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. 2018 Oct 11;18:228. doi: 10.1186/s12870-018-1456-5

Table 2.

RNA-seq analysis of WT plants and CsINV5-OE plants

ID Gene name Description log2FC
WT vs OE Normal vs Cold
Normal Cold WT OE
Specific up-regulated genes
Response to cold
AT1G20020 ATLFNR2 NADP (H) oxidoreductase normal 1.03 normal normal
AT1G55490 CPN60B Chaperonin 60 beta normal 1.94 1.03 2.01
AT1G63940 MDAR6 Monodehydroascorbate reductase 6 normal 1.26 normal normal
AT1G67090 RBCS1A Rubisco small subunit (RBCS) multigene family normal 1.37 normal normal
AT2G35040 AICARFT IMPCHase bienzyme family protein normal 1.09 normal normal
AT2G37190 RPL12A Ribosomal protein L11 family protein normal 1.02 normal normal
AT2G37220 – Encodes a chloroplast RNA binding protein. normal 1.70 normal normal
AT3G08000 – RNA-binding (RRM/RBD/RNP motifs) family protein normal 1.13 normal normal
AT3G13470 CPN60B2 Chaperonin-60 beta2 normal 2.45 normal 2.10
AT3G23700 SRRP1 S1 RNA-binding ribosomal protein 1 normal 1.59 normal normal
AT3G49910 RPL26A Translation protein SH3-like family protein normal 1.04 normal normal
AT3G53460 CP29 Chloroplast RNA-binding protein 29 normal 2.34 normal 1.01
AT3G54050 HCEF1 Chloroplastic fructose 1, 6-bisphosphate phosphatase. normal 1.65 normal normal
AT3G55280 RPL23AB Ribosomal protein L23A normal 1.00 normal 1.13
AT4G04330 – Homologue of cyanobacterial RBCX 1 normal 1.22 normal normal
AT4G24280 cpHsc70–1 Chloroplast heat shock protein 70–1 normal 1.47 normal 1.31
AT5G20720 CPN20 Chaperonin 20 normal 1.71 normal 1.21
AT5G50250 CP31B Chloroplast RNA-binding protein 31B normal 1.17 normal 1.04
AT5G54770 THI1 Thiazole requiring normal 1.12 normal normal
Response to osmotic
AT1G02820 ATLEA3 Late embryogenesis abundant 3 (LEA3) family protein normal 1.40 4.77 4.95
AT1G73570 – HCP-like superfamily protein normal 1.53 normal 1.31
AT2G15970 COR413-PM1 Cold regulated 413 plasma memberane 1 normal 1.13 3.58 4.06
AT2G38230 ATPDX1.1 Pyrodoxine biosynthesis 1.1 normal 1.44 normal normal
AT2G39800 P5CS1 Delta1-pyrroline-5-carboxylate synthase 1 normal 1.46 normal 1.83
AT2G42530 COR15B Cold regulated 15B normal 2.03 6.50 7.60
AT3G04770 RPSAb 40s ribosomal protein SA B normal 1.14 normal normal
AT3G14940 ATPPC3 Cytosolic phosphoenolpyruvate carboxylase 3 normal 1.64 1.03 1.16
AT3G55610 P5CS2 Delta1-pyrroline-5-carboxylate synthase 2 normal 1.57 normal 2.47
AT5G01410 PDX1 Aldolase-type TIM barrel family protein normal 1.09 normal 1.22
AT5G44110 ATPOP1 Arabidopsis thaliana non-intrinsic ABC protein normal 1.05 4.91 5.25
Response to water deprivation
AT1G02205 CER1 Fatty acid hydroxylase superfamily normal 1.12 7.08 4.89
AT2G04030 CR88 Heat shock protein 88 normal 1.81 normal 1.80
AT3G08000 – RNA-binding (RRM/RBD/RNP motifs) family protein normal 1.13 normal normal
Specific down-regulated genes
Response to cold
AT1G01560 ATMPK11 Member of MAP Kinase family normal −1.11 1.19 normal
AT1G18890 ATCDPK1 Calcium-dependent protein kinase 1 normal −1.17 2.02 1.48
AT1G29690 CAD1 Constitutively activated cell death 1 normal −1.82 2.12 normal
AT1G51660 ATMKK4 Mitogen-activated protein kinase kinase 4 normal −1.12 normal normal
AT1G52890 ANAC019 NAC domain containing protein19 normal −2.73 1.98 normal
AT1G66400 CML23 Calmodulin-like protein normal −2.24 2.12 normal
AT2G04430 atnudt5 Nudix hydrolase homolog 5 normal −1.81 2.24 normal
AT2G04450 ATNUDT6 Nucleoside diphosphates linked to some moiety X 6 normal −1.74 3.83 2.12
AT2G17290 CPK6 Calcium-dependent protein kinase family protein normal −1.28 1.13 normal
AT2G22300 CAMTA3 Calcium-binding transcription activator 3 normal −1.04 normal normal
AT2G30250 WRKY25 WRKY DNA-binding protein normal −1.59 1.17 normal
AT2G38470 WRKY33 normal −2.53 2.29 normal
