Combined Metabolome and Transcriptome Analyses Reveal the Effects of Mycorrhizal Fungus Ceratobasidium sp. AR2 on the Flavonoid Accumulation in Anoectochilus roxburghii during Different Growth Stages
Abstract
:1. Introduction
2. Results
2.1. Detecting Mycorrhizal Fungus Colonization in A. roxburghii
2.2. Identification of Metabolites
2.3. Identification of Differentially Accumulated Metabolites and Differentially Accumulated Flavonoids
2.4. Transcriptome Profiles of Mycorrhizal and Non-Mycorrhizal A. roxburghii
2.5. Association Analysis of the DAMs and DEGs
2.6. Dynamic Variations in Flavonoid DAMs
2.7. Dynamic Variations of Expression Levels of Flavonoid Biosynthetic Genes
3. Discussion
4. Materials and Methods
4.1. Plant and Mycorrhizal Fungus Materials
4.2. Symbiotic Cultures of A. roxburghii Plantlets
4.3. Histological Study
4.4. Sample Extraction and Metabolome Analysis
4.4.1. Sample Extraction
4.4.2. Liquid Chromatographic Mass Spectrometry Analysis
4.4.3. Metabolite Identification
4.5. Illumina Sequencing
4.5.1. RNA Extraction, cDNA Library Construction and Sequencing
4.5.2. De Novo Transcriptome Assembly and Annotation
4.6. Determination of the Flavonoid Contents During Different Growth Stages
4.6.1. Preparation of Standard Solutions
4.6.2. Preparation of Sample Solutions
4.6.3. Apparatus and Analytical Conditions
4.7. Expression of the Flavonoid Biosynthesis Related Genes During Different Growth Stages
4.8. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
CE | collision energy |
CUR | curtain gas |
CXP | collision cell exit potential |
DAMs | differentially accumulated metabolites |
DEGs | differentially expressed genes |
DP | de-clustering potential |
EP | entrance potential |
ESI-QTRAP-MS/MS | electrospray ionization-triple quadrupole-linear ion trap MS/MS |
GC-MS | gas chromatography-mass spectrometer |
GO | gene ontology |
GS1 | ion source gas 1 |
GS2 | ion source gas 2 |
HPLC-MS/MS | high-performance liquid chromatography coupled with tandem mass spectrometry |
IS | ion spray voltage |
KEGG | Kyoto encyclopedia of genes and genomes |
LC-MS | liquid chromatograph-mass spectrometer |
LIT | linear ion trap |
LOD | limit of detection |
LOQ | limit of quantification |
NMR | nuclear magnetic resonance |
OPLS-DA | orthogonal partial least squares discriminant |
PCA | principal component analysis |
PC1 | principal component 1 |
PC2 | principal component 2 |
PI | product ions |
QC | quality control |
QQQ | triple quadrupole |
qRT-PCR | quantitative real-time polymerase chain reaction |
RNA-seq | RNA-sequencing |
RSDs | relative standard deviations |
TEM | temperature |
TIC | total ion chromatography |
UPLC-ESI-MS/MS | ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry |
VIP | variable importance in project |
cps | count per second |
MRM | multiple reaction monitoring |
psi | pounds per square inch |
NM | non-mycorrhizal A. roxburghii |
M | mycorrhizal A. roxburghii |
PAL | phenylalanine ammonia-lyase |
C4H | cinnamate 4-hydroxylase |
4CL | 4-coumarate CoA ligase |
CHS | chalcone synthase |
CHI | chalcone isomerase |
F3′H | flavonoid 3′-hydroxylase |
FNS | flavone synthase |
F3H | flavanone 3-hydroxylase |
FLS | flavonol synthase |
GT | flavonoid 3-O-glucosyltransferase |
RT | rhamnosyltransferase |
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Sample | Raw Reads | Clean Reads | Clean Base (G) | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|---|
NM1 | 61,226,728 | 61,071,914 | 9.09 | 0.017 | 97.79 | 93.61 | 48.19 |
NM2 | 60,542,772 | 60,425,910 | 8.99 | 0.016 | 98.11 | 94.42 | 47.93 |
