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Table 2 Confirmation of the RNA-Seq expression profiles with qRT-PCR

From: De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway

Transcript RNA-Seq(CS) RNA-Seq(DS) RNA-Seq(SS) qRT-PCR(CS) qRT-PCR(DS) qRT-PCR(SS) Annotation
Mf53179 5.93 0.69 0.05 9.28 5.01 2.43 DREB protein
Mf40807 3.81 1.30 0.91 4.27 4.06 1.71 GH3
Mf52262 2.79 3.45 2.16 7.24 8.87 5.47 NFR5
Mf44686 2.55 6.14 2.35 7.62 7.03 3.19 ERF
Mf24843 2.45 5.53 3.08 7.28 9.46 5.09 ERF
Mf94524 2.22 3.83 0.66 4.43 3.25 0.45 CYP707A
Mf21376 2.18 1.70 0.40 2.13 1.57 0.33 NCED
Mf89827 2.17 4.92 5.37 1.74 6.17 5.14 Stress-induced receptor
Mf26361 2.11 2.72 1.95 1.84 4.19 0.43 OPCL1
Mf20359 2.04 0.58 1.34 0.15 4.39 2.06 ACS
Mf40505 1.93 3.50 2.66 2.01 5.98 1.40 OPR
Mf51793 1.88 6.03 3.99 5.03 6.35 4.40 Calmodulin binding
Mf23563 1.86 1.12 2.39 1.86 1.12 2.40 CrtZ
Mf84393 1.49 3.81 2.09 3.76 4.96 3.95 JMT
Mf42223 1.48 3.83 1.88 4.74 4.71 1.66 AOS
Mf34249 1.40 1.88 1.29 3.81 1.02 1.43 ACS
Mf84453 1.28 1.53 1.31 −0.16 1.05 −2.60 LOX
Mf31223 1.26 1.52 1.24 1.74 3.19 0.05 AOC
Mf37052 1.24 3.75 3.10 2.81 2.83 1.09 NFR1
Mf19438 1.21 2.24 1.65 5.07 3.66 1.07 SAMS
Mf21208 1.16 1.68 1.12 0.70 3.28 1.34 2-beta-dioxygenase
Mf37096 1.15 4.29 2.69 1.03 3.22 0.23 DMI3
Mf46196 1.09 4.29 5.05 3.56 10.67 9.19 NCED
Mf41585 1.08 1.51 1.14 0.10 1.95 −1.19 SNF1
Mf84582 0.96 −1.01 0.29 −0.52 −2.24 −2.72 cytochrome P450
Mf19924 0.96 3.13 1.70 1.18 0.89 0.64 SAMS
Mf35541 0.83 2.21 1.65 0.26 1.46 −1.00 SNF1
Mf53098 0.75 1.69 1.60 0.32 1.67 0.43 JAR1
Mf52729 0.70 −0.38 0.46 5.19 −0.63 3.87 Cysteine-rich receptor
Mf29322 0.65 0.91 1.75 1.69 1.25 1.20 ACO
Mf32232 0.59 1.13 3.02 −0.04 1.13 3.01 ZEP
Mf46161 0.49 3.69 1.20 2.24 3.79 0.46 ACS
Mf33973 0.42 1.21 0.25 2.01 1.73 0.69 DMI1
Mf22267 0.18 0.45 −0.53 0.43 0.40 −0.87 CrtZ
Mf37546 0.15 1.34 0.78 0.30 0.25 −0.61 JAR1
Mf24274 0.14 −0.68 −0.40 0.07 −1.38 −0.26 20-oxidase
Mf58069 0.11 0.48 1.82 1.03 0.17 1.15 ACO
Mf88132 −0.21 1.26 2.37 −0.66 2.33 2.90 ABF 1
Mf46174 −0.25 −1.17 −0.25 −1.11 −0.95 −0.41 ZEP
Mf23784 −0.77 −0.72 −1.00 −1.93 −0.06 −0.42 NSP11
Mf49154 −0.95 0.58 1.87 −0.56 2.59 3.75 Importin
Mf50824 −0.96 3.51 1.26 −0.79 1.20 0.70 DMI2
Mf54137 −1.11 1.41 0.18 −3.07 5.33 3.96 Nodule receptor kinase
Mf22751 −1.33 −1.76 −0.74 −0.46 −0.73 −1.25 PYR/PYL
Mf11674 −1.36 −2.59 −0.26 −0.68 −1.45 −2.58 Leghemoglobin
Mf24497 −1.49 −0.88 −1.62 −3.93 −0.23 −2.52 ENOD
Mf34644 −1.54 0.43 0.14 −0.55 0.99 0.60 GID1
Mf20666 −1.76 1.26 0.37 −0.16 0.92 0.20 GID1
Mf56011 −1.77 −1.09 −0.47 −2.17 −2.48 −1.62 AAO
Mf38812 −2.21 2.13 2.99 0.52 0.68 0.72 DMI3
Mf17441 −2.26 −1.66 −2.11 −1.45 −0.71 −1.14 AAO
Mf87623 −2.45 −1.08 −1.48 −1.04 −0.35 −2.13 PYR/PYL
Mf49788 −3.16 −2.17 −2.18 −0.70 −0.57 −2.60 NSP2
Mf20500 −3.78 3.32 −0.57 −1.98 5.88 −2.94 ERN2
Mf21830 −4.11 −1.75 −2.31 −1.84 −0.73 −4.88 ENOD
Mf29128 −5.20 1.10 −0.12 −0.46 −0.05 −1.69 3-beta-hydroxylase
  1. The expression levels of CS, DS, SS, and SC were calculated, and pairwise comparisons (CS versus SC, DS versus SC, and SS versus SC) were calculated. Expression ratios for the RNA-Seq data, shown as the fold change, were calculated for cold [RNA-Seq (CS)], dehydration [RNA-Seq (DS)], and high salinity [RNA-Seq (SS)] using the DESeq programme. Ratios for qPCR analyses were calculated for cold [qRT-PCR (CS)], dehydration [qRT-PCR (DS)], and high salinity [qRT-PCR (SS)] using a previously described method [114]. All expression ratios are presented as log2(treatment/standard). Negative values indicate that the standard has a higher expression level than the treatment, and expression ratios of 0 indicate no difference in expression between the treatment and standard