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Table 2 Selected differentially expressed (log 2 -fold) genes in T200 and TME3 used for further discussion in this paper

From: Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection

Gene Cassava accession Arabidopsis AGI accession 12 dpi 32 dpi 67 dpi
    Log2fold p-value Log2fold p-value Log2fold p-value
T200 - Class I resistance genes
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_009831m.g AT5G18350.1 −1.98336   −2.74964 4.62E-04 −3.16827 1.44E-04
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_025981m.g AT4G16960.1 −1.93152   - - - -
Disease resistance protein (TIR-NBS-LRR class) cassava4.1_006736m.g AT1G69550.1 - - −3.93415 2.18E-06 −4.51391 2.55E-07
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_000944m.g AT4G12010.1 - - −2.40348 1.58E-03 −3.38156 3.74E-05
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_000534m.g AT5G36930.2 - - −2.04993 1.14E-02 −2.16756 1.24E-02
Disease resistance protein (TIR-NBS-LRR class), putative cassava4.1_000331m.g AT5G17680.1 - - −1.80402 1.48E-02 −2.20612 4.30E-03
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_001210m.g AT3G44480.1 - - −3.89602 2.04E-05 −3.88410 2.74E-05
Disease resistance protein (TIR-NBS-LRR class) cassava4.1_007699m.g AT1G69550.1 - - −3.68973 8.52E-06 −3.83451 5.23E-06
Disease resistance protein (TIR-NBS-LRR class), putative cassava4.1_031642m.g AT5G17680.1 - - −2.75917 8.32E-04 −3.88542 1.83E-05
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_032672m.g AT4G12010.1 - - −2.28131 3.04E-03 −3.47964 2.50E-05
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_017691m.g AT3G04220.1 - - −3.96304 1.78E-06 −4.09620 3.13E-06
TME3 - Class I Resistance Genes
Disease resistance protein (TIR-NBS-LRR class), putative cassava4.1_031334m.g AT5G17680.1 - - 1.93438 0.016708 - -
Disease resistance protein (TIR-NBS-LRR class) family cassava4.1_023684m.g AT5G41750.2 - - 2.59734 0.027843 - -
T200 - Histone-related genes
Histone H4 cassava4.1_029975m.g AT2G28740.1 2.92352 0.03976 - - 2.92352 2.66E-02
Histone H2A 8 cassava4.1_018866m.g AT2G38810.2 2.28609 0.04821 - - - -
Histone superfamily protein cassava4.1_019888m.g AT1G07820.1 1.74066 0.04304 1.74066 1.86E-02 - -
Histone superfamily protein cassava4.1_018611m.g AT1G08880.1 - - 3.68140 5.09E-03 - -
Histone superfamily protein cassava4.1_028744m.g AT3G27360.1 - - 2.48875 5.18E-03 - -
Histone H2A 10 cassava4.1_026667m.g AT1G51060.1 - - 2.03029 9.65E-03 2.03029 8.78E-03
Histone superfamily protein cassava4.1_030637m.g AT3G27360.1 - - 2.33165 1.04E-02 2.33165 4.00E-02
Histone superfamily protein cassava4.1_024615m.g AT3G27360.1 - - 1.92352 4.00E-02 1.92352 1.77E-02
Histone H2A 7 cassava4.1_018569m.g AT5G27670.1 - - - - 1.68140 5.85E-03
Histone H2A 7 cassava4.1_018568m.g AT5G27670.1 - - - - 3.23092 4.02E-02
Histone H4 cassava4.1_019914m.g AT2G28740.1 - - - - 1.57560 1.63E-02
