 12,588 | ||
| GFLV-infected | RPKM | 464 | 996 | 1 | 74 | 259 | 97 | 147 | 18 | 659 | |
| Genome | 1 | 1 | 0 | 4 | 1 | 1 | 1 | ||||
| EVC56 | 16,543,942 | reads # | 52,660 | 61,265 | 33,687 | 4,202 | 1,048 | 500 | 1,547 | ||
| GFLV-infected | RPKM | 434 | 988 | 1,828 | 29 | 213 | 83 | 15 | 19 | 264 | |
| Genome | 1 | 1 | 1 | 2 | 2 | 2 | 1 | ||||
Number of reads (in bold) and RPKM (Reads Per Kilobase per Million reads mapped to the reference, in italic) for each grapevine viruses and viroids found in the four samples analyzed. Genome: correspond to the number of complete (to near complete) genomes assembled in de novo. GFLV, grapevine fanleaf virus; GRSPaV, grapevine rupestris stem pitting-associated virus; GaTLV, grapevine-associated tymo-like virus; HSVd, Hop stunt viroid, and GYSVd1, grapevine yellow speckle viroid-1.
Reads were mapped on a set of reference viruses previously described as infecting Vitis vinifera. For mapping, a low stringency was used with parameters set to 0.5 for read length and 0.7 for similarity. Size of the sequences tested is noted.