Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance
Abstract
:1. Introduction
2. Results
2.1. Identification of eIF Family Genes in B. rapa and Arabidopsis thaliana
2.2. Phylogenetic Analysis of eIF Family Genes Sequences
2.3. Chromosomal Distribution of eIF Family Genes in B. rapa
2.4. Identification of the Physicochemical Properties of eIF Family Genes
2.5. Evolutionary Analysis of eIF Family Genes in B. rapa
2.6. Conserved Analysis of the Gene Sequences and Gene Structures
2.7. Three-Dimensional (3D) Structure and Sequence Logo Analyses of eIF Proteins
2.8. Expression Characterization of eIF Family Genes in Resistant/Susceptible Brassica rapa Lines
2.9. qRT-PCR Analyses of eIF Family Genes in Resistant/Susceptible B. rapa Lines
2.10. Differential Metabolites Analysis between the Susceptible and Resistant B. rapa Lines
3. Discussion
3.1. Evolution of eIF Family Genes
3.2. eIF Family Genes as Important Resistance Factors against Viruses in Plants
3.3. Effects of the Key Amino Acids at 3D Structure on Resistance
4. Materials and Methods
4.1. Plant Materials and TuMV Inoculation
4.2. Identification and Characterization of eIF Family Genes in A. thaliana and B. rapa
4.3. Phylogenetic Analyses of eIF Family Genes
4.4. Chromosome Distribution of eIF Family Genes
4.5. Analysis of Conserved Motifs, Gene Structures, and Cis-Acting Elements
4.6. Transcriptome Data Analysis, Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), and Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Plant Species | Genes | Effect | References |
---|---|---|---|
Arabidopsis thaliana | eIF4E | Resistance to C1YVV | [11] |
Arabidopsis thaliana | eIF(iso)4E | Resistance to TuMV/LMV | [12,13] |
Arabidopsis thaliana | eIF4G | Resistance to CMV/TCV | [14] |
Brassica rapa | eIF(iso)4E | Resistance to PPV/TuMV | [15,16,17] |
Capsicum spp. | eIF(iso)4E | Resistance to PVMV/ChiVMV | [18] |
Capsicum spp. | eIF4E | Resistance to PVY/TEV/PepMoV | [19,20,21] |
Citrullus lanatus | eIF4E | Resistance to ZYMV | [22] |
Hordeum vulgare | eIF4E | Resistance to BaMMV/BaYMV | [23] |
Lactuca sativa | eIF4E | Resistance to LMY | [24] |
Oryza sativa | eIF4G | Resistance to RTSV | [25] |
Phaseolus vulgaris | eIF4E | Resistance to BCMV/C1YVV | [26] |
Pisum sativum | eIF4E | Resistance to PsBMV/BYMV/C1YVV | [27] |
Prunus armeniaca | eIF4E | Resistance to PPV | [28] |
Prunus domestica | eIF(iso)4E | Resistance to PPV | [29] |
Ryza spp. | eIF(iso)4G | Resistance to RYMV | [30,31,32] |
Solanum habrochaites | eIF4E | Resistance to PVY/TEV | [33] |
Wheat | eIF4G and eIF(iso)4G | Interact with the tobacco etch virus (TEV) 5′ cap; initiate TEV RNA translation | [34] |
Wheat | eIF4G | Resistance to TEV | [34] |
Index | Compound | Formula | Class | Fold Change | Log2FC | Type |
---|---|---|---|---|---|---|
KMW0583 | Trans-beta-Ionone | C13H20O | Terpene | 0.4449 | −1.1685 | Down |