Histone superfamily protein cassava4.1_018874m.g AT3G27360.1 - - - - 2.42885 2.81E-02
Histone H4 cassava4.1_019911m.g AT2G28740.1 - - - - 1.62150 4.14E-02
Histone H4 cassava4.1_019891m.g AT2G28740.1 -- - - - 1.59130 4.43E-02
TME3 - Histone-related genes
Histone acetyltransferase of the MYST family cassava4.1_029570m.g AT5G64610.1 - - - - −3.17558 0.03731
T200 - WRKY genes
WRKY family transcription factor cassava4.1_011089m.g AT4G23810.1 −1.88970 0.03067 −1.88970 2.73E-04 −1.8897 8.23E-06
WRKY DNA-binding protein 70 cassava4.1_013417m.g AT3G56400.1 −1.84402 0.04488 −1.8440 3.53E-03 −1.8440 1.22E-05
WRKY transcription factor family protein cassava4.1_004372m.g AT4G26640.2 2.34337 0.01006 - - - -
WRKY DNA-binding protein 7 cassava4.1_010539m.g AT4G24240.1 2.30203 0.02491 2.30207 8.07E-03 2.30207 5.26E-04
WRKY DNA-binding protein 40 cassava4.1_033249m.g AT1G80840.1 - - −3.71714 7.65E-06 −3.7171 3.60E-03
WRKY family transcription factor cassava4.1_011518m.g AT4G11070.1 - - −2.5359 2.24E-05 −2.5359 7.70E-05
WRKY DNA-binding protein 33 cassava4.1_009059m.g AT2G38470.1 - - −2.0461 2.43E-04 −2.0461 1.25E-03
WRKY family transcription factor cassava4.1_007752m.g AT2G38470.1 - - −2.6020 7.99E-04 −2.6020 2.87E-03
WRKY family transcription factor cassava4.1_010768m.g AT4G23810.1 - - −2.5635 8.93E-04 −2.5635 5.64E-05
WRKY DNA-binding protein 40 cassava4.1_011696m.g AT1G80840.1 -   −2.6405 9.61E-04 - -
WRKY DNA-binding protein 40 cassava4.1_024650m.g AT1G80840.1 - - −2.47729 1.52E-03 −2.4772 6.29E-07
WRKY DNA-binding protein 57 cassava4.1_012575m.g AT1G69310.2 - - −2.60063 2.15E-03 −2.6006 1.51E-02
WRKY DNA-binding protein 40 cassava4.1_012109m.g AT1G80840.1 - - −2.24459 1.10E-02 - -
WRKY DNA-binding protein 51 cassava4.1_016594m.g AT5G64810.1 - - −3.8313 2.23E-02 -  
WRKY DNA-binding protein 70 cassava4.1_012154m.g AT3G56400.1 - - −1.53590 2.26E-02 −1.5359 2.86E-03
WRKY DNA-binding protein 72 cassava4.1_004929m.g AT5G15130.1 - - −3.22549 3.21E-02 - -
WRKY DNA-binding protein 14 cassava4.1_030132m.g AT1G30650.1 - -- −4.0190 3.49E-02 -  
WRKY family transcription factor cassava4.1_016397m.g AT2G44745.1 - - 2.21032 6.78E-03 - -
WRKY DNA-binding protein 23 cassava4.1_011940m.g AT2G47260.1 - - - - −2.9440 2.19E-02
WRKY family transcription factor cassava4.1_024248m.g AT4G01250.1 - - - - 2.2109 4.08E-03
WRKY DNA-binding protein 35 cassava4.1_014297m.g AT2G34830.1 -   -   2.78731 9.64E-03
TME3 – WRKY Genes
WRKY DNA-binding protein 40 cassava4.1_011696m.g AT1G80840.1 2.43773 4.31E-02 2.43773 0.00412 - -
WRKY DNA-binding protein 40 cassava4.1_014368m.g AT1G80840.1 4.24970 1.46E-02 - - - -
WRKY DNA-binding protein 40 cassava4.1_024650m.g AT1G80840.1 - - 2.29778 0.00296 - -
WRKY DNA-binding protein 40 cassava4.1_012109m.g AT1G80840.1 - - 2.08277 0.00524 2.08277 0.02056
WRKY family transcription factor cassava4.1_004331m.g AT1G62300.1 - - 2.28487 0.01171 - -
WRKY family transcription factor cassava4.1_011518m.g AT4G11070.1 - - 1.89948 0.01235 - -
