Physiological and Anatomical Differences and Differentially Expressed Genes Reveal Yellow Leaf Coloration in Shumard Oak
Abstract
:1. Introduction
2. Results
2.1. Color Indices
2.2. SPAD Value and Pigment Content
2.3. Photosynthetic Characteristics and Chlorophyll Fluorescence Parameters
2.4. Anatomical Structures
2.5. Transcriptome Sequencing Results and Quality Assessment
2.6. Functional Annotation for Unigenes
2.7. DEGs Analysis and Verification
2.8. Chlorophyll and Carotenoid Biosynthetic Genes Involved in Leaf Coloration
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Color Indices Measurement
4.3. SPAD Value and Pigment Content Measurement
4.4. Photosynthetic Characteristics and Chlorophyll Fluorescence Parameters Measurement
4.5. Anatomy Observation
4.6. RNA-seq and Data Analysis
4.7. Gene Expression Analysis
4.8. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample | Total Raw Reads (M) | Total Clean Bases (Gb) | GC (%) | Q30 (%) | Adapter (%) | Low Quality (%) |
---|---|---|---|---|---|---|
SO-1 | 52.42 | 7.46 | 40.40 | 93.57 | 0.63 | 4.49 |
SO-2 | 50.78 | 7.28 | 40.40 | 95.23 | 0.56 | 3.89 |
SO-3 | 50.78 | 7.24 | 40.47 | 93.66 | 0.46 | 4.42 |
ZH-1 | 50.78 | 7.25 | 40.45 | 93.73 | 0.52 | 4.24 |
ZH-2 | 50.78 | 7.29 | 40.44 | 95.25 | 0.57 | 3.73 |
ZH-3 | 50.78 | 7.24 | 40.55 | 93.61 | 0.59 | 4.32 |
Average | 51.05 | 7.29 | 40.45 | 94.18 | 0.56 | 4.18 |
No. | Pathway Name | DEGs Num. | Pathway ID |
---|---|---|---|
1 | Carbon metabolism | 773 (5.58%) | ko01200 |
2 | Plant-pathogen interaction | 1419 (10.25%) | ko04626 |
3 | Porphyrin and chlorophyll metabolism | 152 (1.10%) | ko00860 |
4 | Peroxisome | 306 (2.21%) | ko04146 |
5 | alpha-Linolenic acid metabolism | 137 (0.99%) | ko00592 |
6 | Carbon fixation in photosynthetic organisms | 274 (1.98%) | ko00710 |
7 | Mitogen-activated protein kinase (MAPK) signaling pathway - plan | 851 (6.15%) | ko04016 |
8 | Aminoacyl-tRNA biosynthesis | 195 (1.41%) | ko00970 |
9 | Glycolysis / Gluconeogenesis | 334 (2.41%) | ko00010 |
10 | Homologous recombination | 197 (1.42%) | ko03440 |
11 | Carotenoid biosynthesis | 153 (1.11%) | ko00906 |
12 | Plant hormone signal transduction | 645 (4.66%) | ko04075 |
13 | Steroid biosynthesis | 103 (0.74%) | ko00100 |
14 | Fatty acid degradation | 189 (1.37%) | ko00071 |
15 | Glyoxylate and dicarboxylate metabolism | 292 (2.11%) | ko00630 |
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Dong, X.; Huang, L.; Chen, Q.; Lv, Y.; Sun, H.; Liang, Z. Physiological and Anatomical Differences and Differentially Expressed Genes Reveal Yellow Leaf Coloration in Shumard Oak. Plants 2020, 9, 169. https://doi.org/10.3390/plants9020169
Dong X, Huang L, Chen Q, Lv Y, Sun H, Liang Z. Physiological and Anatomical Differences and Differentially Expressed Genes Reveal Yellow Leaf Coloration in Shumard Oak. Plants. 2020; 9(2):169. https://doi.org/10.3390/plants9020169
Chicago/Turabian StyleDong, Xiaoyun, Libin Huang, Qingsheng Chen, Yunzhou Lv, Hainan Sun, and Zhenhai Liang. 2020. "Physiological and Anatomical Differences and Differentially Expressed Genes Reveal Yellow Leaf Coloration in Shumard Oak" Plants 9, no. 2: 169. https://doi.org/10.3390/plants9020169