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Table 1 Cd-regulated differentially expressed genes (DEGs) mapped to the metabolic pathways

From: Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

BinName FPKM Cd1h/ck1h Rice gene annotation
Transcript ID ck1h Cd1h log2FC q_value
Jasmonate synthesis-degradation and signaling
 Os06g11290.1 5.18 435.09 6.39 0.0019 12-oxophytodienoate reductase, OsOPR1
 Os06g11210.1# 58.99 717.03 3.60 0.0019 OsOPR5 [Q69TI0]
 Os06g11240.1 14.15 339.14 4.58 0.0019 OPR
 Os06g11200.1 0.15 2.40 3.98 0.0188 OPR
 Os03g55800.1 29.03 146.45 2.33 0.0019 allene oxide synthase, AOS1
 Os03g12500.1 2.23 13.52 2.60 0.0019 allene oxide synthase, AOS2
 Os12g05440.1* 1.85 58.66 4.98 0.002 cytochrome P450, CYP94C2b
 Os03g08310.1* 1.88 27.26 3.86 0.002 ZIM domain containing protein, OsJAZ9
 Os03g28940.1 38.17 106.38 1.48 0.0019 ZIM domain containing protein
 Os09g02710.1 0.63 4.20 2.73 0.0035 Arabidopsis loss of the timing of Et and JA biosynthesis 1
Abscisic acid synthesis-degradation and signaling
 Os03g44380.1 0.53 5.75 3.43 0.0019 9-cis-epoxycarotenoid dioxygenase, OsNCED3
 Os07g05940.1 0.59 99.97 7.41 0.0019 OsNCED4
 Os12g42280.1 2.63 32.42 3.62 0.0019 OsNCED5
 Os12g29400.1 5.88 14.09 1.26 0.0019 ABA-responsive protein [Q2QQY9]
 Os04g44510.1 51.06 244.45 2.26 0.0019 ABA-responsive protein (GRAM domain)
 Os04g44500.1 17.60 49.88 1.50 0.0019 ABA-responsive protein (GRAM domain)
 Os10g04860.1 5.05 2.26 −1.16 0.0019 aldehyde oxidase
 Os02g52780.2 0.71 14.01 4.30 0.0019 OsbZIP23
Ethylene signaling
 Os07g48630.1 52.93 109.98 1.06 0.002 ethylene-insensitive 3
 Os02g43790.1 41.57 265.23 2.67 0.002 ethylene-responsive transcription factor, OsBIERF3
 Os03g09170.1 20.44 218.22 3.42 0.002 ERF
 Os04g46220.1 44.26 119.27 1.43 0.002 ERF
 Os08g31580.1 102.51 268.56 1.39 0.002 ERF
 Os01g54890.1 4.75 31.18 2.71 0.034 ERF2
 Os01g58420.1 49.28 134.22 1.45 0.002 OsERF3
 Os11g06770.2* 0.10 0.70 2.75 0.027 ERF110
 Os02g43970.1* 2.93 7.61 1.37 0.002 ABA-responsive DREB gene, ARAG1
 Os10g41330.2* 5.79 64.06 3.47 0.002 AP2 domain
 Os06g10780.1* 2.17 6.55 1.59 0.002 AP2 domain
 Os02g43940.1* 1.74 6.56 1.92 0.002 AP2 domain, OsDREB4–1
 Os09g28440.1 0.59 47.37 6.32 0.002 AP2 domain, OsEATB
 Os08g36920.1# 0.76 70.32 6.53 0.002 AP2 domain
 Os03g08460.1 91.75 42.47 −1.11 0.002 AP2 domain
 Os03g08490.1 215.27 81.73 −1.40 0.002 AP2 domain
 Os03g08500.1 538.17 256.44 −1.07 0.002 AP2 domain
 Os04g08740.3 68.92 31.96 −1.11 0.002 ethylene receptor, OsETR2 [Q7XX84]
Gibberellin synthesis-degradation
 Os06g37300.2 0.22 0.01 −2.36 1.1290 ent-kaurene oxidase 4, OsKO4 [Q0DBF4]