WRKY DNA-binding protein 28 cassava4.1_011936m.g AT4G18170.1 - - - - −3.5317 0.00243
WRKY DNA-binding protein 7 cassava4.1_011062m.g AT4G24240.1 - - - - −1.83753 0.03388
T200 - MAP kinase genes
Mitogen-activated protein kinase 3 cassava4.1_010219m.g AT3G45640.1 −2.34215 0.00793 −2.34215 3.97E-06 −2.34215 5.24E-06
MAP kinase 15 cassava4.1_006140m.g AT1G73670.1 −2.46879 0.00884 - - - -
Mitogen-activated protein kinase kinase kinase 19 cassava4.1_020998m.g AT5G67080.1 - - −3.57051 2.45E-05 - -
Mitogen-activated protein kinase kinase kinase 9 cassava4.1_003834m.g AT4G08480.1 - - −3.24143 5.04E-05 −3.24143 5.51E-06
Mitogen-activated protein kinase kinase kinase 15 cassava4.1_008711m.g AT5G55090.1 - - −3.42293 2.97E-03 - -
Mitogen-activated protein kinase kinase kinase 15 cassava4.1_030459m.g AT5G55090.1 - - −2.24639 4.73E-03 −2.24639 7.81E-03
Mitogen-activated protein kinase kinase kinase 19 cassava4.1_010778m.g AT5G67080.1 - - −2.73367 5.11E-03 - -
Mitogen-activated protein kinase kinase kinase 19 cassava4.1_023447m.g AT5G67080.1 - - −3.22549 3.21E-02 - -
MAPK/ERK kinase kinase 1 cassava4.1_025838m.g AT4G08500.1 - - −2.22549 4.27E-02 - -
MAP kinase kinase 7 cassava4.1_028556m.g AT1G18350.1 - - −3.01903 4.81E-02 - -
TME3 - MAP kinase genes
Mitogen-activated protein kinase kinase kinase 19 cassava4.1_020998m.g AT5G67080.1 1.61609 1.45E-03 1.61609 0.034401 - -
Mitogen-activated protein kinase kinase kinase 19 cassava4.1_010778m.g AT5G67080.1 - - 2.59734 0.027843 - -
Mitogen-activated protein kinase kinase kinase 15 cassava4.1_026704m.g AT5G55090.1 - - 3.40470 0.012378 - -
MAP kinase 4 cassava4.1_010005m.g AT4G01370.1 - - 1.64238 0.030164 - -
MAP kinase kinase 9 cassava4.1_011965m.g AT1G73500.1 - - 1.68164 0.037617 - -
T200 - Phytohormone signalling genes
Ethylene responsive element binding factor 5 cassava4.1_012714m.g AT5G47230.1 −2.60003 0.04990 −4.22549 2.937E-05 −2.50424 0.00652
Ethylene responsive element binding factor 5 cassava4.1_012714m.g AT5G47230.1 - - −2.60003 2.94E-05 −2.6000 6.53E-03
Ethylene responsive element binding factor 1 cassava4.1_013138m.g AT4G17500.1 - - −4.01903 3.42E-05 -  
Ethylene responsive element binding factor 6 cassava4.1_032473m.g AT4G17490.1 - - −2.02756 7.71E-05   -
Ethylene responsive element binding factor 4 cassava4.1_015499m.g AT3G15210.1 - - −3.10319 1.12E-04 −3.10318 1.07E-04
Ethylene responsive element binding factor 4 cassava4.1_014721m.g AT3G15210.1 - - −2.80798 2.74E-03 −2.80798 6.10E-03
Ethylene responsive element binding factor 1 cassava4.1_022027m.g AT4G17500.1 - - −3.10709 1.23E-03   
Ethylene response factor 7 cassava4.1_034303m.g AT3G20310.1 - - - - 1.86197 8.31E-03
erf domain protein 9 cassava4.1_032424m.g AT5G44210.1 - - −2.17239 1.13E-05 −2.17239 2.63E-05
erf domain protein 9 cassava4.1_014544m.g AT5G44210.1    −2.97522 1.81E-04 −2.97522 2.54E-04
Jasmonate-zim-domain protein 1 cassava4.1_014096m.g AT1G19180.1 - - −2.27971 3.27E-03 - -