KMW0504 | Benzene, 1-ethenyl-4-methoxy | C9H10O | Aromatic | 2.5819 | 1.3685 | Up |
KMW0499 | 4-Methylthiazole | C4H5NS | Heterocyclic compound | 0.0067 | −7.2183 | Down |
KMW0186 | Octanal | C8H16O | Aldehyde | 2.9778 | 1.5743 | Up |
KMW0361 | Benzaldehyde, 4-ethyl | C9H10O | Aldehyde | 0.4638 | −1.1086 | Down |
KMW0110 | Allyl Isothiocyanate | C4H5NS | Ester | 0.0000 | −16.8360 | Down |
KMW0152 | Butane, 1-isothiocyanato | C5H9NS | Ester | 0.0329 | −4.9257 | Down |
QWM0007 | Butane dioic acid, diethyl ester | C8H14O4 | Ester | 0.0373 | −4.7433 | Down |
WMW0081 | Cis-2-(2-Pentenyl) furan | C9H12O | Heterocyclic compound | 0.4219 | −1.2452 | Down |
XMW0133 | 6-Methyl-6-(5-methylfuran-2-yl) heptan-2-one | C13H20O2 | Ketone | 0.4896 | −1.0303 | Down |
XMW0048 | Phenol, 2-nitro- | C6H5NO3 | Phenol | 7.2955 | 2.8670 | Up |
XMW0376 | 10-Methyltricyclo [4.3.1.1(2,5)] undecan-10-ol | C12H20O | Alcohol | 0.4898 | −1.0297 | Down |
XMW0460 | 1,3-Cyclopentadiene, 5,5-dimethyl-1,2-Dipropyl | C13H22 | Olefin | 0.2946 | −1.7634 | Down |
NMW0073 | Bicyclo-2-ene-2-carboxaldehyde, 6,6-dimethyl | C10H14O | Terpene | 0.4031 | −1.3107 | Down |
NMW0135 | Thiocyanic acid, phenylmethyl ester | C8H7NS | Sulfide | 0.3163 | −1.6605 | Down |
D27 | Benzene, (2-isothiocyanatoethyl) | C9H9NS | Sulfide | 0.0043 | −7.8497 | Down |
D218 | Cyclohexanecarboxylic acid | C7H12O2 | Acid | 0.0614 | −4.0261 | Down |
XMW0811 | Phenethyl isocyanate | C9H9NO | Ester | 0.2005 | −2.3183 | Down |
XMW0812 | Benzene, (1-methyl-1-propylpentyl) | C15H24 | Aromatic | 0.3611 | −1.4697 | Down |
XMW1102 | Vinyl trans-cinnamate | C11H10O2 | Ester | 2.1582 | 1.1099 | Up |
XMW1245 | (+)-2-Carene, 2-isopropenyl | C13H20 | Olefin | 0.4683 | −1.0946 | Down |
XMW1459 | Thiophene, 2-butyl-5-ethyl | C10H16S | Heterocyclic compound | 0.4348 | −1.2017 | Down |
XMW1481 | 5′-Hydroxy-2′,3′,4′-trimethylacetophenone | C11H14O2 | Ketone | 0.3290 | −1.6037 | Down |
D378 | 1-Butene, 4-isothiocyanato | C5H7NS | Sulfide | 0.0012 | −9.6749 | Down |
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Huang, W.; Wang, S.; Zhang, S.; Li, F.; Zhang, H.; Sun, R.; Zhang, S.; Li, G. Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance. Plants 2022, 11, 2248. https://doi.org/10.3390/plants11172248
Huang W, Wang S, Zhang S, Li F, Zhang H, Sun R, Zhang S, Li G. Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance. Plants. 2022; 11(17):2248. https://doi.org/10.3390/plants11172248
Chicago/Turabian StyleHuang, Wenyue, Shaoxing Wang, Shifan Zhang, Fei Li, Hui Zhang, Rifei Sun, Shujiang Zhang, and Guoliang Li. 2022. "Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance" Plants 11, no. 17: 2248. https://doi.org/10.3390/plants11172248
APA StyleHuang, W., Wang, S., Zhang, S., Li, F., Zhang, H., Sun, R., Zhang, S., & Li, G. (2022). Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance. Plants, 11(17), 2248. https://doi.org/10.3390/plants11172248