Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean
Abstract
:1. Introduction
2. Results
2.1. Disease Development
2.2. Quality Control of Transcriptome Analysis
2.3. Differentially Expressed Genes in Response to C. lindemuthianum in Common Bean
2.4. Gene Ontology (GO) Enrichment in Down-Regulated and Up-Regulated DEGs
2.5. Clustering Analysis and Gene Expression Profiles
2.6. Detailed Differences between Incompatible and Compatible Interaction in Response to C. lindemuthianum in Common Bean
2.7. Expression of Pathogenesis-Related (PRs) Proteins and NLRs in Response to C. lindemuthianum
2.8. Defense-Related Plant Hormones
2.9. Validation of RNA-Seq Results with Quantitative Real-Time PCR (RT-qPCR)
3. Discussion
3.1. PR Proteins and Hemibiotrophic Pathogens
3.2. Importance of PR10/Bet vI in Common Bean Defense
3.3. In Infected Common Bean, SA Accumulation Is Based on the PAL Pathway
3.4. Up-Regulation of NLR after Pathogen Infection
3.5. C. lindemuthianum Resistance in Common Bean Involved Down-Regulation of Photosynthesis, Ubiquitination-Mediated Proteolysis and Cell Wall Modifications
4. Materials and Methods
4.1. Biological Material and Plant Inoculation
4.2. RNA Isolation, Library Preparation and Sequencing
4.3. Analysis of Differentially Expressed Genes
4.4. Gene Ontology Enrichment
4.5. Real-Time Quantitative PCR (RT-qPCR)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Incompatible | Compatible | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
C531 vs. Mock 48 hpi | C531 vs. Mock 72 hpi | Strain 100 vs. Mock 48 hpi | Strain 100 vs. Mock 72 hpi | ||||||||||||||
Gene ID | Annotation | Methylation Status | 24nt siRNA | LogFC | FDR | LogFC | FDR | LogFC | FDR | LogFC | FDR | ||||||
Phvul.002G098200 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.96 | 4.56E-03 | 1.95 | 9.53E-04 | 1.45 | 7.98E-02 | 1.78 | 3.97E-03 | ||||||
Phvul.011G201900 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.85 | 1.08E-02 | 0.39 | 6.31E-01 | 0.37 | 8.23E-01 | 0.57 | 4.26E-01 | ||||||
Phvul.002G133400 | PTHR23155:SF633 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.62 | 2.71E-03 | 1.46 | 2.05E-03 | 1.58 | 5.42E-03 | 1.33 | 7.01E-03 | ||||||
Phvul.008G020700 | PTHR23155:SF497 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.45 | 1.74E-02 | 2.38 | 1.40E-06 | 1.52 | 1.67E-02 | 1.94 | 1.36E-04 | ||||||
Phvul.005G117900 | PTHR23155:SF497 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.41 | 4.96E-02 | 1.93 | 3.73E-04 | 1.33 | 9.20E-02 | 1.73 | 2.47E-03 | ||||||
Phvul.011G014400 | PTHR23155:SF402 DISEASE RESISTANCE PROTEIN RPP13-RELATED | UM | None | 1.08 | 5.96E-03 | 1.05 | 2.16E-03 | 0.92 | 3.83E-02 | 1.10 | 2.06E-03 | ||||||
Phvul.010G024100 | PF00931//PF01582 NB-ARC domain (NB-ARC)//TIR domain (TIR) | UM | None | 0.95 | 8.43E-03 | 0.70 | 2.90E-02 | 0.64 | 1.60E-01 | 0.43 | 2.22E-01 | ||||||
Phvul.009G233700 | PTHR23155:SF402 DISEASE RESISTANCE PROTEIN RPP13-RELATED | UM | None | 0.84 | 3.76E-02 | 1.27 | 6.95E-05 | 0.82 | 5.69E-02 | 1.35 | 2.94E-05 | ||||||
Phvul.007G254700 | PTHR23155:SF563 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 1.74 | 6.79E-02 | 1.75 | 1.53E-02 | 1.25 | 2.87E-01 | 2.04 | 6.30E-03 | ||||||
Phvul.002G171400 | PTHR11945:SF169 MADS-BOX FAMILY PROTEIN | UM | None | 1.54 | 7.79E-02 | 1.78 | 1.06E-02 | 0.74 | 5.56E-01 | 1.78 | 1.36E-02 | ||||||
Phvul.008G020900 | PTHR23155:SF497 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 2.17 | 6.08E-02 | 1.74 | 3.75E-02 | 1.89 | 1.59E-01 | 1.40 | 1.15E-01 | ||||||
Phvul.008G020750 | PTHR23155:SF497 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | N.A | N.A | 1.33 | 1.35E-01 | 1.71 | 8.52E-03 | 1.32 | 1.83E-01 | 0.92 | 2.23E-01 | ||||||