Jasmonate-zim-domain protein 1 cassava4.1_013620m.g AT1G19180.1 - - −2.21310 3.52E-03 -  
Jasmonate-zim-domain protein 8 cassava4.1_018315m.g AT1G30135.1 - - −6.29587 1.07E-05 −6.29587 2.06E-02
Jasmonate-zim-domain protein 10 cassava4.1_017020m.g AT5G13220.1 - - −2.40606 4.51E-03 - -
Jasmonate-zim-domain protein 12 cassava4.1_015456m.g AT5G20900.1 - - −2.12735 5.94E-03 −2.12735 2.85E-03
Jasmonate-zim-domain protein 3 cassava4.1_009349m.g AT3G17860.1 - - −2.02736 6.81E-03 −2.02736 5.89E-03
Jasmonate-zim-domain protein 1 cassava4.1_031135m.g AT1G19180.1 - - −3.19306 1.85E-02 - -
Jasmonate-zim-domain protein 8 cassava4.1_019045m.g AT1G30135.1 - - −3.01903 4.81E-02 - -
Gibberellin-regulated family protein cassava4.1_019648m.g AT1G74670.1 - - 3.13766 2.57E-04 3.13766 1.14E-02
Gibberellin-regulated family protein cassava4.1_019838m.g AT5G14920.1 - - 3.71114 4.32E-04 3.71114 2.67E-03
Gibberellin-regulated family protein cassava4.1_019810m.g AT1G74670.1 -   2.09802 5.52E-04 2.09802 1.25E-04
Gibberellin-regulated family protein cassava4.1_028672m.g AT1G22690.2 - - 2.06102 2.78E-03 - -
Gibberellin 2-oxidase 8 cassava4.1_024994m.g AT4G21200.3 - - 3.89085 6.87E-03 - -
Brassinosteroid-responsive RING-H2 cassava4.1_017699m.g AT3G61460.1 - - −1.94589 1.70E-05 - -
Auxin response factor 16 cassava4.1_002960m.g AT4G30080.1 - - 2.89517 9.36E-04 - -
Auxin response factor 16 cassava4.1_009838m.g AT4G30080.1 - - 2.43627 8.52E-03 - -
Auxin-responsive GH3 family protein cassava4.1_004196m.g AT4G03400.1    1.70739 2.98E-02 - -
TME3 - Phytohormone signalling genes
erf domain protein 9 cassava4.1_032424m.g AT5G44210.1 −1.88098 1.82E-02 - - - -
Ethylene responsive element binding factor 1 cassava4.1_013138m.g AT4G17500.1 - - 2.2302 0.003676 - -
Ethylene response factor 1 cassava4.1_015673m.g AT3G23240.1 - - 2.01957 0.016286 - -
Ethylene responsive element binding factor 4 cassava4.1_014721m.g AT3G15210.1 - - - - −1.5327 0.040184
Jasmonate-zim-domain protein 1 cassava4.1_014096m.g AT1G19180.1 −2.15968 0.00471 1.79727 4.71E-03 - -
Jasmonate-zim-domain protein 1 cassava4.1_013620m.g AT1G19180.1 - - 2.42433 0.00506 - --
Jasmonate-zim-domain protein 1 cassava4.1_031135m.g AT1G19180.1 - - 2.0092 0.02233 - -
Jasmonate-zim-domain protein 8 cassava4.1_018315m.g AT1G30135.1 1.62177 2.48E-02 1.62177 0.032334 - -
Jasmonate-zim-domain protein 8 cassava4.1_019045m.g AT1G30135.1 - - 2.5862 0.007889 2.58620 0.031204
Jasmonate-zim-domain protein 8 cassava4.1_026855m.g AT1G30135.1 - - 3.31981 0.007962 - --
Jasmonate-zim-domain protein 10 cassava4.1_016821m.g AT5G13220.1 - - 3.06848 0.000172 3.06848 0.034474
Jasmonate-zim-domain protein 12 cassava4.1_015456m.g AT5G20900.1 - - 1.64996 0.045744 - -
Brassinosteroid-responsive RING-H2 cassava4.1_017695m.g AT3G61460.1 −2.22022 3.82E-02 - - - -
Brassinosteroid-responsive RING-H2 cassava4.1_018087m.g AT3G61460.1 - - 2.56082 0.003351 - -