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Table 2 Mapping the universal Cd-responsive DEGs in co-expression network 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 Log2Foldchange Rice gene annotation
Transcript ID Cd1h MCd1 MCdD Cd24h
Stress protein
 Os03g16020.1 4.78 8.93 8.95 6.76 hsp20/alpha crystallin family protein
Abscisic acid synthesis
 Os07g05940.1 5.63 8.61 8.60 7.32 9-cis-epoxycarotenoid dioxygenase, OsNCED4
Jasmonate synthesis and signaling
 Os06g11290.1 5.06 6.25 5.76 4.72 12-oxophytodienoate reductase, OsOPR1
 Os06g11240.1 4.52 5.13 4.38 4.79 OPR
 Os06g11210.1# 3.55 5.19 4.91 3.34 OsOPR5
 Os10g25290.1# 2.72 5.54 4.66 2.97 ZIM domain containing protein, OsJAZ12
 Os03g08330.1 3.36 7.21 6.93 2.02 OsJAZ10
 Os10g25230.1 4.89 7.43 7.38 4.45 OsJAZ13
 Os03g08310.1* 2.99 5.56 4.67 1.86 OsJAZ9
 Os12g05440.1* 4.09 6.83 5.28 4.33 cytochrome P450, CYP94C2b
Ethylene signal transduction
 Os08g36920.1# 5.16 8.29 8.90 5.47 AP2 domain containing protein
 Os07g22730.1 3.17 5.98 7.58 3.40 AP2 domain
 Os09g39850.1 3.71 5.30 5.72 2.72 AP2 domain
 Os09g28440.1 4.67 7.54 7.97 6.41 AP2 domain, OsEATB
 Os02g43790.1 2.57 3.89 4.36 2.09 ethylene-responsive transcription factor, OsBIERF3
 Os05g34730.1 4.99 7.43 8.95 4.88 ethylene-responsive transcription factor, SERF1
Transcription factor family
 Os01g09100.1 2.44 4.65 4.68 3.14 OsWRKY10
 Os01g01870.1 2.53 3.48 1.77 1.58 HLH DNA-binding domain containing protein
 Os01g49160.1 1.91 4.07 3.91 2.11 MYB family transcription factor
 Os01g19330.1 4.33 7.48 7.53 5.03 MYB
 Os02g41510.1# 2.96 4.31 3.82 3.01 MYB
 Os03g60080.1# 3.67 5.08 5.16 3.48 SNAC1
 Os07g12340.1 4.93 6.26 5.91 3.04 OsNAC3
 Os09g31390.1 −1.25 −1.46 −2.64 −1.64 OsbZIP74
Zinc finger proteins
 Os09g21710.1# 2.71 6.17 6.95 2.94 AN1-like zinc finger domain containing protein
 Os03g32230.1# 5.04 7.77 6.03 3.61 ZOS3–12 - C2H2 zinc finger protein
 Os03g60560.1 7.11 9.63 11.52 5.82 ZOS3–21, ZFP182
 Os12g39400.1 2.36 5.08 5.67 2.75 ZOS12–09, ZFP252
 Os03g60570.1 5.12 9.13 8.86 5.79 ZOS3–22
 Os02g45780.1 2.74 5.76 5.24 2.48 zinc finger, C3HC4 type
 Os09g29310.1 3.83 6.05 5.86 2.33 zinc finger, C3HC4 type
Glutathione S transferases
 Os10g22070.1* 2.42 3.04 3.92 2.07 glutathione S-transferase, GST
 Os09g20220.1# 6.43 7.67 7.73 8.32 GST
 Os10g38340.1 6.40 11.52 13.14 7.08 GSTU6
 Os10g38720.1 2.87 5.78 7.45 4.64 GST
 Os03g57200.1 2.10 2.66 2.93 1.35 GST
 Os10g38314.1 5.71 7.11 8.28 5.29 GST
 Os10g38350.1 1.97 3.07 1.94 2.20 GST
ROS regulation-related genes
 Os07g08840.3 5.09 5.39 3.94 4.17 apoplastic H-type thioredoxin, OsTRXh1
 Os04g33390.1* 1.98 3.42 2.26 2.24 prephenate dehydratase / arogenate dehydratase
 Os11g42989.1* 5.09 5.40 6.16 3.81 exo70 exocyst complex subunit
Transporters
 Os01g42380.1# 2.07 4.51 4.56 4.00 ABCG36/OsPDR9
 Os02g37300.1 2.33 4.56 7.04 3.61 HMAD
 Os02g37330.1 4.25 7.19 8.63 4.43 HMAD
 Os03g11900.1 1.15 2.78 2.58 1.99 monosaccharide transporter, OsMST4
others DEGs with Cd-upregulated homologs
 Os02g50730.1 1.90 2.67 3.49 4.41 APK_ORTHOMCL1642, metalloendoproteinase
 Os06g13180.1 3.03 1.88 5.44 5.03 APK_ORTHOMCL1642, metalloendoproteinase
 Os08g04350.1 4.22 4.28 7.54 7.52 APK_ORTHOMCL3089, plastocyanin-like
 Os08g04360.1 4.76 4.90 7.71 8.40 APK_ORTHOMCL3089, plastocyanin-like
 Os08g04370.1 3.04 3.02 5.56 4.75 APK_ORTHOMCL3089, plastocyanin-like
 Os12g18560.1 2.53 3.31 4.95 4.96 APK_ORTHOMCL14694, pectin methylesterase inhibitor
others novel DEGs
 Os01g61990.1* 1.42 1.55 1.15 1.70 ankyrin repeat-containing protein, OsNPR4
 Os03g08520.1* 2.79 4.38 5.32 2.02 DUF581 domain containing protein
 Os03g41330.1* −1.59 −2.77 −3.08 −1.97 DUF260 domain containing protein
 Os02g25700.1* −1.31 −2.17 −3.04 −1.23 O-acyltransferase
 Os03g08720.1* −1.57 −1.75 −3.10 −3.27 transferase family protein
 Os04g43710.1* −1.23 −2.12 −2.30 −2.63 CAMK, Ca/CaM-depedent protein kinases
 Os06g11030.1* 2.13 4.94 4.84 2.38 EF hand family protein
 Os08g42490.1* 3.47 4.65 7.06 3.91 DC1 domain containing protein
 Os12g43870.1* 3.05 4.39 3.81 3.20 expressed protein
  1. Rice seedling roots samples of medium Cd stress (50 μM) for 1 h and 24 h (designated MCd1 and MCdD, respectively), high Cd pressure (100 μM) for 24 h (labeled as Cd24h) and 1 h (Cd1h, prepared in our lab), and their corresponding control are compared in couples to analyze DEGs using the limma package. The DEGs marked with stars are the uniquely identified DEGs in our RNAseq samples (Cd1h). Those marked with pound signs were also upregulated by medium and low Cd stress in rice seedling roots in 3 previous reports [21, 27, 48], and those with triangle were regulated uniformly by Cd treatments in the two high-throughput studies [21, 27], whereas those labeled M were detected only in the microarray analysis [21]. Those labeled C were general stress-responsive genes that were commonly upregulated by multiple stresses as previously reported [27]. Rice genes with experimentally verified functions are presented in bold fonts, and the homologous DEGs can be categorized into orthologous groups are presented with APK_ORTHOMCL number [86]