Table 2

DEGs and highly transcribed genes related to ion transport *
GeneID C21 RPKM T43 RPKM Fold change Homologous species GeneID C21 RPKM T43 RPKM Fold change Homologous species
HKT1 SOS
Ug20631 28.6 9.5 −1.6 P. trichocarpa Ug798 27.2 34.5 +0.3 C. quinoa
Ug4890 139.4 64.2 −1.1 P. trichocarpa Ug35995 0.5 0.0 −8.9 C. quinoa
Ug27586 70.8 30.8 −1.2 M. crystallinum Ug35827 3.4 0.9 −1.9 M. crystallinum
CNGC NHX
Ug3965 141.8 101.0 −0.5 A. thaliana Ug20634 23.2 44.6 +0.9 C. reticulata
Ug7183 112.6 86.2 −0.4 G. hirsutum Ug5272 10.1 23.7 +1.2 S. komarovii
Ug24497 9.8 4.6 −1.1 A. lyrata Ug8445 47.3 39.3 −0.3 M. crystallinum
Ug61678 0.0 3.2 +11.7 A. lyrata Ug752 28.7 21.7 −0.4 T. tetragonioides
Ug54762 0.0 0.8 +9.6 A. lyrata Nha-like protein
Ug39788 1.3 0.0 −10.3 V. vinifera Ug16859 223.0 311.2 +0.5 T. octandrum
KUP V-H+-ATPase
Ug14170 231.6 124.1 −0.9 V. vinifera Ug63112 0.0 0.3 +8.4 A. lyrata
Ug26051 103.6 63.8 −0.7 M. crystallinum Ug15764 0.0 0.3 +8.4 A. lyrata
Ug41960 15.6 33.5 +1.1 G. hirsutum Ug13159 12.2 23.7 +1.0 G. max
Ug65296 3.3 13.7 +2.0 G. hirsutum Ug8615 69.1 112.3 +0.7 C. sinensis
Ug61613 3.6 13.3 +1.9 G. hirsutum Ug32194 16.8 24.8 +0.6 G. max
Ug29610 4.9 10.5 +1.1 V. vinifera Ug14517 149.2 193.3 +0.4 C. limon
Ug5469 3.3 10.1 +1.6 A. thaliana Ug48766 86.3 108.1 +0.3 E. guineensis
Ug33474 3.3 9.9 +1.6 A. thaliana Ug23403 16.4 20.4 +0.3 A. lyrata
Ug4060 5.4 2.0 −1.5 A. thaliana Ug27100 86.4 106.0 +0.3 A. lyrata
Ug41099 4.2 0.7 −2.5 A. thaliana Ug5921 64.1 78.6 +0.3 A. lyrata
AKT Ug38012 38.0 46.3 +0.3 Z. mays
Ug20360 3.3 7.0 +1.1 P. tenuiflora Ug18074 52.5 63.8 +0.3 C. unshiu
Ug57424 0.0 5.6 +12.5 P. euphratica Ug5444 35.8 41.4 +0.2 D. carota
Ug63704 3.9 7.8 +1.0 E. camaldulensis Ug8331 96.0 104.3 +0.1 E. guineensis
Ug63924 1.0 5.9 +2.6 V. vinifera Ug6864 97.1 104.6 +0.1 G. hirsutum
Ug47159 3.0 0.8 −2.0 S. tuberosum Ug14833 77.6 83.3 +0.1 Z. mays
Ug4060 5.4 2.0 −1.5 A. thaliana Ug32662 113.7 119.2 +0.1 Z. mays
Ug41099 4.2 0.7 −2.5 A. thaliana Ug18679 58.5 59.7 +0.0 A. thaliana
HAK Ug14939 58.5 59.7 +0.0 A. thaliana
Ug27946 36.3 74.8 +1.0 M. crystallinum Ug13111 50.8 51.3 +0.0 H. caspica
Ug28118 13.8 31.4 +1.2 A. thaliana Ug27358 137.8 138.0 +0.0 C. unshiu
Ug65080 3.2 8.0 +1.3 O. sativa Ug31534 107.4 106.3 +0.0 A. thaliana