Phvul.003G129700 | PTHR11017:SF169 DISEASE RESISTANCE PROTEIN-RELATED | UM | None | 1.32 | 3.43E-01 | 2.33 | 1.07E-02 | 1.49 | 3.04E-01 | 2.63 | 5.49E-03 | ||||||
Phvul.010G028200 | PF00931//PF13676 NB-ARC domain (NB-ARC) TIR domain (TIR_2) | UM | None | 1.24 | 1.03E-01 | 1.21 | 3.57E-02 | 0.81 | 4.07E-01 | 1.10 | 7.08E-02 | ||||||
Phvul.001G132301 | PTHR23155:SF563 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | N.A | N.A | 1.17 | 3.09E-01 | 1.66 | 4.42E-02 | 0.94 | 5.13E-01 | 2.21 | 6.15E-03 | ||||||
Phvul.011G014500 | PTHR23155:SF402 DISEASE RESISTANCE PROTEIN RPP13-RELATED | UM | None | 0.92 | 1.00E-01 | 1.24 | 3.83E-03 | 0.94 | 1.12E-01 | 1.43 | 1.11E-03 | ||||||
Phvul.002G133600 | PTHR23155:SF633 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | CG-Meth | None | 0.68 | 3.15E-01 | 1.24 | 6.35E-03 | 0.55 | 4.80E-01 | 1.36 | 4.14E-03 | ||||||
Phvul.004G048000 | PTHR23155:SF554 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | Yes | 0.60 | 6.64E-01 | 1.94 | 1.71E-02 | 0.41 | 8.17E-01 | 2.54 | 2.22E-03 | ||||||
Phvul.004G013300 | K00122 Formate dehydrogenase (FDH) | C-Meth | Yes | 0.59 | 2.29E-01 | 0.81 | 1.61E-02 | 0.18 | 8.26E-01 | 0.61 | 9.14E-02 | ||||||
Phvul.003G247200 | PTHR23155:SF543 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 0.57 | 1.32E-01 | 1.01 | 3.58E-04 | 0.50 | 2.52E-01 | 1.02 | 4.75E-04 | ||||||
Phvul.011G136130 | K14488 SAUR family protein (SAUR) | N.A | N.A | 0.47 | 3.47E-01 | 0.75 | 2.44E-02 | 0.14 | 8.59E-01 | 0.44 | 2.35E-01 | ||||||
Phvul.004G140700 | PF05729//PF13676 NACHT domain (NACHT)//TIR domain | UM | None | 0.42 | 3.74E-01 | 0.81 | 8.70E-03 | 0.38 | 4.65E-01 | 0.85 | 7.76E-03 | ||||||
Phvul.003G072500 | PTHR12565:SF107 TRANSCRIPTION FACTOR BPE | UM | None | 0.35 | 3.25E-01 | 0.50 | 4.40E-02 | 0.20 | 6.79E-01 | 0.61 | 1.35E-02 | ||||||
Phvul.010G054400 | PF01582 TIR domain (TIR) | UM | None | 0.33 | 8.02E-01 | 2.10 | 1.81E-03 | 0.60 | 6.28E-01 | 1.89 | 7.60E-03 | ||||||
Phvul.001G134100 | PTHR23155:SF563 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | Yes | 0.32 | 7.09E-01 | 0.94 | 4.28E-02 | 0.26 | 8.04E-01 | 0.74 | 1.37E-01 | ||||||
Phvul.004G140800 | PTHR11017:SF171 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.31 | 6.65E-01 | 1.14 | 4.47E-03 | 0.23 | 7.93E-01 | 1.01 | 1.78E-02 | ||||||
Phvul.002G131000 | PTHR23155:SF505 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.31 | 3.72E-01 | 0.48 | 3.37E-02 | 0.14 | 7.72E-01 | 0.54 | 1.91E-02 | ||||||
Phvul.011G202900 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.30 | 5.76E-01 | 0.79 | 2.01E-02 | 0.24 | 7.14E-01 | 0.27 | 5.26E-01 | ||||||
Phvul.001G018800 | PTHR23155:SF543 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 0.30 | 3.21E-01 | 0.51 | 1.53E-02 | 0.36 | 2.55E-01 | 0.47 | 3.37E-02 | ||||||
Phvul.011G172100 | PTHR23155:SF554 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.27 | 7.89E-01 | 0.79 | 1.77E-01 | −0.56 | 5.97E-01 | 1.21 | 2.48E-02 | ||||||
Phvul.002G021700 | PTHR23155:SF543 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 0.25 | 6.57E-01 | 0.79 | 1.48E-02 | 0.24 | 7.03E-01 | 0.78 | 2.15E-02 | ||||||
Phvul.010G101200 | PTHR11017:SF174 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.23 | 7.79E-01 | 1.07 | 1.51E-02 | 0.11 | 9.26E-01 | 1.29 | 4.25E-03 | ||||||
Phvul.002G166400 | PTHR23155:SF506 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 0.22 | 5.45E-01 | 0.55 | 1.51E-02 | 0.29 | 4.27E-01 | 0.66 | 3.80E-03 | ||||||
