Table 2 Selected differentially expressed (log 2 -fold) genes in T200 and TME3 used for further discussion in this paper
Gene | Cassava accession | Arabidopsis AGI accession | 12 dpi | 32 dpi | 67 dpi | |||
|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | 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 | - | Â | - | Â | 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 | - | Â | 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 | Â | Â | 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 | - | - |