Transcriptome Analysis of Apple Leaves in Response to Powdery Mildew (Podosphaera leucotricha) Infection
Abstract
:1. Introduction
2. Results
2.1. Statistical Analysis of RNA-seq Results from Different Time Points after PM Inoculation
2.2. DEG Profiles in Response to PM Infection
2.3. Pathway Enrichment Analysis at Different Infection Stages
2.4. DEGs Involved in Phytohormone Signaling
2.5. DEGs Involved in Plant-fungal interaction
2.6. TFs Related to PM Responses
2.7. Validation of RNA-Seq Data by Quantitative Real Time (qRT)-PCR
2.8. Changes in Physiological Characteristics of Apple Leaves after Infection with PM
3. Discussion
4. Materials and Methods
4.1. Plant Materials, Fungal Collection and Inoculation
4.2. RNA Quantification and Qualification
4.3. Library Preparation
4.4. RNA-Seq DataAnalysis
4.5. Differential Expression Analysis
4.6. GO and KEGG Pathway Enrichment Analysis
4.7. qRT-PCR Validation and Analysis
4.8. Effects of PM on Physiological Indexes
4.9. Effects of PM on the Accumulation of Defense-Related Enzyme
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
Abbreviations
PM | Powdery mildew |
DEG | Differentially expressed gene |
HPI | Hours post inoculation |
DPI | Days post inoculation |
PCR | Polymerase chain reaction |
qRT-PCR | Quantitative real time PCR |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
KO | KEGG Orthology |
ZF-TFs | Zinc finger-transcription factors |
PR5 | Thaumatin protein |
PR10 | Ribonucleases |
PR14 | Lipid-transfer protein |
CYPs | Cytochrome P450 genes |
ET | Ethylene |
SA | Salicylic acid |
JA | Jasmonic acid |
GA | Gibberellin |
AUX | Auxin |
BR | brassionosteroid |
NBT | Nitro blue tetrazolium |
DAB | Diaminobenzidine |
Pro | Proline |
MDA | Malondialdehyde |
POD | Peroxidase |
SOD | Superoxide dismutase |
CAT | Catalase |
β-1,3-GA | β-1,3-glucanase |
CHI | Chitinase |
PAL | Phenylalanine ammonia-lyase |
ROS | Reactive oxygen species |
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Samples | Time Points | Total Reads | Q20 Percentage (%) | Q30 Percentage (%) | Mapped Reads | Mapping Rate (%) |
---|---|---|---|---|---|---|
CK01 | 0 hpi | 60,137,610 | 97.4 | 93.65 | 48,293,530 | 80.31 |
CK02 | 0 hpi | 61,254,152 | 97.5 | 93.83 | 49,772,328 | 81.26 |
CK03 | 0 hpi | 58,546,454 | 97.46 | 93.77 | 47,250,937 | 80.71 |
CK121 | 12 hpi | 48,161,690 | 97.55 | 94.05 | 37,977,254 | 78.85 |
CK122 | 12 hpi | 60,404,448 | 96.95 | 92.80 | 47,385,808 | 78.85 |
CK123 | 12 hpi | 62,016,814 | 97.29 | 93.41 | 49,706,083 | 80.15 |
CK241 | 24 hpi | 54,165,314 | 96.78 | 92.46 | 42,586,645 | 78.62 |
CK242 | 24 hpi | 64,515,854 | 96.86 | 92.67 | 51,035,900 | 79.11 |
CK243 | 24 hpi | 70,503,200 | 96.76 | 92.47 | 55,360,754 | 78.52 |
CK481 | 48 hpi | 64,182,946 | 97.06 | 92.98 | 51,398,939 | 80.08 |
CK482 | 48 hpi | 56,164,490 | 96.91 | 92.69 | 44,903,336 | 79.95 |
CK483 | 48 hpi | 56,864,248 | 96.76 | 92.42 | 44,919,501 | 78.99 |
T01 | 0 hpi | 68,815,498 | 97.41 | 93.67 | 56,225,369 | 78.99 |
T02 | 0 hpi | 60,247,576 | 97.12 | 93.17 | 48,129,005 | 78.99 |
T03 | 0 hpi | 60,534,844 | 97.13 | 93.16 | 48,533,584 | 78.99 |
