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.

Dang et al. BMC Genomics 2013 14:29   doi:10.1186/1471-2164-14-29

Open Data