Phvul.003G247651 | PTHR23155:SF543 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | N.A | N.A | 0.21 | 6.91E-01 | 0.78 | 1.01E-02 | 0.36 | 4.79E-01 | 0.98 | 1.48E-03 | ||||||
Phvul.011G202966 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | N.A | N.A | 0.21 | 5.19E-01 | 0.49 | 1.49E-02 | 0.08 | 8.70E-01 | 0.42 | 4.95E-02 | ||||||
Phvul.011G014301 | PTHR23155:SF402 DISEASE RESISTANCE PROTEIN RPP13-RELATED | N.A | N.A | 0.16 | 5.14E-01 | 0.36 | 2.02E-02 | 0.16 | 5.40E-01 | 0.34 | 3.65E-02 | ||||||
Phvul.011G195100 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | None | 0.12 | 9.27E-01 | 1.56 | 1.68E-02 | 0.75 | 3.86E-01 | 1.29 | 6.74E-02 | ||||||
Phvul.002G323200 | PTHR11017:SF162 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | 0.03 | 9.71E-01 | 0.33 | 3.24E-01 | −0.05 | 9.45E-01 | 0.62 | 4.08E-02 | ||||||
Phvul.011G193600 | PF00931//PF13855 NB-ARC domain (NB-ARC)//Leucine rich repeat | C-Meth | None | 0.00 | 9.96E-01 | −0.44 | 9.41E-02 | −0.13 | 8.05E-01 | −0.53 | 4.40E-02 | ||||||
Phvul.010G026400 | PF00931//PF13676 NB-ARC domain (NB-ARC)//TIR domain | C-Meth | None | −0.04 | 9.39E-01 | 0.58 | 2.51E-02 | −0.15 | 7.78E-01 | 0.44 | 1.12E-01 | ||||||
Phvul.011G074800 | 1.3.99.12 2-methylacyl-CoA dehydrogenase/Branched-chain acyl-CoA | UM | None | −0.09 | 9.24E-01 | 0.90 | 2.50E-02 | −0.08 | 9.37E-01 | 0.56 | 2.06E-01 | ||||||
Phvul.002G075400 | KOG4308 LRR-containing protein | N.A | N.A | −0.13 | 7.13E-01 | −0.31 | 1.48E-01 | −0.17 | 6.38E-01 | −0.52 | 1.26E-02 | ||||||
Phvul.011G193100 | PTHR23155:SF414 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | C-Meth | −0.20 | 5.50E-01 | −0.39 | 7.92E-02 | −0.27 | 4.25E-01 | −0.44 | 4.87E-02 | |||||||
Phvul.011G198400 | PF00931//PF13855 NB-ARC domain (NB-ARC)//Leucine rich repeat | C-Meth | −0.28 | 4.49E-01 | −0.19 | 5.43E-01 | −0.62 | 4.66E-02 | −0.18 | 5.54E-01 | |||||||
Phvul.008G072300 | PTHR23155:SF590 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | −0.45 | 4.26E-01 | 0.03 | 9.67E-01 | −1.00 | 3.95E-02 | −0.02 | 9.76E-01 | ||||||
Phvul.002G075000 | PTHR23155:SF505 LEUCINE-RICH REPEAT-CONTAINING PROTEIN | UM | None | −0.47 | 6.08E-01 | −0.67 | 3.39E-01 | −1.51 | 4.62E-02 | −0.63 | 3.63E-01 | ||||||
Phvul.011G191600 | PF13191//PF13855 AAA ATPase domain//Leucine rich repeat | C-Meth | None | −0.60 | 3.96E-02 | −0.03 | 9.38E-01 | −0.65 | 3.26E-02 | −0.18 | 5.65E-01 | ||||||
Phvul.005G005000 | PTHR32472 P-LOOP CONTAINING NUCLEOSIDE TRIPHOSPHATE HYDROLASES SUPERFAMILY PROTEIN | UM | None | −1.81 | 3.97E-02 | −1.50 | 1.40E-01 | −2.54 | 4.87E-03 | −3.78 | 2.70E-03 | ||||||
N.A: Not available; UM: Unmethylated; C-Meth: CHG or CHH gene-body methylated; CG-Meth: CG gene-body methylated: Underlined (purple): Methylation due to a TE inserted in an intron; Underlined (green): Methylation due to an associated repeat located in an intron. | |||||||||||||||||
FDR | |||||||||||||||||
1.00E-10 | 1.00E-08 | 0.05 | 0.00 | ||||||||||||||
Log2FC | |||||||||||||||||
−2.50 | −1.50 | −1.00 | −0.5 | 0.00 | 0.5 | 1.00 | 1.50 | 2.50 |
Incompatible | Compatible | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
C531 vs. Mock 48 hpi | C531 vs. Mock 72 hpi | Strain 100 vs. Mock 48 hpi | Strain 100 vs. Mock 72 hpi | ||||||||
Gene ID | Annotation | LogFC | FDR | LogFC | FDR | LogFC | FDR | LogFC | FDR | ||
Phvul.002G209500 * | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 4.53 | 2.34E-19 | 2.80 | 3.29E-08 | 3.06 | 2.94E-08 | 1.91 | 3.09E-04 | ||
Phvul.003G109603 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 4.31 | 4.94E-04 | 2.99 | 3.98E-03 | 3.51 | 1.48E-02 | 2.21 | 4.48E-02 | ||
Phvul.003G109200 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 4.18 | 8.46E-10 | 2.94 | 1.54E-05 | 2.69 | 5.41E-04 | 2.30 | 1.31E-03 | ||