T121 | 12 hpi | 55,781,200 | 96.74 | 92.89 | 44,030,266 | 78.99 |
T122 | 12 hpi | 68,568,070 | 97.03 | 92.94 | 54,673,257 | 78.99 |
T123 | 12 hpi | 53,809,766 | 97.21 | 93.29 | 43,094,498 | 80.09 |
T241 | 24 hpi | 66,547,810 | 96.74 | 92.47 | 52,184,112 | 78.42 |
T242 | 24 hpi | 55,181,416 | 97.03 | 92.96 | 43,627,644 | 79.06 |
T243 | 24 hpi | 43,835,550 | 96.86 | 92.63 | 34,502,703 | 78.71 |
T481 | 48 hpi | 56,609,920 | 96.89 | 92.69 | 45,122,462 | 79.71 |
T482 | 48 hpi | 52,151,048 | 96.9 | 92.77 | 40,989,977 | 78.60 |
T483 | 48 hpi | 71,638,240 | 96.81 | 92.55 | 56,853,084 | 79.36 |
Average | 59,609,923 | 97.05 | 93.02 | 47,439,874 | 79.35 |
Pathway Name | Number of Genes with Pathway Annotation | ||||
---|---|---|---|---|---|
No. | Pathway ID | G12 | G24 | G48 | |
Plant hormone signal transduction | P1 | KO 04075 | 15 | 10 | 5 |
Plant-pathogen interaction | P2 | KO 04626 | 11 | 8 | 1 |
Phenylpropanoid biosynthesis | P3 | KO 00940 | 10 | 8 | 5 |
Cyanoamino acid metabolism | P4 | KO 00460 | 7 | 8 | 3 |
ABC transporters | P5 | KO 02010 | 6 | 7 | 1 |
Protein processing in endoplasmic reticulum | P6 | KO 04141 | 5 | 7 | 1 |
Starch and sucrose metabolism | P7 | KO 00500 | 4 | 5 | 3 |
Cysteine and methionine metabolism | P8 | KO 00270 | 4 | 4 | 7 |
Phagosome | P9 | KO 04145 | 4 | 3 | 1 |
Phenylalanine metabolism | P10 | KO 00360 | 3 | 3 | 2 |
Endocytosis | P11 | KO 04144 | 3 | 3 | 1 |
Stilbenoid, diarylheptanoid and gingerol biosynthesis | P12 | KO 00945 | 3 | 3 | 1 |
alpha-Linolenic acid metabolism | P13 | KO 00592 | 3 | 3 | 0 |
Ubiquitin mediated proteolysis | P14 | KO 04120 | 3 | 3 | 0 |
DNA replication | P15 | KO 03030 | 3 | 3 | 0 |
Lysine degradation | P16 | KO 00310 | 3 | 3 | 0 |
Linoleic acid metabolism | P17 | KO 00591 | 3 | 3 | 0 |
Glutathione metabolism | P18 | KO 00480 | 2 | 3 | 1 |
Sesquiterpenoid and triterpenoid biosynthesis | P19 | KO 00909 | 2 | 1 | 1 |
Biosynthesis of amino acids | P20 | KO 01230 | 2 | 0 | 1 |
Glycine, serine and threonine metabolism | P21 | KO 00260 | 2 | 1 | 1 |
Arginine and proline metabolism | P22 | KO 00330 | 2 | 1 | 1 |
Steroid biosynthesis | P23 | KO 00100 | 2 | 1 | 3 |
Carbon metabolism | P24 | KO 01200 | 2 | 2 | 0 |
SNARE interactions in vesicular transport | P25 | KO 04130 | 2 | 1 | 0 |
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Tian, X.; Zhang, L.; Feng, S.; Zhao, Z.; Wang, X.; Gao, H. Transcriptome Analysis of Apple Leaves in Response to Powdery Mildew (Podosphaera leucotricha) Infection. Int. J. Mol. Sci. 2019, 20, 2326. https://doi.org/10.3390/ijms20092326
Tian X, Zhang L, Feng S, Zhao Z, Wang X, Gao H. Transcriptome Analysis of Apple Leaves in Response to Powdery Mildew (Podosphaera leucotricha) Infection. International Journal of Molecular Sciences. 2019; 20(9):2326. https://doi.org/10.3390/ijms20092326
Chicago/Turabian StyleTian, Xiaomin, Li Zhang, Shuaishuai Feng, Zhengyang Zhao, Xiping Wang, and Hua Gao. 2019. "Transcriptome Analysis of Apple Leaves in Response to Powdery Mildew (Podosphaera leucotricha) Infection" International Journal of Molecular Sciences 20, no. 9: 2326. https://doi.org/10.3390/ijms20092326