Table 2.
Summary of transcriptomes related to plant responses to fungal pathogens where expression profile of genes involved in ROS/RNS and redox-related categories were analysed using bioinformatics
| Biotic stress | Fungus | Plant | Expression gene analysis | Reference | ||||
|---|---|---|---|---|---|---|---|---|
| ID | Species | Timing | Species | Tissue | Culture condition | Type | Threshold | |
| Fo _L_P_1 (a–b) | F. oxysporum (1×106 spores ml–1) | 1, 6 dpi | A. thaliana | Plant | MS+ sucrose 3% (2 w) | RNA-seq | RPKM >1 | Zhu et al., 2013 |
| Fg_L_L_1 | F. graminearum (1×105 spores ml–1) | 3 dpi | A. thaliana | Leaves | Soil (flowering plants) | Microarray (Agilent) | P adj <0.05, –1>log2FC >1 * | Miwa et al., 2017 |
| Bc_L_L_1 (a–d) | B. cinerea (5×104 spores ml–1) | 18, 22 hpi | A. thaliana | Leaves | Soil (4 w) | Microarray (NimbleGen) | P adj <0.05, –1>log2FC>1 * | Ingle et al., 2015 |
| Bc_L_L_2 (a–c) | B. cinerea (1×105 spores ml–1) | 12, 18, 24 hpi | A. thaliana | Leaves | River sand+ Hoag. (4–5 w) | RNA-seq | FDR <0.05, –1>log2FC>1 | Coolen et al., 2016 |
| Bc_S_L_3 (a–b) | B. cinerea (1–5×105 spores ml–1) | 6, 48 hpi | A. thaliana | Leaves | Soil (4 w) | Microarray (Agilent) | P adj <0.05, –1>log2FC>1 * | Wang et al., 2018 |
| Mo_L_S_1 | M. oryzae (1×105 spores ml–1) | 36 hpi | O. sativa | Sheath | Soil (3 w) | Microarray (Agilent) | FC >50, P<2.2× 106 | Mosquera et al., 2009 |
| Mo_L_L_2 (a–d) | M. oryzae (1×105 spores ml–1) | 1, 2 dpi | O. sativa L. cv. LTH (compatible), IRBL1 (incompatible) | Leaves | Soil (2 w) | Microarray (Agilent) | P logratio >0.05, 0.9<FC<1.2 | Kato et al., 2009 |
| Mo_L_L_3 | M. oryzae (1×105 spores ml–1) | 2 dpi | O. sativa L. cv. Nipponbare | Leaves | Soil (2 w) | Microarray (Agilent) | P adj <0.05, –1>log2FC>1 * | Chujo et al., 2013 |
| Mo_L_L_4 (a-h) | M. oryzae (1×105 spores ml–1) | 1, 2, 3, 5 dpi | O. sativa cv. Nipponbare NP/++ (compatible), NP/Pia (incompatible) | Leaves | Hydroponic, specific NS (2 w) | Microarray (Agilent) | P adj <0.05, –1>log2FC>1 * | Tanabe et al., 2014 |
| Mo_L_L_5 | M. oryzae (1×105 spores ml–1) | 2 dpi | O. sativa cv. Tainung67, japonica | Leaves | Soil (3–4 leaves stage) | RNA-seq | FDR <0.05, –1<log2FC<1 | Sánchez-Sanuy et al., 2019 |
The code of each paper appears in the first column and in the abscissa axis of Figs 2, 4 and 5. The main conditions used in each paper have been summarized as fungi (Fo: Fusarium oxysporum, Fg: Fusarium graminearum, Bc: Botrytis cinerea; Mo: Magnaporthe oryzae); time of the treatment (S, short, <6 h; L, long, >6 h); tissue used (L, leaves; P, plant; R, root; S, sheath; C, cell culture); number of the paper by chronological order. For Zhu et al.: Fo _L_P_1a (1 dpi); Fo_L_P_1b (6 dpi). For Ingle et al.: Bc_L_L_1a (D 18 dpi); Bc_L_L_1b (D 22 dpi); Bc_L_L_1c (N 18 dpi); Bc_L_L_1d (N 22 dpi). For Coolen et al.: Bc_L_L_2a (12 hpi); Bc_L_L_2b (18 hpi); Bc_L_L_2c (24 hpi). For Wang et al.: Bc_S_L_3a (6 h); Bc_L_L_3b (48 h). For Kato et al.: Mo_L_L_2a (comp, LTH-24 h), Mo_L_L_2b (comp LTH-48 h), Mo_L_L_2c (incomp IRBL-24 h), Mo_L_L_2d (incomp IRBL-48 h). For Tanabe et al.: Mo_L_L_4a (1 d incomp), Mo_L_L_4b (2 d incomp), Mo_L_L_4c (3 d incomp), Mo_L_L_4d (5 d incomp), Mo_L_L_4e (1 d comp), Mo_L_L_4f (2 d comp), Mo_L_L_4g (3 d comp), Mo_L_L_4h (5 d comp). dpi, days post infection; hpi, hours post infection; w, weeks. Asterisks indicate data analysed for this review by using the GEO2R web tool (http://www.ncbi.nlm.nih.gov/geo/info/geo2r.html).