NM3 | 67,559,786 | 67,410,292 | 10.05 | 0.016 | 98.07 | 94.28 | 48.43 |
M1 | 55,632,192 | 55,492,010 | 8.28 | 0.016 | 98.02 | 94.20 | 49.06 |
M2 | 65,007,376 | 64,859,884 | 9.68 | 0.016 | 98.19 | 94.58 | 48.10 |
M3 | 67,125,158 | 66,965,132 | 9.99 | 0.016 | 98.09 | 94.34 | 48.23 |
No. | Name | Precursor Ion (m/z) | Product Ions (m/z) | DP (V) | CE (V) | EP (V) | CXP (V) | IS (V) | Ionization Mode | Retention Time (min) | |
---|---|---|---|---|---|---|---|---|---|---|---|
PI q | PI i | ||||||||||
1 | nobiletin | 402.9 | 373.1 | 388.1 | 20 | 33 | 10 | 13 | 5500 | ESI+ | 4.56 |
2 | narcissin | 624.9 | 316.7 | 479.6 | 50 | 25 | 10 | 13 | 5500 | ESI+ | 3.51 |
3 | isorhamnetin-3-O-beta-d-glucoside | 479.3 | 317 | 253 | 150 | 34 | 10 | 13 | 5500 | ESI+ | 3.53 |
4 | tangeretin | 372.8 | 343.1 | 358.1 | 10 | 32 | 10 | 13 | 5500 | ESI+ | 4.67 |
5 | rutin | 609 | 299.9 | 279.5 | −50 | −43 | −10 | −15 | −4500 | ESI− | 3.44 |
6 | quercetin | 301 | 150.8 | 178.9 | −100 | −35 | −10 | −15 | −4500 | ESI− | 3.69 |
7 | isorhamnetin | 314.8 | 300 | 150.8 | −150 | −30 | −10 | −15 | −4500 | ESI− | 3.84 |
8 | quercetin-7-O-glucoside | 462.9 | 300.9 | 342.9 | −50 | −28 | −10 | −15 | −4500 | ESI− | 3.43 |
9 | kaempferol-3-O-glucoside | 592.9 | 284.9 | 255 | −50 | −40 | −10 | −15 | −4500 | ESI− | 3.50 |
No. | Name | Linearity | LOD (ng/mL) | LOQ (ng/mL) | Stability (RSD, %) | Precision (RSD, %) | Repeatability (RSD, %) | ||
---|---|---|---|---|---|---|---|---|---|
Regression Equations | R2 | Ranges (ng/mL) | |||||||
1 | nobiletin | y = 62,293,800x − 1,576,600 | 0.9968 | 7.81–1000 | 0.488 | 0.977 | 3.05 | 1.43 | 4.44 |
2 | narcissin | y = 3,029,650x − 314,384 | 0.9942 | 31.25–4000 | 7.81 | 15.63 | 3.26 | 3.22 | 2.26 |
3 | isorhamnetin-3-O- beta-d-glucoside | y = 279,387x − 11,500 | 0.9973 | 62.5–4000 | 15.63 | 31.25 | 4.22 | 4.37 | 4.93 |
4 | tangeretin | y = 4,034,570x − 18,086 | 0.9902 | 3.91–250 | 0.488 | 0.977 | 1.94 | 1.76 | 4.87 |
5 | rutin | y = 3,089,740x − 61,316 | 0.9978 | 15.63–1000 | 7.81 | 31.25 | 2.99 | 3.71 | 1.74 |
6 | quercetin | y = 17,556,400x − 169,184 | 0.9921 | 15.63–500 | 7.81 | 15.63 | 3.82 | 4.03 | 4.9 |
7 | isorhamnetin | y = 116,434,300x − 149,754 | 0.9903 | 7.81–250 | 3.91 | 7.81 | 2.53 | 2.94 | 2.82 |
8 | quercetin-7-O- glucoside | y = 5,857,970x − 144,514 | 0.9989 | 31.25–1000 | 7.81 | 15.63 | 3.26 | 3.31 | 2.39 |
9 | kaempferol-3-O- glucoside | y = 4,499,260x − 117,172 | 0.9901 | 31.25–1000 | 7.81 | 15.63 | 2.06 | 4.49 | 4.9 |
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Zhang, Y.; Li, Y.; Chen, X.; Meng, Z.; Guo, S. Combined Metabolome and Transcriptome Analyses Reveal the Effects of Mycorrhizal Fungus Ceratobasidium sp. AR2 on the Flavonoid Accumulation in Anoectochilus roxburghii during Different Growth Stages. Int. J. Mol. Sci. 2020, 21, 564. https://doi.org/10.3390/ijms21020564
Zhang Y, Li Y, Chen X, Meng Z, Guo S. Combined Metabolome and Transcriptome Analyses Reveal the Effects of Mycorrhizal Fungus Ceratobasidium sp. AR2 on the Flavonoid Accumulation in Anoectochilus roxburghii during Different Growth Stages. International Journal of Molecular Sciences. 2020; 21(2):564. https://doi.org/10.3390/ijms21020564
Chicago/Turabian StyleZhang, Ying, Yuanyuan Li, Xiaomei Chen, Zhixia Meng, and Shunxing Guo. 2020. "Combined Metabolome and Transcriptome Analyses Reveal the Effects of Mycorrhizal Fungus Ceratobasidium sp. AR2 on the Flavonoid Accumulation in Anoectochilus roxburghii during Different Growth Stages" International Journal of Molecular Sciences 21, no. 2: 564. https://doi.org/10.3390/ijms21020564