The Reason for Growth Inhibition of Ulmus pumila ‘Jinye’: Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy
Abstract
:1. Introduction
2. Results and Analysis
2.1. Growth and Physiological Factors Analysis
2.2. Photosynthetic Rate and Chlorophyll Fluorescence Analysis
2.3. Cellular Microstructure Analysis
2.4. RNA Sequencing Analysis
2.4.1. DEG Analysis
2.4.2. COG Classification of DEGs
2.4.3. KOG Classification of DEGs
2.4.4. KEGG Metabolism Pathway Analysis
2.4.5. DEG Pathway Analysis
2.4.6. qPCR Verification Analysis
3. Materials and Methods
3.1. Materials
3.2. Determination of Physiological Factors
3.3. Photosynthetic Rate and Chlorophyll Fluorescence Analysis
3.4. Cellular Microstructure Analysis
3.5. RNA Extraction, Library Construction, and Sequencing
3.6. Illumina Sequencing, Assembly, and Functional Annotation
3.7. Real Time Q-PCR Verification
4. Discussion and Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Formulae and Terms | U. pumila L. | U. pumila ’Jinye’ | |
---|---|---|---|
Net photosynthetic rate | Pn | 17.41 ± 1.42 a | 12.57 ± 2.80 b |
Fluorescence intensity | Fo | 5695.32 ± 468.22 a | 2657.62 ± 248.74 b |
Fm | 21,337.45 ± 715.39 a | 5686.73 ± 482.54 b | |
Fv | 15,642.73 ± 657.22 a | 3029.86 ± 397.61 b | |
Yields or flux ratios | φPo | 0.73 ± 0.13 a | 0.53 ± 0.08 b |
ψO | 0.84 ± 0.11 a | 0.73 ± 0.11 b | |
φEo | 0.62 ± 0.07 a | 0.39 ± 0.04 b | |
φDo | 0.27 ± 0.04 b | 0.47 ± 0.05 a | |
Phenomenological energy fluxes | ABS/CSO | 5695.73 ± 451.35 a | 2657.06 ± 426.33 b |
TRO/CSO | 4174.96 ± 391.57 a | 1415.42 ± 206.54 b | |
ETO/CSO | 3523.71 ± 299.36 a | 1039.25 ± 255.32 b | |
DIO/CSO | 1520.04 ± 268.13 a | 1241.58 ± 143.68 b | |
Density of reaction centers | RC/CSO | 2823.42 ± 162.47 a | 890.16 ± 118.67 b |
Samples | Read Number | Base Number | GC Content | % ≥ Q30 | Mapped Reads | Mapped Ratio |
---|---|---|---|---|---|---|
U. pumila L. | 25,920,122 | 7,815,753,169 | 45.72% | 92.08% | 21,715,012 | 83.78% |
U. pumila ‘Jinye’ | 26,788,118 | 8,080,109,712 | 45.70% | 92.40% | 22,450,089 | 83.81% |
KEGG Pathway | DEG | Total | Enrichment Factor | p-Value | Corrected p-Value |
---|---|---|---|---|---|
Carbon metabolism | 13 | 643 | 1.22 | 0.27 | 1.00 |
Glycolysis/Gluconeogenesis | 11 | 315 | 2.11 | 0.02 | 1.00 |
Ribosome | 10 | 823 | 0.73 | 0.89 | 1.00 |
Amino sugar and nucleotide sugar metabolism | 9 | 192 | 2.83 | 0.00 | 0.30 |
Methane metabolism | 8 | 178 | 2.71 | 0.01 | 0.63 |
Plant–pathogen interaction | 8 | 239 | 2.02 | 0.04 | 1.00 |
Biosynthesis of amino acids | 7 | 480 | 0.88 | 0.69 | 1.00 |
Galactose metabolism | 6 | 114 | 3.18 | 0.01 | 0.77 |
Starch and sucrose metabolism | 6 | 265 | 1.37 | 0.28 | 1.00 |
Pyruvate metabolism | 6 | 254 | 1.43 | 0.24 | 1.00 |
Phenylpropanoid biosynthesis | 6 | 171 | 2.12 | 0.06 | 1.00 |
RNA transport | 6 | 317 | 1.14 | 0.43 | 1.00 |
Plant hormone signal transduction | 6 | 189 | 1.92 | 0.09 | 1.00 |
Protein processing in endoplasmic reticulum | 6 | 402 | 0.90 | 0.66 | 1.00 |
Phenylalanine metabolism | 5 | 116 | 2.60 | 0.04 | 1.00 |
ABC transporters | 5 | 56 | 5.39 | 0.00 | 0.15 |
RNA degradation | 5 | 208 | 1.45 | 0.26 | 1.00 |
Spliceosome | 5 | 350 | 0.86 | 0.69 | 1.00 |
HIF-1 signaling pathway | 5 | 150 | 2.01 | 0.10 | 1.00 |
Pentose and glucuronate interconversions | 4 | 140 | 1.73 | 0.20 | 1.00 |
Ascorbate and aldarate metabolism | 4 | 90 | 2.68 | 0.06 | 1.00 |
Pyrimidine metabolism | 4 | 221 | 1.09 | 0.50 | 1.00 |
Cyanoamino acid metabolism | 4 | 67 | 3.61 | 0.02 | 1.00 |
