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Table 4 Sequence similarity of cucumber PlasTi-microarray probes to plastid genomes of other plants

From: A tiling microarray for global analysis of chloroplast genome expression in cucumber and 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.%)

  1. 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.