Transcriptomic Analysis of Antimony Response in Tall Fescue (Festuca arundinacea)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Growth and Treatment
2.2. Measurement of Physiological Index
2.2.1. Determination of Chlorophyll Content
2.2.2. Determination of Peroxidase (POD) and Catalase (CAT) Activities
2.2.3. Measurement of Electrical Leakage (EL)
2.2.4. Measurement of Plant Height, Root Length, and Biomass
2.3. RNA Extraction and Preparation of cDNA Libraries
2.4. Raw Sequence Procession, Assembly and Functional Annotation
2.5. Gene Expression Level Quantification and Differential Expression Analysis
2.6. Function Assessment of DEGs
2.7. Statistical Analysis
3. Results
3.1. Effects of Sb on the Physiology of Tall Fescue
3.2. Sequence Analysis and Assembly
3.3. Identification of Differentially Expressed Genes (DEGs)
3.4. Functional Annotation and Classification
3.5. Functions and Processes Influenced by the Sb Treatment
3.6. DEGs Involved in Root and Leave of Tall Fescue Response to Sb Stress
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sample | Library | Raw_Reads | Raw_Bases | Clean_Reads | Clean_Bases | Error_Rate | Q20 | Q30 | GC_pct |
---|---|---|---|---|---|---|---|---|---|
Sb72h_L1 | FRAS220313374-1b | 22,116,740 | 6.64G | 21,741,555 | 6.52G | 0.03 | 97.04 | 91.97 | 53.46 |
Sb72h_L2 | FRAS220313375-2r | 22,687,115 | 6.81G | 20,303,984 | 6.09G | 0.03 | 97.4 | 92.96 | 53.01 |
Sb72h_L3 | FRAS220313376-2r | 23,069,812 | 6.92G | 22,507,637 | 6.75G | 0.03 | 96.66 | 91.42 | 53.34 |
Sb72h_R1 | FRAS220313377-2r | 20,604,720 | 6.18G | 20,219,043 | 6.07G | 0.03 | 96.3 | 90.67 | 54.35 |
Sb72h_R2 | FRAS220313378-1r | 22,914,468 | 6.87G | 22,554,162 | 6.77G | 0.03 | 95.87 | 89.81 | 55.18 |
Sb72h_R3 | FRAS220313379-1r | 22,641,644 | 6.79G | 22,273,629 | 6.68G | 0.03 | 95.9 | 89.84 | 55.04 |
Sample Name | Total Reads | Total Mapped |
---|---|---|
Sb72h_L1 | 21,741,555 | 14,385,010 (66.16%) |
Sb72h_L2 | 20,303,984 | 12,102,770 (59.61%) |
Sb72h_L3 | 22,507,637 | 14,895,776 (66.18%) |
Sb72h_R1 | 20,219,043 | 13,167,615 (65.12%) |
Sb72h_R2 | 22,554,162 | 14,825,164 (65.73%) |
Sb72h_R3 | 22,273,629 | 14,589,959 (65.50%) |
Category | ID | Description | GeneRatio | BgRatio | p Value | p Adj | Count |
---|---|---|---|---|---|---|---|
KEGG | ko03010 | Ribosome | 1788|9794 | 3422|26,033 | 6.51 × 10−40 | 2.30 × 10−37 | 1788 |
KEGG | ko00940 | Phenylpropanoid biosynthesis | 349|9794 | 609|26,033 | 6.04 × 10−12 | 1.07 × 10−9 | 349 |
KEGG | ko00360 | Phenylalanine metabolism | 139|9794 | 212|26,033 | 5.54 × 10−8 | 6.53 × 10−6 | 139 |
KEGG | ko04626 | Plant-pathogen interaction | 381|9794 | 805|26,033 | 7.36 × 10−6 | 0.000651484 | 381 |
KEGG | ko00195 | Photosynthesis | 65|9794 | 89|26,033 | 1.69 × 10−5 | 0.001199096 | 65 |
KEGG | ko00196 | Photosynthesis—antenna proteins | 39|9794 | 48|26,033 | 0.000172271 | 0.010163989 | 39 |
KEGG | ko00500 | Starch and sucrose metabolism | 318|9794 | 700|26,033 | 0.000365297 | 0.018473587 | 318 |
KEGG | ko05130 | Pathogenic Escherichia coli infection | 121|9794 | 234|26,033 | 0.000906485 | 0.033381022 | 121 |
KEGG | ko05204 | Chemical carcinogenesis | 116|9794 | 223|26,033 | 0.00097187 | 0.033381022 | 116 |
KEGG | ko00591 | Linoleic acid metabolism | 51|9794 | 79|26,033 | 0.001021212 | 0.033381022 | 51 |
KEGG | ko00906 | Carotenoid biosynthesis | 50|9794 | 77|26,033 | 0.001037263 | 0.033381022 | 50 |
KEGG | ko00982 | Drug metabolism—cytochrome P450 | 116|9794 | 225|26,033 | 0.001230914 | 0.03488579 | 116 |
KEGG | ko00980 | Metabolism of xenobiotics by cytochrome P450 | 118|9794 | 230|26,033 | 0.001281117 | 0.03488579 | 118 |
KEGG | ko04540 | Gap junction | 96|9794 | 180|26,033 | 0.001412409 | 0.035713782 | 96 |