Glyoxylate and dicarboxylate metabolism | 4 | 187 | 1.29 | 0.37 | 1.00 |
Fatty acid metabolism | 4 | 178 | 1.36 | 0.34 | 1.00 |
NF-kappa B signaling pathway | 4 | 79 | 3.06 | 0.04 | 1.00 |
Apoptosis | 4 | 110 | 2.20 | 0.11 | 1.00 |
Toll-like receptor signaling pathway | 4 | 111 | 2.18 | 0.11 | 1.00 |
Neurotrophin signaling pathway | 4 | 165 | 1.46 | 0.29 | 1.00 |
Ubiquinone and other terpenoid-quinone biosynthesis | 3 | 48 | 3.78 | 0.04 | 1.00 |
Purine metabolism | 3 | 300 | 0.60 | 0.88 | 1.00 |
Lysine degradation | 3 | 98 | 1.85 | 0.22 | 1.00 |
Tryptophan metabolism | 3 | 99 | 1.83 | 0.23 | 1.00 |
Glycerolipid metabolism | 3 | 116 | 1.56 | 0.30 | 1.00 |
Inositol phosphate metabolism | 3 | 103 | 1.76 | 0.24 | 1.00 |
Glycerophospholipid metabolism | 3 | 143 | 1.27 | 0.42 | 1.00 |
Propanoate metabolism | 3 | 98 | 1.85 | 0.22 | 1.00 |
Carbon fixation in photosynthetic organisms | 3 | 163 | 1.11 | 0.51 | 1.00 |
Carbon fixation pathways in prokaryotes | 3 | 110 | 1.65 | 0.27 | 1.00 |
Terpenoid backbone biosynthesis | 3 | 75 | 2.42 | 0.13 | 1.00 |
Zeatin biosynthesis | 3 | 23 | 7.88 | 0.01 | 0.41 |
Ribosome biogenesis in eukaryotes | 3 | 183 | 0.99 | 0.59 | 1.00 |
RNA polymerase | 3 | 74 | 2.45 | 0.12 | 1.00 |
AMPK signaling pathway | 3 | 213 | 0.85 | 0.69 | 1.00 |
Bile secretion | 3 | 64 | 2.83 | 0.09 | 1.00 |
Fructose and mannose metabolism | 2 | 109 | 1.11 | 0.54 | 1.00 |
Fatty acid degradation | 2 | 129 | 0.94 | 0.63 | 1.00 |
Photosynthesis | 2 | 56 | 2.16 | 0.24 | 1.00 |
Valine, leucine, and isoleucine degradation | 2 | 128 | 0.94 | 0.63 | 1.00 |
Glutathione metabolism | 2 | 133 | 0.91 | 0.65 | 1.00 |
Riboflavin metabolism | 2 | 24 | 5.03 | 0.06 | 1.00 |
Carotenoid biosynthesis | 2 | 29 | 4.17 | 0.08 | 1.00 |
Nitrogen metabolism | 2 | 43 | 2.81 | 0.16 | 1.00 |
Flavonoid biosynthesis | 2 | 38 | 3.18 | 0.13 | 1.00 |
Stilbenoid, diarylheptanoid, and gingerol biosynthesis | 2 | 24 | 5.03 | 0.06 | 1.00 |
Tropane, piperidine, and pyridine alkaloid biosynthesis | 2 | 46 | 2.63 | 0.18 | 1.00 |
Aminoacyl-tRNA biosynthesis | 2 | 123 | 0.98 | 0.61 | 1.00 |
Biosynthesis of unsaturated fatty acids | 2 | 84 | 1.44 | 0.41 | 1.00 |
Degradation of aromatic compounds | 2 | 23 | 5.25 | 0.05 | 1.00 |
DNA replication | 2 | 92 | 1.31 | 0.45 | 1.00 |
Protein export | 2 | 78 | 1.55 | 0.37 | 1.00 |
Cell cycle | 2 | 228 | 0.53 | 0.90 | 1.00 |
Ubiquitin mediated proteolysis | 2 | 220 | 0.55 | 0.88 | 1.00 |
Endocytosis | 2 | 211 | 0.57 | 0.87 | 1.00 |
Insulin signaling pathway | 2 | 220 | 0.55 | 0.88 | 1.00 |
Estrogen signaling pathway | 2 | 125 | 0.97 | 0.62 | 1.00 |
Thyroid hormone synthesis | 2 | 56 | 2.16 | 0.24 | 1.00 |
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Zuo, L.; Zhang, S.; Liu, Y.; Huang, Y.; Yang, M.; Wang, J. The Reason for Growth Inhibition of Ulmus pumila ‘Jinye’: Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy. Int. J. Mol. Sci. 2019, 20, 4227. https://doi.org/10.3390/ijms20174227
Zuo L, Zhang S, Liu Y, Huang Y, Yang M, Wang J. The Reason for Growth Inhibition of Ulmus pumila ‘Jinye’: Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy. International Journal of Molecular Sciences. 2019; 20(17):4227. https://doi.org/10.3390/ijms20174227
Chicago/Turabian StyleZuo, Lihui, Shuang Zhang, Yichao Liu, Yinran Huang, Minsheng Yang, and Jinmao Wang. 2019. "The Reason for Growth Inhibition of Ulmus pumila ‘Jinye’: Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy" International Journal of Molecular Sciences 20, no. 17: 4227. https://doi.org/10.3390/ijms20174227