Table 4.
Sequence similarity of cucumber PlasTi-microarray probes to plastid genomes of other plants
| Organism | PlasTi- microarray probes matching target plastid genome with E < 1 × 10-3 | PlasTi- microarray probes matching target plastid genome with E ≤ 1 × 10-10 | ||||
|---|---|---|---|---|---|---|
| All | SC coding | SC non-coding | IR coding | IR non-coding | ||
| C.sa | 1629 | 262 | 1062 | 53 | 252 | 1629 |
| A.tha | 1188 (72.9%) | 246 (93.9%) | 638 (60.1%) | 53 (100%) | 251 (99.6%) | 1035 (63.5%) |
| N.tab | 1253 (76.9%) | 250 (95.4%) | 706 (66.5%) | 53 (100%) | 244 (96.8%) | 1108 (68.0%) |
| S.lyc | 1212 (74.4%) | 250 (95.4%) | 666 (62.7%) | 53 (100%) | 243 (96.4%) | 1086 (66.7%) |
| S.ole | 927 (56.9%) | 214 (81.7%) | 470 (44.3%) | 49 (92.5%) | 194 (77.0%) | 807 (49.5%) |
| L.sat | 1225 (75.2%) | 252 (96.2%) | 682 (64.2%) | 52 (98.1%) | 239 (94.8%) | 1078 (66.2%) |
| M.tru | 1101 (67.6%) | 238 (90.8%) | 615 (57.9%) | 52 (98.1%) | 196 (77.8%) | 944 (57.9%) |
| L.jap | 1164 (71.4%) | 247 (94.3%) | 625 (58.9%) | 52 (98.1%) | 240 (95.2%) | 1032 (63.4%) |
| P.tri | 1287 (79.0%) | 245 (93.5%) | 740 (69.7%) | 53 (100%) | 249 (98.8%) | 1142 (70.1%) |
| H.vul | 927 (56.9%) | 219 (83.6%) | 474 (44.6%) | 49 (92.5%) | 185 (73.4%) | 802 (49.2.%) |
Each probe was used as a query in a blastn search against each plastid genome, with the E value threshold set at 1 × 10-3. C.sa - Cucumis sativus [GenBank: NC_007144], A. tha - Arabidopsis thaliana [GenBank: NC_000932], N.tab - Nicotiana tabacum [GenBank: NC_001879], S.lyc - Solanum lycopersicon [GenBank: NC_007898], S.ole - Spinacia oleracea [GenBank: NC_002202], L.sat - Lactuca sativa [GenBank: NC_007578], M.tru - Medicago truncatula [GenBank: NC_003119], L.jap - Lotus japonicus [GenBank: NC_002694], P.tri - Populus trichocarpa [GenBank: NC_009143], H.vul - Hordeum vulgare [GenBank: NC_008590]. For each genome, number of probes matching with E value lower than the threshold as well as number of probes matching with E ≤ 1 × 10-10 is reported.