An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple
Abstract
:1. Introduction
2. Results
2.1. Histological Analysis of Russeting Apple
2.2. General Characterization of Transcriptome Data
2.3. General Characterization of Proteome Data
2.4. Proteome and Transcriptome Correlation Analysis
2.5. Identification of Transcription Factors Involved in Lignin Biosynthesis
2.6. Quantitative Real-Time PCR Confirmation of Selected Genes
2.7. Functional Identification of MD15G1068200
3. Discussion
3.1. Histologic Change of Russeted Skin
3.2. Changes in Related Genes of Lignin Biosynthesis
3.3. Proteome and Transcriptome Correlation Analysis
3.4. Regulatory Factors of Lignin Biosynthesis Related Genes
4. Materials and Methods
4.1. Plant Materials
4.2. Scanning Electron Microscope for Epidermis Structure
4.3. Light Microscopy for Epidermis Cell
4.4. RNA Extraction and Sequencing
4.5. Protein Extraction, iTRAQ Labeling, and Mass Spectrometry Analysis
4.6. Protein and RNA Correlation Analysis
4.7. Quantitative Real-time PCR Validation
4.8. Functional Association Network
4.9. Phylogenetic Analysis
4.10. Electrophoretic Mobility Shift Assay
4.11. Luciferase Reporter Assays in Nicotiana Benthamiana Leaves
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
DAF | days after flowering |
SEM | scanning electron microscopy |
LM | light microscope |
PAL | phenylalanine ammonia-lyase |
CCR | cinnamyl CoA reductase |
CAD | cinnamyl-alcohol dehydrogenase |
POD | peroxidase |
PRX | peroxidase |
C4H | cinnamate hydroxylase |
C3H | coumaric acid 3-hydroxylase |
4CL | 4-coumaric acid- CoA ligase |
PDC | pyruvate decarboxylase |
HCT | shikimate O-hydroxycinnamoyl transferase |
PDA | phospholipid: diacylglycerol acyltransferase |
DEGs | differentially expressed genes |
DEPs | differentially expressed proteins |
qPCR | Quantitative real-time PCR |
iTRAQ | isobaric tags for relative and absolute quantitation |
RNA-Seq | RNA sequencing |
NR | NCBI non-redundant protein sequences |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
Ko | KEGG ortholog |
GO | Gene ontology |
TF | transcription factor |
HPLC | high-performance liquid chromatography |
MS/MS | tandem mass spectrometry |
NJ | Neighbor-joining |
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Gene ID | Gene Length (bp) | Log2(T/CK) | Description | Ko Number |
---|---|---|---|---|
MD01G1042500 | 2011 | −2.41 | CAD, cinnamyl-alcohol dehydrogenase [EC:1.1.1.195] | K00083 |
MD01G1042800 | 1779 | −2.66 | CAD, cinnamyl-alcohol dehydrogenase [EC:1.1.1.195] | K00083 |
MD02G1161000 | 2472 | −2.02 | PDA, phospholipid: diacylglycerol acyltransferase [EC:2.3.1.158] | K00679 |
MD03G1126700 | 5941 | −1.39 | PDC, pyruvate decarboxylase [EC:4.1.1.1] | K01568 |
MD04G1096200 | 3458 | −1.81 | PAL, phenylalanine ammonia-lyase [EC:4.3.1.24] | K10775 |
MD06G1194000 | 1697 | −2.24 | UBR4, E3 ubiquitin-protein ligase [EC:2.3.2.27] | K10691 |
MD11G1153800 | 3440 | −1.56 | PDA, phospholipid: diacylglycerol acyltransferase [EC:2.3.1.158] | K00679 |
MD11G1210200 | 1645 | −2.72 | UBR4, E3 ubiquitin-protein ligase UBR4 [EC:2.3.2.27] | K10691 |
MD11G1214800 | 2056 | −1.86 | PDA, phospholipid: diacylglycerol acyltransferase [EC:2.3.1.158] | K00679 |
MD12G1252500 | 2161 | 1.32 | PDA, phospholipid: diacylglycerol acyltransferase [EC:2.3.1.158] | K00679 |
MD17G1157600 | 2990 | −2.25 | HCT, shikimate O-hydroxycinnamoyl transferase [EC:2.3.1.133] | K13065 |
Gene ID | Gene Length (bp) | Log2(T/CK) | Log2(RAE/WAE) | Description | Ko Number |
