Table 3 |
|||||||||
| DEGs and highly transcribed genes related to ROS scavenging system | |||||||||
| GeneID | C21 RPKM | T43 RPKM | Fold change | Homologous species | GeneID | C21 RPKM | T43 RPKM | Fold change | Homologous species |
| GLR | Ug30784 | 2.2 | 4.9 | +1.1 | P. trichocarpa | ||||
| Ug33573 | 239.7 | 239.4 | +0.0 | S. tuberosum | Ug39822 | 1.6 | 4.2 | +1.4 | G. max |
| Ug7889 | 215.9 | 207.0 | −0.1 | P. trichocarpa | Ug46671 | 3.1 | 4.0 | +0.3 | P. trichocarpa |
| Ug5332 | 224.8 | 159.1 | −0.5 | A. lyrata | Ug34203 | 5.5 | 3.9 | −0.5 | P. trichocarpa |
| Ug20320 | 59.6 | 137.6 | +1.2 | P. trichocarpa | Ug39974 | 0.9 | 3.8 | +2.0 | C. chinense |
| Ug2849 | 17.2 | 48.0 | +1.5 | P. trichocarpa | Ug49935 | 0.3 | 3.1 | +3.3 | P. trichocarpa |
| Ug64057 | 0.6 | 46.6 | +6.2 | R. australe | Ug49935 | 0.3 | 3.1 | +3.3 | P. trichocarpa |
| Ug6417 | 6.5 | 28.5 | +2.1 | P. trichocarpa | Ug51894 | 1.1 | 2.9 | +1.4 | P. juliflora |
| Ug64851 | 5.1 | 26.3 | +2.4 | P. trichocarpa | Ug55860 | 0.9 | 2.6 | +1.5 | G. max |
| Ug35505 | 9.3 | 19.1 | +1.0 | P. trichocarpa | Ug35988 | 7.0 | 2.5 | −1.5 | P. trichocarpa |
| Ug64791 | 0.0 | 17.1 | +14.1 | R. australe | Ug56737 | 0.6 | 1.0 | +0.8 | P. trichocarpa |
| Ug25907 | 26.2 | 5.0 | −2.4 | A. thaliana | Ug36012 | 2.8 | 0.8 | −1.8 | -- |
| Ug421 | 13.9 | 4.9 | −1.5 | V. vinifera | POD | ||||
| Ug41652 | 13.3 | 2.8 | −2.2 | A. lyrata | Ug16495 | 502.4 | 158.5 | −1.7 | A. lyrata |
| Ug9652 | 5.9 | 2.5 | −1.3 | A. lyrata | Ug14936 | 346.9 | 113.9 | −1.6 | G. hirsutum |
| Ug42510 | 1.2 | 0.5 | −1.2 | R. communis | Ug9314 | 420.9 | 71.7 | −2.6 | L. chinensis |
| Ug38396 | 1.6 | 0.0 | −10.7 | A. thaliana | Ug31805 | 135.2 | 54.4 | −1.3 | T. hispida |
| Ug42531 | 2.9 | 0.0 | −11.5 | P. trichocarpa | Ug28717 | 143.6 | 49.1 | −1.5 | L. chinensis |
| Ug45519 | 2.4 | 0.0 | −11.2 | A. thaliana | Ug21658 | 127.8 | 45.9 | −1.5 | L. chinensis |
| APX | Ug24487 | 110.2 | 44.3 | −1.3 | A. thaliana | ||||
| Ug44406 | 422.1 | 448.6 | +0.1 | R. australe | Ug8366 | 216.0 | 38.5 | −2.5 | L. chinensis |
| Ug47495 | 171.9 | 210.3 | +0.3 | T. hispida | Ug58048 | 187.9 | 33.6 | −2.5 | O. sativa |
| Ug17786 | 324.5 | 199.7 | −0.7 | N. tabacum | Ug17264 | 74.8 | 25.4 | −1.6 | T. hispida |
| Ug13095 | 315.9 | 183.3 | −0.8 | F. ananassa | Ug26097 | 75.6 | 21.7 | −1.8 | T. hispida |
| Ug57465 | 336.9 | 167.6 | −1.0 | C. sinensis | Ug56728 | 2.9 | 18.3 | +2.6 | T. hispida |
| Ug25879 | 201.8 | 166.0 | −0.3 | A. thaliana | Ug555 | 45.7 | 14.3 | −1.7 | B. gymnorhiza |
| Ug10954 | 241.7 | 143.2 | −0.8 | S. nigrum | Ug33872 | 37.9 | 11.6 | −1.7 | T. hispida |
| Ug26707 | 48.4 | 98.9 | +1.0 | M. crystallinum | Ug21205 | 35.9 | 9.5 | −1.9 | P. trichocarpa |
| Ug46803 | 98.4 | 43.9 | −1.2 | T. hispida | Ug8210 | 21.3 | 7.0 | −1.6 | T. hispida |
| Ug28905 | 8.9 | 3.9 | −1.2 | Z. aethiopica | Ug26203 | 12.8 | 5.4 | −1.2 | O. sativa |
| MDAR | Ug23427 | 22.2 | 4.8 | −2.2 | A. thaliana | ||||
| Ug33304 | 347.9 | 300.5 | −0.2 | P. sativum | Ug61313 | 0.0 | 4.5 | +12.1 | O. sativa |
| Ug64013 | 1.3 | 5.2 | +2.0 | A. lyrata | Ug55297 | 0.9 | 4.5 | +2.3 | G. hirsutum |
| DHAR | Ug13312 | 16.7 | 4.4 | −1.9 | A. thaliana | ||||
| Ug42162 | 275.1 | 196.6 | −0.5 | M. pumila | Ug63541 | 1.1 | 3.6 | +1.7 | A. thaliana |