 Os03g63970.1* 18.68 0.00 −1.12 40.5099 gibberellin 20 oxidase 1
 Os05g48700.1 2.84 0.01 1.34 1.1252 gibberellin 2-beta-dioxygenase
Metal binding, chelation and storage
 Os04g57200.1 54.50 169.43 1.64 0.002 heavy metal transport/detoxification protein
 Os04g57200.2 3.10 47.85 3.95 0.002
 Os04g17100.1 2.63 32.28 3.62 0.0063 heavy metal-associated domain protein, HMAD
HMAD
 Os04g17100.2 43.72 123.38 1.50 0.0019
 Os03g05750.1 0.54 89.45 7.38 0.003 HMAD
 Os03g05750.2 9.01 212.68 4.56 0.002
 Os02g37290.1 38.65 132.69 1.78 0.002 HMAD
 Os02g37300.1 11.63 66.20 2.51 0.002 HMAD
 Os02g37330.1 3.99 98.49 4.63 0.002 HMAD
 Os04g39350.1 4.57 33.87 2.89 0.002 HMAD
 Os04g39010.1 0.94 3.69 1.97 0.022 HMAD
 Os02g37320.1 2.57 19.20 2.90 0.002 HMAD
 Os02g37320.2 9.45 84.16 3.15 0.002
 Os01g48710.1 116.94 46.15 −1.34 0.002 HMAD
 Os03g64340.1* 5.31 12.44 1.23 0.0050 HMAD
Divalent cations transporters
 Os08g10630.1 19.33 6.55 −1.56 0.0019 ZRT/IRT-like protein, OsZIP4 [Q6ZJ91]
 Os05g10940.1 40.47 19.81 −1.03 0.0019 OsZIP7 [Q6L8F7]
 Os05g39560.1 5.37 1.36 −1.98 0.0113 OsZIP5 [Q6L8G0]
 Os05g39560.2 40.35 9.21 −2.13 0.002
 Os06g37010.1 5.56 2.13 −1.39 0.0050 OsZIP10 [Q5Z653]
 Os05g39540.2* 97.22 25.45 −1.93 0.0019 OsZIP9 [Q0DHE3]
 Os03g46470.1* 14.68 2.46 −2.58 0.0076 Iron-regulated transporter 1, OsIRT1
ABC transporters and pleiotropic drug resistance proteins
 Os01g42380.1# 1.35 5.99 2.15 0.0019 ABCG36/OsPDR9 , pleiotropic drug resistance protein
 Os01g42410.1 3.66 21.96 2.59 0.0050 ABCG37/OsPDR8 [Q8GU89]
 Os02g11760.1 0.34 2.90 3.10 0.0019 ABCG39/OsPDR7 [Q8GU88]
 Os01g42370.1 0.28 0.91 1.68 0.0019 ABCG35/OsPDR11 [Q8GU92]
 Os08g29570.1 0.32 8.42 4.72 0.0101 ABCG44/OsPDR17 [Q6YW62]
 Os08g29570.2 4.95 18.57 1.91 0.002
 Os01g61940.1* 10.43 25.90 1.31 0.0019 ABC transporter family protein
MATE family of citrate/H+ antiport transporters
 Os08g43654.1* 1.05 2.52 1.26 0.026 MATE efflux family protein
 Os12g03260.1* 1.50 4.33 1.53 0.047 MATE
 Os04g48290.1 3.72 8.19 1.14 0.002 MATE
 Os02g45380.1 1.23 8.37 2.76 0.002 MATE
other transporters
 Os12g25200.1 123.93 50.25 −1.30 0.002 chloride transporter
 Os02g36414.1 162.32 70.28 −1.21 0.002 transporter family protein
 Os04g37970.1 118.36 43.01 −1.46 0.002 transporter family protein
 Os07g24230.1 1.26 0.38 −1.71 0.014 integral membrane transporter family protein
 Os01g14520.1 131.86 45.76 −1.53 0.002 dicarboxylate /malic acid transport protein
 Os09g31130.1 1.58 7.13 2.17 0.035 citrate transporter
 Os10g30790.1 26.30 94.24 1.84 0.046 inorganic phosphate transporter, OsPT8
 Os10g30790.3* 25.00 80.55 1.69 0.016
Mitochondrial electron transport
 Os07g37730.1 0.15 9.07 5.96 0.0035 NADH-ubiquinone oxidoreductase