Phvul.002G209400 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 4.15 | 6.68E-10 | 2.84 | 9.35E-06 | 3.02 | 1.03E-04 | 2.14 | 1.57E-03 | ||
Phvul.003G109800 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 3.63 | 2.12E-03 | 2.84 | 1.29E-03 | 1.68 | 4.46E-01 | 1.92 | 6.28E-02 | ||
Phvul.003G109000 | PTHR31339—PECTIN LYASE-LIKE SUPERFAMILY PROTEIN (Bet v 1) (PR10) | 3.46 | 7.35E-05 | 2.52 | 1.14E-03 | 2.81 | 3.85E-03 | 2.85 | 3.11E-04 | ||
Phvul.003G109100 | PTHR22847:SF361—JOUBERIN Bet v I family (PR10) | 3.44 | 6.18E-09 | 2.62 | 1.13E-05 | 2.66 | 7.18E-05 | 1.83 | 3.14E-03 | ||
Phvul.002G155500 | PF00314—Thaumatin family (Thaumatin) Pathogenesis-related (PR5) | 2.23 | 9.47E-07 | 1.89 | 2.78E-05 | 1.84 | 2.63E-04 | 1.55 | 1.02E-03 | ||
Phvul.006G196900 ** | K13449—pathogenesis-related protein 1 (PR1) | 2.21 | 2.31E-05 | 1.28 | 1.19E-02 | 1.88 | 1.00E-03 | 0.99 | 6.97E-02 | ||
Phvul.002G286600 | KOG4837—Uncharacterized conserved protein Pathogenesis-related (PR5) | 1.97 | 2.35E-01 | 2.15 | 2.43E-02 | 1.71 | 3.75E-01 | 2.28 | 2.30E-02 | ||
Phvul.006G197500 | PTHR10334—CYSTEINE-RICH SECRETORY PROTEIN (PR1) | 1.37 | 3.91E-02 | 0.41 | 5.58E-01 | 0.90 | 2.96E-01 | 0.63 | 3.13E-01 | ||
Phvul.011G183900 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.95 | 5.62E-02 | 0.94 | 2.09E-02 | 0.73 | 2.20E-01 | 0.97 | 2.33E-02 | ||
Phvul.011G183766 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.94 | 1.02E-01 | 0.86 | 6.71E-02 | 0.78 | 2.45E-01 | 1.03 | 2.97E-02 | ||
Phvul.011G183700 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.88 | 4.05E-02 | 0.86 | 1.79E-02 | 0.70 | 1.66E-01 | 0.83 | 2.80E-02 | ||
Phvul.011G183832 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.83 | 8.87E-02 | 0.89 | 2.25E-02 | 0.71 | 2.08E-01 | 0.92 | 2.39E-02 | ||
Phvul.002G286500 | PF00314—Thaumatin family (Thaumatin) (PR5) | 0.79 | 4.56E-01 | 2.01 | 3.32E-03 | 0.51 | 7.00E-01 | 2.15 | 2.57E-03 | ||
Phvul.011G184200 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.77 | 1.00E-02 | 0.86 | 9.60E-04 | 0.62 | 7.75E-02 | 0.78 | 4.18E-03 | ||
Phvul.011G183400 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.53 | 2.24E-02 | 0.27 | 2.33E-01 | 0.40 | 1.49E-01 | 0.30 | 1.78E-01 | ||
Phvul.006G197200 | PTHR10334—CYSTEINE-RICH SECRETORY PROTEIN (PR1) | 0.20 | 9.41E-01 | 2.34 | 4.93E-02 | 0.20 | 9.54E-01 | 2.62 | 3.09E-02 | ||
Phvul.011G183000 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | 0.15 | 9.29E-01 | 0.76 | 3.94E-01 | −0.39 | 8.07E-01 | 1.82 | 2.40E-02 | ||
Phvul.008G166500 | [NAD(+)], CYTOPLASMIC Pathogenesis-related (PR5) | −0.72 | 1.21E-01 | −1.06 | 1.65E-02 | −0.52 | 3.45E-01 | −0.27 | 5.96E-01 | ||
Phvul.009G082100 | Pathogenesis-related protein p14a (PR1-like) | −0.76 | 2.41E-01 | −1.73 | 1.89E-04 | −0.65 | 3.79E-01 | −1.44 | 2.73E-03 | ||
Phvul.011G182900 | PF00407—Pathogenesis-related protein Bet v I family (PR10) | −0.89 | 2.05E-02 | −1.05 | 3.12E-03 | −0.82 | 5.06E-02 | −0.60 | 1.16E-01 | ||
Phvul.001G016700 | PTHR31048:SF10—PATHOGENESIS-RELATED PROTEIN 5-RELATED (PR5) | −0.93 | 2.16E-01 | −2.26 | 1.62E-04 | −0.64 | 4.84E-01 | −1.27 | 3.64E-02 | ||
Phvul.011G034200 | PROTEIN AGD2-RELATED Pathogenesis-related (PR5) | −0.98 | 3.90E-01 | −2.19 | 6.17E-03 | −0.60 | 6.76E-01 | −1.48 | 7.49E-02 | ||
*; **: Bet v I (PR10) and PR1 are presented in bold and underlined, respectively, while PR5 encoding genes appears in normal character. | |||||||||||
FDR | |||||||||||
1.00E-10 | 1.00E-08 | 0.05 | 0.00 | ||||||||
Log2FC | |||||||||||
−2.50 | −1.50 | −1.00 | −0.5 | 0.00 | 0.5 | 1.00 | 1.50 | 2.50 |