| GR | Ug3944 | 15.1 | 2.9 | −2.4 | S. oleracea | ||||
| Ug8218 | 279.8 | 259.3 | −0.1 | R. australe | Ug47499 | 5.7 | 1.4 | −2.0 | I. batatas |
| Ug3408 | 310.6 | 233.2 | −0.4 | V. unguiculata | Ug34920 | 12.0 | 1.0 | −3.5 | A. thaliana |
| GST | Ug43924 | 7.6 | 1.0 | −3.0 | S. oleracea | ||||
| Ug48125 | 250.3 | 477.2 | +0.9 | J. curcas | Ug43247 | 2.2 | 0.5 | −2.2 | A. thaliana |
| Ug63119 | 313.4 | 336.6 | +0.1 | Z. mays | Ug46420 | 4.1 | 0.4 | −3.3 | S. oleracea |
| Ug12484 | 217.4 | 220.3 | +0.0 | T. androssowii | Ug47065 | 3.9 | 0.4 | −3.3 | G. max |
| Ug42162 | 275.1 | 196.6 | −0.5 | M. pumila | Ug40929 | 2.5 | 0.0 | −11.3 | A. thaliana |
| Ug48024 | 184.0 | 195.6 | +0.1 | P. trichocarpa | PrxR | ||||
| Ug32254 | 115.3 | 191.7 | +0.7 | T. androssowii | Ug63275 | 487.7 | 279.7 | −0.8 | Z. mays |
| Ug1025 | 114.0 | 155.9 | +0.5 | M. pusilla | Ug61053 | 226.7 | 215.5 | −0.1 | I. batatas |
| Ug20784 | 117.7 | 139.8 | +0.2 | P. trichocarpa | Trx | ||||
| Ug6700 | 96.3 | 138.9 | +0.5 | E. guineensis | Ug12493 | 200.7 | 353.6 | +0.8 | H. brasiliensis |
| Ug8174 | 84.6 | 127.3 | +0.6 | A. thaliana | Ug17142 | 502.1 | 339.8 | −0.6 | L. bicolor |
| Ug18987 | 160.0 | 109.0 | −0.6 | E. guineensis | Ug7940 | 214.0 | 177.2 | −0.3 | A. thaliana |
| Ug62570 | 203.9 | 106.5 | −0.9 | A. hypogaea | Ug34328 | 221.6 | 169.4 | −0.4 | S. tuberosum |
| Ug28190 | 62.6 | 102.6 | +0.7 | A. thaliana | Ug2658 | 404.1 | 157.1 | −1.4 | P. trichocarpa |
| Ug7332 | 135.4 | 64.2 | −1.1 | L. bicolor | Ug21241 | 18.5 | 79.8 | +2.1 | M. truncatula |
| Ug27980 | 52.8 | 58.8 | +0.2 | P. trichocarpa | Ug16795 | 5.7 | 37.4 | +2.7 | N. alata |
| Ug27203 | 41.0 | 57.6 | +0.5 | P. trichocarpa | Ug37125 | 15.1 | 32.9 | +1.1 | M. truncatula |
| Ug19050 | 69.7 | 28.3 | −1.3 | N. tabacum | Ug65122 | 3.3 | 30.9 | +3.2 | G. max |
| Ug4112 | 38.2 | 17.2 | −1.1 | J. curcas | Ug14501 | 43.7 | 18.6 | −1.2 | A. thaliana |
| Ug28720 | 6.3 | 13.2 | +1.1 | G. max | Ug49635 | 0.6 | 18.4 | +4.8 | Z. mays |
| Ug53783 | 3.6 | 12.4 | +1.8 | P. trichocarpa | Ug27430 | 1.0 | 10.0 | +3.3 | M. truncatula |
| Ug14715 | 11.7 | 11.7 | +0.0 | P. trichocarpa | Ug58332 | 18.6 | 8.8 | −1.1 | N. benthamiana |
| Ug8711 | 2.8 | 10.1 | +1.8 | P. trichocarpa | Ug32797 | 9.5 | 4.0 | −1.2 | A. thaliana |
| Ug8711 | 2.8 | 10.1 | +1.8 | P. trichocarpa | Ug61925 | 0.9 | 3.1 | +1.8 | Z. mays |
| Ug58658 | 1.1 | 8.1 | +2.9 | G. max | SOD | ||||
| Ug56087 | 2.7 | 5.9 | +1.1 | T. androssowii | Ug23472 | 332.4 | 348.8 | +0.1 | N. nucifera |
| Ug6808 | 5.3 | 5.9 | +0.1 | P. trichocarpa | Ug8340 | 247.0 | 265.8 | +0.1 | T. androssowii |
| Ug28520 | 11.9 | 5.4 | −1.1 | Z. jujuba | Ug18352 | 78.3 | 36.8 | −1.1 | M. crystallinum |
| Ug30784 | 2.2 | 4.9 | 1.1 | P. trichocarpa | Ug57351 | 0.6 | 1.5 | +1.4 | G. max |
*DEG was filtered by using threshold of false discovery rate (FDR) ≤ 0.001 and absolute value of log2Ratio ≥ 1. Ug represents unigene. RPKM means RPKM values of unigenes in C21 or T43. “Fold change” equals to log2 (T43-RPKM/C21-RPKM). “+” indicates up-regulated transcription and “-” represents down-regulated transcription. Homologous species is that identified from BLAST search of nr database using cut-off E-value of ≤ 10-5.
Dang et al. BMC Genomics 2013 14:29 doi:10.1186/1471-2164-14-29