Ug54929 1.9 7.0 +1.9 O. sativa Ug31417 116.0 114.7 +0.0 K. foliatum
Ug64325 1.5 6.1 +2.0 V. vinifera Ug12019 68.3 67.4 +0.0 G. hirsutum
Ug35034 2.0 4.3 +1.1 O. sativa Ug46409 15.4 14.6 −0.1 Z. mays
Ug64584 0.0 4.2 +12.1 O. sativa Ug31885 133.0 124.2 −0.1 S. salsa
Ug48231 9.3 2.5 −1.9 H. vulgare Ug9415 7.9 7.3 −0.1 A. lyrata
CHX Ug30783 220.6 202.0 −0.1 Z. marina
Ug64193 2.2 6.1 +1.5 P. trichocarpa Ug9762 54.3 48.2 −0.2 A. lyrata
Ug64762 0.0 5.3 +12.4 P. trichocarpa Ug23822 289.1 241.7 −0.3 P. acutifolius
Ug22739 10.4 4.8 −1.1 A. thaliana Ug28038 166.2 135.7 −0.3 S. oleracea
Ug62951 6.4 2.5 −1.4 M. truncatula Ug14408 57.5 45.4 −0.3 G. hirsutum
Ug47929 7.6 1.0 −2.9 A. thaliana Ug1235 57.5 45.4 −0.3 G. hirsutum
Ug47939 2.7 1.0 −1.4 A. thaliana Ug14963 116.2 87.3 −0.4 M. crystallinum
Ug35886 1.1 0.5 −1.2 P. trichocarpa Ug27790 18.8 14.1 −0.4 A. thaliana
KEA Ug58281 139.3 103.6 −0.4 I. lactea
Ug39703 3.0 0.8 −2.0 A. thaliana Ug62214 45.5 32.7 −0.5 A. lyrata
Ug43622 5.5 2.4 −1.2 A. thaliana Ug3474 8.4 5.9 −0.5 O. sativa
Ug53119 3.5 8.9 +1.3 A. thaliana Ug27883 47.2 33.0 −0.5 M. truncatula
Ug54277 2.6 7.3 +1.5 A. thaliana Ug26948 62.4 36.4 −0.8 G. hirsutum
KOC PM-H+-ATPase
Ug23367 3.0 6.4 +1.1 N. tabacum Ug248 79.8 240.3 +1.6 D. carota
Ug37885 2.4 0.8 −1.6 H. brasiliensis Ug15650 143.1 376.9 +1.4 P. persica
Ug43016 1.7 0.5 −1.8 -- Ug1087 171.3 265.1 +0.6 S. lycopersicum
Ug19269 6.7 12.6 +0.9 P. trichocarpa Ug47575 285.8 402.4 +0.5 C. sativus
Ug8178 9.1 10.3 +0.2 P. trichocarpa Ug7564 205.5 243.9 +0.2 A. lyrata
Ug56865 6.4 8.3 +0.4 P. trichocarpa Ug24901 199.6 218.9 +0.1 A. thaliana
Ug9256 32.1 55.3 +0.8 P. trichocarpa V-H+-PPase
Ug20095 7.3 7.8 +0.1 P. trichocarpa Ug12515 188.6 156.3 −0.3 A. lyrata
Ug22675 44.6 25.4 −0.8 P. trichocarpa Ug14495 251.2 184.2 −0.4 P. communis
Ug40263 4.4 3.4 −0.4 P. trichocarpa Ug16866 276.0 268.2 +0.0 N. tabacum
Ug50188 3.7 3.5 −0.1 P. trichocarpa Ug61784 320.3 237.0 −0.4 V. radiata
Ug39519 0.9 0.5 −0.9 P. trichocarpa Ug8875 197.0 221.1 +0.2 M. truncatula
Ug25217 20.7 18.6 −0.2 P. trichocarpa

*DEG was filtered using threshold of false discovery rate (FDR) ≤ 0.001 and absolute value of log2Ratio ≥ 1. Ug represents unigene. RPKM indicates 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 the 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