 Os04g51150.1 14.41 35.47 1.30 0.0019 AOX1A, alternative oxidase
 Os04g51160.1 0.66 46.99 6.15 0.0019 AOX1B
 Os10g39870.1 10.79 29.33 1.44 0.0019 Arabidopsis Transmembrane protein G1P-related 1
 Os05g09550.1 1.37 4.81 1.81 0.0482 Der1-like family domain containing protein
 Os02g37000.1* 6.37 16.29 1.35 0.0019 mitochondrial prohibitin complex protein 1
Heat-shock transcription factor (HSF) family
 Os09g35790.1* 0.76 6.99 3.20 0.0168 OsHsfB2c [Q652B0]
 Os09g35790.2* 9.03 26.10 1.53 0.0019
 Os02g32590.1 1.21 7.07 2.55 0.0019 OsHsfA3 [Q6H6Q7]
 Os02g32590.2 0.38 2.76 2.88 0.0218
 Os04g48030.1 3.05 14.05 2.20 0.0178 OsHsfB2a [Q7XRX3]
 Os10g28340.1 0.62 12.76 4.36 0.0019 OsHsfA2c
 Os10g28340.2 3.72 15.96 2.10 0.0135
 Os03g12370.3 0.40 4.95 3.65 0.0101 OsHsfA9 [Q10PR4]
 Os08g43334.2 2.45 44.04 4.17 0.0019 OsHsfB2b [Q6Z9C8]
 Os02g13800.1 15.01 50.05 1.74 0.0019 OsHsfC2a [Q6EUG4]
NAC domain transcription factor family   
 Os01g50360.1* 2.52 1.09 −1.21 0.026 NAC domain containing protein
 Os11g03300.2 16.07 38.93 1.28 0.002 OsNAC10
 Os01g60020.1 5.77 25.25 2.13 0.002 OsNAC4
 Os07g12340.1 12.81 455.79 5.15 0.002 OsNAC3 [Q7EZT1]
 Os03g60080.1# 88.35 942.97 3.42 0.002 SNAC1
WRKY domain transcription factor family
 Os02g08440.1# 2.03 125.38 5.95 0.0019 WRKY71
 Os02g08440.4 24.26 179.27 2.89 0.0019
 Os05g27730.1 101.45 430.59 2.09 0.0019 OsWRKY53
 Os01g61080.1 6.51 92.36 3.83 0.0019 OsWRKY24
 Os01g09100.1 29.32 195.59 2.74 0.0019 OsWRKY10
 Os05g50610.2 0.89 2.44 1.45 0.0317 WRKY8
 Os08g13840.2 130.82 404.49 1.63 0.0019 WRKY25
 Os05g09020.1 1.47 13.65 3.21 0.0019 WRKY67
 Os05g09020.2 9.62 51.47 2.42 0.0019
 Os11g29870.1 5.02 15.26 1.60 0.0019 WRKY72
 Os09g25060.1 3.11 24.14 2.95 0.0019 OsWRKY76
 Os01g60600.1* 0.42 1.68 1.99 0.0323 WRKY108
  1. The Cuffdiff utility was used to evaluate the transcript differential expression between ck1h and Cd1h samples. The DEGs uniquely identified in our RNAseq samples are marked with stars. Rice genes with experimentally verified functions are presented in bold fonts. Rice gene annotation was also referred from UniProt (square brackets contain the accession number). The DEGs marked with pound signs were also upregulated by medium and low Cd stress in rice seedling roots in 3 previous reports [21, 27, 48]. The DEGs marked with sigma were also upregulated uniformly by the lowest Cd treatment [48] as well as in one of the two high-throughput transcriptome study [21, 27]. Those marked with triangle were regulated uniformly by Cd treatment in the two high-throughput studies, and those labeled M were detected only in the microarray analysis [21]