Table 1.
Summary of eRTBVL-D Segments in the Oryza sativa Genome
| ID | Previous Namea | Positions in Rice Genome |
Positions in Viral Genomeb |
Length (bp) | Disruptive Mutation Numberc | Distances to Neighbor Genes |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Start | End | Strand | Start | End | Left | Right | ||||
| d1 | JaE1-4 | 1 | 5,193,920 | 5,194,407 | + | 6,880 | 7,353 | 488 | NA | 43,579 | 7,455 |
| d2 | JaE1-4 | 1 | 5,194,744 | 5,195,008 | + | 108 | 359 | 265 | 0 | 44,403 | 6,854 |
| d3 | JaE1-4 | 1 | 5,195,124 | 5,198,055 | + | 4,259 | 7,180 | 2,932 | 9 | 44,783 | 3,807 |
| d4 | NA | 2 | 12,120,385 | 12,120,601 | + | 6,540 | 6,758 | 217 | NA | 5,419 | 7,312 |
| d5 | NA | 2 | 12,120,644 | 12,121,245 | − | 6,539 | 7,184 | 602 | NA | 5,678 | 6,668 |
| d6 | NA | 4 | 18,488,307 | 18,488,450 | + | 6,873 | 7,021 | 144 | NA | 8,092 | 1,903 |
| d7 | NA | 4 | 18,488,544 | 18,488,674 | − | 6,852 | 6,984 | 131 | NA | 8,329 | 1,679 |
| d8 | NA | 4 | 21,097,520 | 21,097,778 | − | 6,952 | 7,196 | 259 | NA | 86,783 | 85,199 |
| d9 | NA | 5 | 6,506,720 | 6,507,050 | − | 6,953 | 7,278 | 331 | NA | 8,332 | 7,696 |
| d10 | JaE7-4 | 7 | 8,906,209 | 8,907,980 | + | 5,547 | 7,343 | 1,772 | 5 | 27,304 | 18,154 |
| d11 | JaE7-5/7-6 | 7 | 8,909,007 | 8,920,257 | − | 4,817 | 7,341 | 11,251 | 9 | 30,102 | 5,877 |
| d12 | NA | 9 | 16,726,920 | 16,727,025 | + | 32 | 137 | 106 | 0 | 5,997 | 1,153 |
| d13 | NA | 10 | 9,099,571 | 9,099,688 | − | 2,584 | 2,696 | 118 | 1 | 5,282 | 2,080 |
| d14 | JaE11-2 | 11 | 5,069,912 | 5,072,964 | + | 3,580 | 6,416 | 3,053 | 19 | 5,378 | 243 |
| d15 | JaE11-5 | 11 | 11,654,495 | 11,657,114 | − | 3,806 | 6,413 | 2,620 | 15 | 2,608 | 4,216 |
a
Previous names of six segments (JaE1-4, 7-4, 7-5, 7-6, 11-2, and 11-5) are from Liu et al. (2012).
b
Segments were mapped to the reconstructed viral genomes.
c
Single nucleotide polymorphisms and insertion/deletion-induced nonsense mutations and frameshift mutations.
NA, not available for intergenic regions; Chr, chromosome.