---|---|---|---|---|---|
MD03G1073600 | 1904 | −2.79 | 3.97 | CYP86A1, long-chain fatty acid omega-monooxygenase [EC:1.14.14.80] | K15401 |
MD08G1058900 | 1808 | 1.67 | - | HHT1, omega-hydroxypalmitate O-feruloyl transferase [EC:2.3.1.188] | K15400 |
MD09G1007600 | 1797 | −2.23 | - | HHT1, omega-hydroxypalmitate O-feruloyl transferase [EC:2.3.1.188] | K15400 |
MD13G1004700 | 2106 | −2.84 | 4.75 | CYP86B1, fatty acid omega-hydroxylase [EC:1.14.-.-] | K15402 |
MD17G1011500 | 1790 | −2.27 | - | HHT1, omega-hydroxypalmitate O-feruloyl transferase [EC:2.3.1.188] | K15400 |
Protein ID | Mass (kD) | Mean Ratio (T/CK) | Description | Ko ID |
---|---|---|---|---|
MD01G1205400 | 33.79 | 0.60 | At4g11410, WW domain-containing oxidoreductase | K19329 |
MD02G1009300 | 53.71 | 0.67 | At2g24270, glyceraldehyde-3-phosphate dehydrogenase (NADP+) [EC:1.2.1.9] | K00131 |
MD02G1157800 | 35.27 | 0.58 | -, photosystem II oxygen-evolving enhancer protein 1 | K02716 |
MD05G1122100 | 42.35 | 0.65 | At1g68010, hydroxypyruvate reductase 1 [EC:1.1.1.29] | K15893 |
MD05G1209300 | 40.59 | 0.63 | At3g14420, (S)-2-hydroxy-acid oxidase [EC:1.1.3.15] | K11517 |
MD08G1007200 | 16.92 | 0.67 | -, plastocyanin | K02638 |
MD08G1168600 | 48.75 | 0.60 | At5g08640, flavonol synthase [EC:1.14.20.6] | K05278 |
MD09G1050500 | 49.97 | 0.74 | At5g39830, HtrA serine peptidase 2 [EC:3.4.21.108] | K08669 |
MD09G1252100 | 20.72 | 0.58 | -, ribulose-bisphosphate carboxylase [EC:4.1.1.39] | K01602 |
MD09G1262800 | 41.17 | 0.65 | At1g66430, fructokinase [EC:2.7.1.4] | K00847 |
MD10G1011900 | 19.93 | 0.59 | At4g03520, thioredoxin 1 | K03671 |
MD10G1195700 | 52.49 | 0.55 | At3g14420, (S)-2-hydroxy-acid oxidase [EC:1.1.3.15] | K11517 |
MD14G1219000 | 41.45 | 0.69 | -, chitinase domain-containing protein 1 | K17525 |
MD15G1006300 | 16.86 | 0.72 | -, plastocyanin | K02638 |
MD15G1222600 | 23.68 | 0.64 | At3g26060, peroxiredoxin Q/BCP [EC:1.11.1.15] | K03564 |
MD15G1272500 | 35.24 | 0.53 | -, photosystem II oxygen-evolving enhancer | K02716 |
MD15G1307200 | 56.88 | 0.53 | At4g37930, glycine hydroxymethyl transferase | K00600 |
MD15G1421500 | 27.39 | 0.69 | -, exocyst complex component 2 | - |
MD17G1020900 | 32.92 | 0.67 | At4g24770, nucleolin | K11294 |
MD17G1132900 | 28.77 | 0.56 | -, photosystem II oxygen-evolving enhancer | K02717 |
ID | Protein | Gene | Description | Ko ID |
---|---|---|---|---|
T/CK | Log2(T/CK) | |||
MD00G1116600 | 1.72 | −1.77 | UBR4, E3 ubiquitin-protein ligase | K00679 |
MD03G1059200 | 0.67 | 1.31 | PRX, Peroxidase | K00430 |
MD08G1009200 | 0.84 | −1.21 | CAD, Cinnamyl-alcohol dehydrogenase | K00083 |
MD17G1092400 | 1.42 | −1.85 | PRX, Peroxidase | K00430 |
MD17G1225100 | 1.00 | 1.12 | HCT, Shikimate O-hydroxycinnamoyl transferase | K13065 |
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Yuan, G.; Bian, S.; Han, X.; He, S.; Liu, K.; Zhang, C.; Cong, P. An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple. Int. J. Mol. Sci. 2019, 20, 4462. https://doi.org/10.3390/ijms20184462
Yuan G, Bian S, Han X, He S, Liu K, Zhang C, Cong P. An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple. International Journal of Molecular Sciences. 2019; 20(18):4462. https://doi.org/10.3390/ijms20184462
Chicago/Turabian StyleYuan, Gaopeng, Shuxun Bian, Xiaolei Han, Shanshan He, Kai Liu, Caixia Zhang, and Peihua Cong. 2019. "An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple" International Journal of Molecular Sciences 20, no. 18: 4462. https://doi.org/10.3390/ijms20184462