Incompatible | Compatible | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
C531 vs. Mock 48 hpi | C531 vs. Mock 72 hpi | Strain 100 vs. Mock 48 hpi | Strain 100 vs. Mock 72 hpi | ||||||||
Gene ID | Annotation | LogFC | FDR | LogFC | FDR | LogFC | FDR | LogFC | FDR | ||
Auxins | |||||||||||
Phvul.009G103800 | K14488—SAUR family protein (SAUR) | 2.45 | 4.37E-02 | 0.26 | 8.47E-01 | 2.01 | 1.59E-01 | 0.16 | 9.15E-01 | ||
Phvul.006G186600 | PTHR11772//PTHR11772:SF19—ASPARAGINE SYNTHETASE | 1.10 | 9.08E-02 | 1.03 | 5.09E-02 | 0.92 | 2.24E-01 | 1.13 | 3.62E-02 | ||
Phvul.009G001800 | K14488—SAUR family protein (SAUR) | 1.02 | 1.72E-01 | 2.39 | 3.71E-05 | 1.12 | 1.52E-01 | 2.41 | 4.03E-05 | ||
Phvul.006G142300 | PTHR23130:SF80-AUXIN-INDUCED IN ROOT CULTURES PROTEIN 12 | 0.85 | 4.61E-02 | 1.38 | 5.42E-05 | 0.91 | 3.76E-02 | 1.44 | 3.37E-05 | ||
Phvul.009G001500 | K14488—SAUR family protein (SAUR) | 0.65 | 5.15E-01 | 1.31 | 5.46E-02 | −0.08 | 9.65E-01 | 1.59 | 2.06E-02 | ||
Phvul.011G108500 | PTHR10641//PTHR10641—MYB-LIKE DNA-BINDING PROTEIN MYB | 0.51 | 6.36E-01 | 1.28 | 4.44E-02 | 0.50 | 6.76E-01 | 1.12 | 9.11E-02 | ||
Phvul.010G117500 | K14488—SAUR family protein (SAUR) | 0.41 | 5.20E-01 | 1.10 | 3.96E-03 | 0.19 | 8.32E-01 | 0.99 | 1.52E-02 | ||
Phvul.001G147300 | K14487—auxin responsive GH3 gene family (GH3) | 0.34 | 8.10E-01 | 1.57 | 3.47E-02 | −0.34 | 8.43E-01 | 0.79 | 3.60E-01 | ||
Phvul.007G219500 | PTHR12899//PTHR12899:SF4—39S RIBOSOMAL PROTEIN L18 | 0.34 | 6.94E-01 | 0.99 | 4.84E-02 | 0.47 | 5.83E-01 | 1.41 | 4.67E-03 | ||
Phvul.011G037300 | PTHR23334—CCAAT/ENHANCER BINDING PROTEIN | 0.11 | 9.10E-01 | −1.39 | 1.16E-02 | −0.19 | 8.46E-01 | −0.40 | 4.98E-01 | ||
Phvul.002G209300 | PTHR23335:SF12—CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 1 | 0.05 | 8.70E-01 | 0.26 | 9.24E-02 | 0.01 | 9.80E-01 | 0.44 | 2.91E-03 | ||
Phvul.011G037900 | PTHR24015:SF364—ATPASE EXPRESSION PROTEIN 3 | −0.22 | 8.14E-01 | −1.18 | 1.58E-02 | −0.10 | 9.41E-01 | −0.93 | 7.20E-02 | ||
Phvul.002G147300 | PTHR31933:SF3—O-FUCOSYLTRANSFERASE FAMILY PROTEIN | −0.26 | 3.65E-01 | −0.44 | 2.80E-02 | −0.29 | 3.46E-01 | −0.39 | 6.39E-02 | ||
Phvul.008G286600 | PF03188//PF04526—Eukaryotic cytochrome b561 (Cytochrom B561) | −0.30 | 6.39E-01 | −0.94 | 5.06E-02 | −0.23 | 7.54E-01 | −1.05 | 3.26E-02 | ||
Phvul.010G125400 | PF02519—Auxin responsive protein (Auxin inducible) | −0.36 | 6.75E-01 | −0.93 | 7.57E-02 | −0.18 | 8.70E-01 | −1.17 | 2.67E-02 | ||
Phvul.003G190900 | PF03634—TCP family transcription factor (TCP) | −0.37 | 2.34E-01 | −0.61 | 7.03E-03 | −0.31 | 3.93E-01 | −0.42 | 8.54E-02 | ||
Phvul.003G127801 | PTHR31374:SF22—AUXIN-RESPONSIVE PROTEIN-LIKE PROTEIN | −0.50 | 4.07E-01 | −1.12 | 7.57E-03 | −0.26 | 7.45E-01 | −0.95 | 3.01E-02 | ||
Phvul.009G188100 | PF03634—TCP family transcription factor (TCP) | −0.50 | 2.34E-01 | −0.65 | 4.12E-02 | −0.37 | 4.60E-01 | −0.54 | 1.06E-01 | ||
Phvul.006G113100 | PF13639//PF13947//PF14380—Ring finger domain (zf-RING 2) | −1.02 | 1.63E-02 | −0.84 | 6.39E-02 | −0.62 | 2.45E-01 | −0.02 | 9.76E-01 | ||
Brassinosteroids | |||||||||||
Phvul.003G187200 | PF00069//PF00560//PF08263—Protein kinase domain (Pkinase) | 2.12 | 7.49E-03 | 1.99 | 2.30E-03 | 2.14 | 9.73E-03 | 2.09 | 2.40E-03 | ||
Phvul.002G207000 | K13416—brassinosteroid insensitive 1-associated receptor kinase 1 | 1.39 | 1.98E-02 | 1.80 | 2.92E-04 | 1.47 | 1.75E-02 | 1.87 | 2.77E-04 | ||
Phvul.002G158800 | PTHR14155—RING FINGER DOMAIN-CONTAINING | 0.51 | 1.13E-01 | 0.12 | 7.38E-01 | 0.70 | 2.17E-02 | 0.30 | 2.96E-01 | ||