AT2G40140 CZF1 Salt-inducible zinc finger 2 normal −1.38 2.93 2.30
AT3G03050 CSLD3 Cellulose synthase like D3 normal −1.02 1.04 normal
AT3G05360 AtRLP30 Receptor like protein 30 normal −1.84 2.77 1.86
AT3G11820 SYP121 Syntaxin related protein 1 normal −1.42 1.28 normal
AT3G49530 ANAC062 NAC domain containing protein 62 normal −1.70 2.41 1.03
AT3G52400 SYP122 Syntaxin of plants 122 normal −2.56 2.19 normal
AT4G02330 ATPMEPCRB Pectin methylesterase 41 normal −1.63 2.54 1.27
AT4G08500 MEKK1 MAPK/ERK Kinase Kinase 1 normal −1.33 1.22 normal
AT4G25490 CBF1 C-repeat/DRE binding factor 1 normal −1.26 4.98 3.72
AT4G26120 NPR2 Ankyrin repeat family protein normal −2.03 1.99 normal
AT5G01600 ATFER1 Arabidopsis thaliana ferretin 1 normal −1.45 1.84 1.03
AT5G01820 ATSR1 Serine/Threonine protein Kinase 1 normal −1.16 1.47 normal
AT5G02490 MED37D Heat shock protein 70 (Hsp 70) family protein normal −2.12 4.70 3.01
AT5G13320 PBS3 AVRPPHB susceptible 3 normal −3.20 3.67 normal
AT5G16910 ATCSLD2 Cellulose-synthase like D2 normal −1.40 1.61 1.08
AT5G26920 CBP60G CAM-binding protein 60-like G normal −3.69 3.62 normal
AT5G42050 NRP Asparagine-rich protein normal −1.33 1.58 normal
AT5G57560 TCH4 Xyloglucan endotransglucosylase/hydrolase 22 normal −2.72 2.65 1.22
AT5G58670 ATPLC1 Arabidopsis thaliana phospholipase C normal −1.04 normal normal
AT5G67340 PUB2 ARM repeat superfamily protein normal −2.32 3.82 2.01
Response to osmotic
AT1G15520 PDR12 Arabidopsis thaliana ATP-binding cassette G40 normal −3.13 2.13 normal
AT1G57560 AtMYB50 MYB domain protein nd −2.90 2.63 normal
AT3G06490 MYB108 normal −2.81 1.42 normal
AT3G10500 anac053 NAC domain containing protein 53 normal −1.38 normal normal
AT3G14050 RSH2 RELA/SPOT homolog 2 normal −2.10 2.21 1.04
AT3G22160 JAV1 Jasmonate-associated VQ motif gene 1 normal −1.19 1.04 normal
AT3G28210 PMZ Encodes a putative zinc finger protein normal −2.91 3.00 normal
AT4G15120 – VQ motif-containing protein normal −2.57 3.07 normal
AT4G34390 XLG2 Extra-large GTP-binding protein 2 normal −2.27 1.80 normal
AT4G36990 HSF4 Haliana heat shock factor 4 normal −1.19 0.51 normal
AT5G13170 SAG29 Senescense-associated gene29 normal −3.53 6.25 3.12
AT5G39720 AIG2L Avirulence induced protein 2 like protein nd −2.90 2.82 normal
Response to water deprivation
AT1G08920 ESL1 Early response to dehydration SIX-like 1 normal −1.76 3.42 2.14
AT1G02930 GSTF6 Arabidopsis thaliana gluatione s-transferase F3 normal −1.54 normal normal
AT1G32870 ANAC13 NAC domain containing protein 13 normal −1.12 2.56 1.74
AT1G32940 ATSBT3.5 Subtilase family protein normal −1.82 2.37 1.42
AT1G32950 – normal −3.30 4.69 1.15
AT1G54160 NFYA5 Nuclear factor Y A5 normal −1.29 1.80 1.20
AT2G38340 DREB19 Dehyration response element-binding protein 19 normal −2.62 2.20 normal
AT2G45570 CYP76C2 Cytochrome P450 normal −2.14 2.71 1.41
AT3G56880 – VQ motif-containing protein normal −1.33 1.80 normal
AT4G12250 GAE5 UDP-D-glucuronate 4-epimerase normal −1.26 1.50 normal
AT5G54730 ATATG18F Yeast autophagy 18 F-like protein normal −1.04 1.26 normal

Differentially expressed genes (FDR < 0.05, log2FC) between WT plants and CsINV5-OE plants under cold conditions were annotated with the GO terms ‘response to cold’, ‘response to osmotic stress’ and ‘response to water deprivation’. The log2FC values between WT plants and CsINV5-OE plants under normal conditions, and log2FC values in CsINV5-OE plants or WT plants between normal and cold condition are also shown

“—” indicates the gene has not been named; “nd” represents that the FC value was not detected in DEGs expression analysis results. “normal” indicates the gene was not differentially expressed between these two conditions. The negative value represents the gene was down-regulated, and the positive value represents the gene was up-regulated