KEGG | ko03320 | PPAR signaling pathway | 179|9794 | 398|26,033 | 0.008182979 | 0.170398495 | 179 |
KEGG | ko00941 | Flavonoid biosynthesis | 58|9794 | 108|26,033 | 0.009944045 | 0.185273251 | 58 |
Category | ID | Description | GeneRatio | BgRatio | p Value | p Adj | Count |
---|---|---|---|---|---|---|---|
KEGG | ko00280 | “Valine, leucine and isoleucine degradation” | 3|15 | 315|26,033 | 0.000702478 | 0.013792724 | 3 |
KEGG | ko00260 | “Glycine, serine and threonine metabolism” | 3|15 | 329|26,033 | 0.000795734 | 0.013792724 | 3 |
KEGG | ko00300 | Lysine biosynthesis | 2|15 | 65|26,033 | 0.000636832 | 0.013792724 | 2 |
KEGG | ko00340 | Histidine metabolism | 2|15 | 109|26,033 | 0.001732706 | 0.02252518 | 2 |
KEGG | ko00053 | Ascorbate and aldarate metabolism | 2|15 | 164|26,033 | 0.003816051 | 0.034527213 | 2 |
KEGG | ko00310 | Lysine degradation | 2|15 | 195|26,033 | 0.00532411 | 0.034527213 | 2 |
KEGG | ko00410 | beta-Alanine metabolism | 2|15 | 206|26,033 | 0.005915116 | 0.034527213 | 2 |
KEGG | ko00380 | Tryptophan metabolism | 2|15 | 222|26,033 | 0.006825951 | 0.034527213 | 2 |
KEGG | ko05204 | Chemical carcinogenesis | 2|15 | 223|26,033 | 0.006884872 | 0.034527213 | 2 |
KEGG | ko00982 | Drug metabolism—cytochrome P450 | 2|15 | 225|26,033 | 0.007003413 | 0.034527213 | 2 |
KEGG | ko00980 | Metabolism of xenobiotics by cytochrome P450 | 2|15 | 230|26,033 | 0.007303833 | 0.034527213 | 2 |
KEGG | ko00561 | Glycerolipid metabolism | 2|15 | 278|26,033 | 0.010477595 | 0.041066837 | 2 |
KEGG | ko00330 | Arginine and proline metabolism | 2|15 | 283|26,033 | 0.010837745 | 0.041066837 | 2 |
KEGG | ko01524 | Platinum drug resistance | 2|15 | 286|26,033 | 0.011056456 | 0.041066837 | 2 |
KEGG | ko00071 | Fatty acid degradation | 2|15 | 297|26,033 | 0.011875103 | 0.041167023 | 2 |
KEGG | ko00480 | Glutathione metabolism | 2|15 | 429|26,033 | 0.023639005 | 0.072307545 | 2 |
Category | ID | Description | GeneRatio | BgRatio | p Value | p Adj | Count |
---|---|---|---|---|---|---|---|
KEGG | ko00052 | Galactose metabolism | 6|25 | 301|26,033 | 6.07 × 10−7 | 3.83 × 10−5 | 6 |
KEGG | ko00860 | Porphyrin and chlorophyll metabolism | 3|25 | 155|26,033 | 0.000543294 | 0.017113772 | 3 |
KEGG | ko00500 | Starch and sucrose metabolism | 4|25 | 700|26,033 | 0.005334744 | 0.044867681 | 4 |
KEGG | ko05145 | Toxoplasmosis | 4|25 | 717|26,033 | 0.005799291 | 0.044867681 | 4 |
KEGG | ko05162 | Measles | 4|25 | 722|26,033 | 0.005940919 | 0.044867681 | 4 |
KEGG | ko05164 | Influenza A | 4|25 | 738|26,033 | 0.006409669 | 0.044867681 | 4 |
KEGG | ko00280 | “Valine, leucine and isoleucine degradation” | 3|25 | 315|26,033 | 0.004004421 | 0.044867681 | 3 |
KEGG | ko00260 | “Glycine, serine and threonine metabolism” | 3|25 | 329|26,033 | 0.004514999 | 0.044867681 | 3 |
KEGG | ko04010 | MAPK signaling pathway | 3|25 | 349|26,033 | 0.005310248 | 0.044867681 | 3 |
KEGG | ko00982 | Drug metabolism—cytochrome P450 | 2|25 | 225|26,033 | 0.021912355 | 0.092748505 | 2 |
KEGG | ko00980 | Metabolism of xenobiotics by cytochrome P450 | 2|25 | 230|26,033 | 0.022818884 | 0.092748505 | 2 |
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Li, X.; Wu, F.; Xiang, Y.; Fan, J. Transcriptomic Analysis of Antimony Response in Tall Fescue (Festuca arundinacea). Agriculture 2024, 14, 1504. https://doi.org/10.3390/agriculture14091504
Li X, Wu F, Xiang Y, Fan J. Transcriptomic Analysis of Antimony Response in Tall Fescue (Festuca arundinacea). Agriculture. 2024; 14(9):1504. https://doi.org/10.3390/agriculture14091504
Chicago/Turabian StyleLi, Xiaoqin, Fangming Wu, Yuanhang Xiang, and Jibiao Fan. 2024. "Transcriptomic Analysis of Antimony Response in Tall Fescue (Festuca arundinacea)" Agriculture 14, no. 9: 1504. https://doi.org/10.3390/agriculture14091504