Phvul.009G184500 | PF00069//PF00560//PF08263—Protein kinase domain (Pkinase) | 0.43 | 6.22E-01 | 1.05 | 4.16E-02 | 0.70 | 3.92E-01 | 1.17 | 2.65E-02 | ||
Phvul.006G208100 | K13416—brassinosteroid insensitive 1-associated receptor kinase 1 | 0.28 | 5.13E-01 | 0.56 | 4.35E-02 | 0.23 | 6.55E-01 | 0.60 | 3.50E-02 | ||
Phvul.002G216900 | Squalene monooxygenase/Squalene epoxidase | 0.04 | 9.81E-01 | −1.82 | 8.58E-03 | −0.44 | 7.44E-01 | −1.24 | 8.65E-02 | ||
Phvul.004G067300 | no data | 0.00 | 9.97E-01 | −0.79 | 1.24E-02 | −0.16 | 8.18E-01 | −0.88 | 6.79E-03 | ||
Phvul.009G056400 | K14503—brassinosteroid resistant 1/2 (BZR1 2) | −0.21 | 6.34E-01 | −0.52 | 5.11E-02 | −0.05 | 9.43E-01 | −0.59 | 3.16E-02 | ||
Phvul.007G223700 | PTHR10015:SF164—HEAT STRESS TRANSCRIPTION FACTOR A-3 | −0.37 | 2.47E-01 | −0.54 | 2.36E-02 | −0.26 | 5.06E-01 | −0.47 | 6.13E-02 | ||
Phvul.011G031700 | PTHR31388:SF37—PEROXIDASE 4-RELATED | −0.50 | 3.99E-01 | −1.06 | 7.79E-03 | −0.45 | 4.93E-01 | −1.05 | 1.09E-02 | ||
Phvul.009G020000 | Cycloartenol 24-C-methyltransferase/Sterol C-methyltransferase | −0.52 | 2.28E-01 | −0.66 | 4.08E-02 | −0.09 | 9.05E-01 | −0.45 | 1.97E-01 | ||
Phvul.002G291800 | PF00651—BTB/POZ domain (BTB) | −0.83 | 2.68E-01 | −2.01 | 1.17E-03 | −0.32 | 7.56E-01 | −0.82 | 1.84E-01 | ||
Phvul.010G064300 | K02728—20S proteasome subunit alpha 3 (PSMA4) | −1.57 | 4.87E-02 | −2.23 | 2.24E-03 | −1.70 | 3.67E-02 | −2.21 | 2.72E-03 | ||
Abscisic acid | |||||||||||
Phvul.011G096800 | KOG0725—Reductases with broad range of substrate specificities | 5.47 | 1.30E-02 | 3.10 | 2.02E-02 | 2.86 | 3.51E-01 | 2.10 | 1.43E-01 | ||
Phvul.009G218800 | PTHR11926:SF242—UDP-GLYCOSYLTRANSFERASE 71B2-RELATED | 1.54 | 5.86E-03 | 1.45 | 2.20E-03 | 1.35 | 3.08E-02 | 1.14 | 2.62E-02 | ||
Phvul.004G138600 | PF02893—GRAM domain (GRAM) | 1.02 | 4.17E-01 | 1.83 | 3.34E-02 | 1.33 | 2.91E-01 | 2.11 | 1.89E-02 | ||
Phvul.008G209900 | K00423—L-ascorbate oxidase (E1.10.3.3) | 0.91 | 9.81E-02 | 1.05 | 1.53E-02 | 0.81 | 1.94E-01 | 1.06 | 1.90E-02 | ||
Phvul.001G153200 | PF04570—zinc-finger of the FCS-type, C2-C2 (zf-FLZ) | 0.56 | 4.41E-01 | 1.28 | 6.08E-03 | 0.30 | 7.60E-01 | 0.83 | 1.02E-01 | ||
Phvul.001G087100 | Pleckstrin-homology domain (PH domain) | 0.54 | 7.67E-02 | 0.54 | 3.23E-02 | 0.37 | 3.44E-01 | 0.75 | 2.35E-03 | ||
Phvul.011G097200 | KOG0725—Reductases with broad range of substrate specificities | 0.48 | 1.39E-01 | 0.73 | 2.86E-03 | 0.62 | 4.72E-02 | 0.53 | 4.50E-02 | ||
Phvul.002G122200 | PTHR24286:SF10—ABSCISIC ACID 8’-HYDROXYLASE 1-RELATED | 0.15 | 8.58E-01 | 1.06 | 6.51E-03 | 0.33 | 6.45E-01 | 1.13 | 5.44E-03 | ||
Phvul.003G191100 | PTHR12300:SF52—HVA22-LIKE PROTEIN A-RELATED | −0.30 | 4.45E-01 | −0.74 | 5.03E-03 | −0.42 | 2.80E-01 | −0.55 | 5.38E-02 | ||
Phvul.002G086700 | PTHR12300:SF51—HVA22-LIKE PROTEIN C | −0.39 | 5.77E-01 | −1.03 | 1.99E-02 | −0.16 | 8.70E-01 | −0.84 | 7.18E-02 | ||
Phvul.001G007300 | PTHR12300:SF26—HVA22-LIKE PROTEIN G-RELATED | −0.48 | 1.91E-01 | −1.07 | 9.85E-05 | −0.51 | 1.90E-01 | −0.75 | 9.87E-03 | ||
Phvul.008G190500 | PTHR12300:SF27—HVA22-LIKE PROTEIN F | −0.54 | 3.84E-01 | −1.32 | 3.11E-03 | −0.58 | 3.77E-01 | −1.28 | 5.12E-03 | ||
Ethylene | |||||||||||
Phvul.007G273000 | PTHR31190:SF15—ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 1B | 3.66 | 1.42E-02 | 2.21 | 1.88E-02 | 3.00 | 1.19E-01 | 2.77 | 3.24E-03 | ||
Phvul.001G160100 | PTHR31190:SF26—ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR | 2.62 | 1.16E-03 | 1.51 | 2.97E-02 | 1.94 | 5.00E-02 | 0.23 | 8.06E-01 | ||
Phvul.002G326600 | PTHR18934:SF112—DEA(D/H)-BOX RNA HELICASE FAMILY PROTEIN | 2.29 | 5.13E-04 | 2.25 | 2.29E-04 | 2.31 | 8.01E-04 | 2.44 | 8.86E-05 | ||
Phvul.010G003300 | no data | 1.95 | 1.13E-02 | 2.72 | 3.41E-05 | 2.02 | 9.54E-03 | 3.37 | 2.34E-07 | ||
Phvul.007G127800 | PTHR31153:SF3—HISTONE H1FLK-LIKE PROTEIN-RELATED | 1.94 | 9.04E-05 | 1.34 | 4.47E-03 | 1.65 | 2.51E-03 | 1.06 | 3.46E-02 | ||
Phvul.004G081900 | PTHR13690:SF86—TRANSCRIPTION FACTOR VIP1 | 1.90 | 3.97E-04 | 1.82 | 1.62E-04 | 1.40 | 3.11E-02 | 1.43 | 5.37E-03 | ||
Phvul.004G081900 | PTHR13690:SF86—TRANSCRIPTION FACTOR VIP1 | 1.90 | 3.97E-04 | 1.82 | 1.62E-04 | 1.40 | 3.11E-02 | 1.43 | 5.37E-03 | ||
Phvul.003G020100 | PTHR10209- OXIDOREDUCTASE, 2OG-FE II OXYGENASE | 1.67 | 8.68E-03 | 1.42 | 9.56E-03 | 1.10 | 1.76E-01 | 1.29 | 2.38E-02 | ||
Phvul.003G020000 | 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase/ | 1.13 | 1.11E-01 | 1.65 | 2.01E-03 | 0.82 | 3.46E-01 | 1.52 | 6.29E-03 | ||
Phvul.009G066980 | PTHR31729:SF0—ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR | 1.06 | 7.49E-03 | 0.79 | 2.74E-02 | 1.13 | 4.87E-03 | 0.81 | 2.84E-02 | ||
Phvul.003G020200 | PTHR10209—OXIDOREDUCTASE, 2OG-FE II OXYGENASE FAMILY PROTEIN | 1.05 | 1.92E-01 | 1.18 | 5.48E-02 | 0.97 | 2.76E-01 | 1.47 | 1.85E-02 | ||
Phvul.008G127500 | PTHR15898:SF1—GLUCOSE-INDUCED DEGRADATION PROTEIN 4 | 1.01 | 7.54E-02 | 1.27 | 4.09E-03 | 0.82 | 2.26E-01 | 0.88 | 6.61E-02 | ||
Phvul.009G003400 | PTHR10209:SF107 FE(II)-DEPENDENT OXYGENASE-LIKE PROTEIN-RELATED | 0.93 | 2.96E-01 | 1.50 | 1.11E-02 | 1.02 | 2.85E-01 | 1.34 | 3.11E-02 | ||
Phvul.006G183100 | PF00847—AP2 domain (AP2) | 0.86 | 1.59E-02 | 1.05 | 5.42E-04 | 0.75 | 6.43E-02 | 0.57 | 9.01E-02 | ||
Phvul.003G020300 | PTHR10209//PTHR10209:SF148—OXIDOREDUCTASE, 2OG-FE II | 0.81 | 1.34E-01 | 0.94 | 2.76E-02 | 0.75 | 2.20E-01 | 0.94 | 3.16E-02 | ||
Phvul.011G125200 | no data | 0.73 | 3.90E-02 | 0.65 | 2.54E-02 | 0.70 | 6.39E-02 | 0.63 | 3.61E-02 | ||
Phvul.001G225300 | PF00582—Universal stress protein family (Usp) | 0.69 | 1.23E-01 | 0.75 | 2.57E-02 | 0.41 | 4.92E-01 | 0.55 | 1.32E-01 | ||
Phvul.007G241600 | K06228—fused (FU) | 0.63 | 1.18E-01 | 0.86 | 5.28E-03 | 0.80 | 4.05E-02 | 0.79 | 1.58E-02 | ||
Phvul.002G055800 | K09286—EREBP-like factor (EREBP) | 0.54 | 7.35E-02 | 0.84 | 2.93E-04 | 0.79 | 3.33E-03 | 0.85 | 3.09E-04 | ||
Phvul.002G293000 | K11135—Pin2-interacting protein X1 (PINX1) | 0.52 | 5.51E-01 | 1.22 | 2.66E-02 | 0.59 | 5.20E-01 | 1.33 | 2.07E-02 | ||
Phvul.004G120700 | Deacetoxyvindoline 4-hydroxylase/Desacetyoxyvindoline-17-hydroxylase | 0.42 | 3.34E-01 | 0.65 | 2.94E-02 | 0.20 | 7.33E-01 | 0.50 | 1.15E-01 | ||
Phvul.002G055700 | PTHR31190:SF30—ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 15 | 0.41 | 2.09E-01 | 0.69 | 3.15E-03 | 0.70 | 1.35E-02 | 0.68 | 5.09E-03 | ||
Phvul.003G223624 | K09286—EREBP-like factor (EREBP) | 0.33 | 3.16E-01 | 0.73 | 9.51E-04 | 0.59 | 3.47E-02 | 0.88 | 5.54E-05 | ||
Phvul.003G223686 | PTHR31190:SF30—ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 15 | 0.32 | 4.19E-01 | 0.81 | 1.53E-03 | 0.57 | 9.77E-02 | 0.69 | 1.12E-02 | ||
Phvul.003G150900 | K19044—E3 ubiquitin-protein ligase XBAT32/33 (XBAT32 33) | 0.09 | 7.77E-01 | 0.36 | 4.76E-02 | 0.08 | 8.30E-01 | 0.36 | 5.50E-02 | ||
Phvul.002G209300 | PTHR23335:SF12—CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 1 | 0.05 | 8.70E-01 | 0.26 | 9.24E-02 | 0.01 | 9.80E-01 | 0.44 | 2.91E-03 | ||
Phvul.006G179800 | PF00847—AP2 domain (AP2) | −0.07 | 9.15E-01 | 0.64 | 3.41E-02 | 0.21 | 7.26E-01 | 0.84 | 5.53E-03 | ||
Phvul.004G121000 | Deacetoxyvindoline 4-hydroxylase | −0.30 | 5.72E-01 | −0.77 | 2.09E-02 | −0.24 | 7.02E-01 | −0.40 | 2.64E-01 | ||
Phvul.003G241700 | PTHR31729:SF0- ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR | −0.34 | 4.94E-01 | −0.65 | 4.84E-02 | −0.20 | 7.54E-01 | −0.63 | 6.26E-02 | ||
Salicylic acid | |||||||||||
Phvul.008G057600 | Caffeine synthase/Dimethylxanthine methyltransferase | 5.07 | 2.40E-05 | 2.95 | 1.04E-03 | 4.41 | 1.11E-03 | 1.77 | 7.16E-02 | ||
Phvul.001G177700 | K10775—Phenylalanine ammonia-lyase (PAL) | 1.61 | 6.78E-03 | 2.19 | 2.35E-05 | 1.55 | 1.37E-02 | 2.45 | 3.25E-06 | ||
Phvul.001G177800 | K10775—Phenylalanine ammonia-lyase (PAL) | 1.59 | 2.83E-02 | 2.27 | 1.72E-04 | −0.13 | 1.00E+00 | 2.28 | 2.39E-04 | ||
Phvul.010G011700 | 5.4.4.2—Isochorismate synthase/Isochorismate synthetase | −0.02 | 9.77E-01 | −0.60 | 6.19E-02 | −0.08 | 1.00E+00 | −0.61 | 6.64E-02 | ||
Jasmonic acid | |||||||||||
Phvul.010G134700 | K15718—linoleate 9S-lipoxygenase (LOX1 5) | 1.70 | 1.99E-02 | 2.25 | 2.48E-04 | 1.52 | 6.13E-02 | 1.84 | 3.96E-03 | ||
Phvul.006G016900 | no data | 1.43 | 1.85E-04 | 1.44 | 5.50E-05 | 1.18 | 5.46E-03 | 1.23 | 1.02E-03 | ||
Phvul.001G000800 | PTHR22893//PTHR22893:SF62- NADH OXIDOREDUCTASE-RELATED | 0.98 | 1.58E-01 | 1.03 | 4.90E-02 | 0.98 | 1.91E-01 | 1.01 | 6.17E-02 | ||
Phvul.005G156800 | K15718—linoleate 9S-lipoxygenase (LOX1 5) | 0.88 | 6.18E-01 | −2.52 | 2.72E-02 | 0.19 | 9.46E-01 | −1.01 | 4.37E-01 | ||
Phvul.009G262900 | PTHR11771:SF38—LIPOXYGENASE 3, CHLOROPLASTIC-RELATED | 0.86 | 1.27E-01 | 1.20 | 4.91E-03 | 0.70 | 2.92E-01 | 1.04 | 2.11E-02 | ||
Phvul.003G021000 | PTHR33077:SF7—PROTEIN TIFY 6A-RELATED | 0.70 | 6.11E-02 | 0.34 | 3.54E-01 | 0.56 | 2.06E-01 | 0.81 | 1.25E-02 | ||
Phvul.003G111500 | Delta(4)-3-oxosteroid 5-beta-reductase | 0.55 | 9.25E-02 | 0.64 | 1.21E-02 | 0.54 | 1.28E-01 | 0.42 | 1.30E-01 | ||
Phvul.005G156900 | K15718—linoleate 9S-lipoxygenase (LOX1 5) | 0.31 | 8.49E-01 | −1.89 | 2.13E-02 | −0.15 | 9.44E-01 | −0.86 | 3.63E-01 | ||
Phvul.003G129200 | PTHR33077:SF13—PROTEIN TIFY 10A-RELATED | 0.19 | 8.87E-01 | 0.29 | 7.73E-01 | 0.39 | 7.54E-01 | 1.72 | 9.46E-03 | ||
Phvul.009G225300 | PTHR33077:SF13—PROTEIN TIFY 10A-RELATED | 0.18 | 6.26E-01 | 0.62 | 5.05E-03 | 0.24 | 5.20E-01 | 0.78 | 4.37E-04 | ||
Phvul.003G131600 | PTHR22893:SF67—12-OXOPHYTODIENOATE REDUCTASE 3 | −0.39 | 2.89E-01 | −0.58 | 2.82E-02 | −0.19 | 7.10E-01 | −0.25 | 4.15E-01 | ||
Phvul.002G175500 | PTHR11771:SF60—LIPOXYGENASE 6, CHLOROPLASTIC | −0.47 | 3.22E-01 | −0.71 | 4.38E-02 | −0.39 | 4.76E-01 | −0.33 | 4.10E-01 | ||
Phvul.004G072000 | PTHR31942:SF29—MLO-LIKE PROTEIN 12-RELATED | −0.60 | 9.00E-02 | −0.62 | 3.84E-02 | −0.36 | 4.23E-01 | −0.59 | 5.63E-02 | ||
Phvul.010G032300 | PTHR11771//PTHR11771:SF59—LIPOXYGENASE | −1.26 | 4.20E-03 | −0.48 | 3.32E-01 | −0.34 | 6.23E-01 | −0.14 | 8.13E-01 | ||
FDR | |||||||||||
1.00E-10 | 1.00E-08 | 0.05 | 0.00 | ||||||||
Log2FC | |||||||||||
−2.50 | −1.50 | −1.00 | −0.5 | 0.00 | 0.5 | 1.00 | 1.50 | 2.50 |
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Alvarez-Diaz, J.C.; Laugé, R.; Delannoy, E.; Huguet, S.; Paysant-Le Roux, C.; Gratias, A.; Geffroy, V. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. Plants 2022, 11, 1995. https://doi.org/10.3390/plants11151995
Alvarez-Diaz JC, Laugé R, Delannoy E, Huguet S, Paysant-Le Roux C, Gratias A, Geffroy V. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. Plants. 2022; 11(15):1995. https://doi.org/10.3390/plants11151995
Chicago/Turabian StyleAlvarez-Diaz, Juan C., Richard Laugé, Etienne Delannoy, Stéphanie Huguet, Christine Paysant-Le Roux, Ariane Gratias, and Valérie Geffroy. 2022. "Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean" Plants 11, no. 15: 1995. https://doi.org/10.3390/plants11151995