Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Meta-Analysis of Data from the Genome-Wide Transcriptome
2.2. Differential Expression Analyses
2.3. One-Sample Proportions Test for SDGs Screening
2.4. Bioinformatics Analyses
2.5. Functional and Pathway Enrichment Analyses of SDGs
2.6. Principal Component Analyses
2.7. Plant Ontology
3. Results
3.1. Meta-Analysis of Data from the Genome-Wide Transcriptome
3.2. Global Drought Genes Screening
3.3. IWGSC Gene IDs Identification
3.4. Identification of Analyzed Genes Transcripts
3.5. Mapping of SDGs on Wheat Genome
3.6. Expression Analyses
3.7. Statistical Analysis
3.8. GO Categorization of SDGs
3.9. Gene Annotation from PlantRegMap Database
3.10. Plant Ontology Annotation Using Annotated Reference Genomes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sr # | GSE45563 | GSE47090 | GSE70443 | GSE87325 | Coutif | p-Value |
---|---|---|---|---|---|---|
1 | 31369563 | 31369563 | 31369563 | 31369563 | 4 | 4.16 × 10−23 |
2 | 25245708 | 25245708 | 25245708 | #N/A | 3 | 9.58 × 10−7 |
3 | 31369545 | 31369545 | 31369545 | #N/A | 3 | 9.58 × 10−7 |
4 | 25232126 | 25232126 | 25232126 | #N/A | 3 | 9.58 × 10−7 |
5 | #N/A | 19959095 | 19959095 | 19959095 | 3 | 9.58 × 10−7 |
6 | 14320 | 14320 | 14320 | #N/A | 3 | 9.58 × 10−7 |
7 | 25550165 | 25550165 | 25550165 | #N/A | 3 | 9.58 × 10−7 |
8 | 25270582 | 25270582 | 25270582 | #N/A | 3 | 9.58 × 10−7 |
9 | 20313737 | 20313737 | 20313737 | #N/A | 3 | 9.58 × 10−7 |
10 | 20334251 | 20334251 | 20334251 | #N/A | 3 | 9.58 × 10−7 |
11 | 25231635 | 25231635 | 25231635 | #N/A | 3 | 9.58 × 10−7 |
Genes | Accession Numbers | IWGSC Genes | Score | E-Value | Identity (%) | Chromosome | Start | End |
---|---|---|---|---|---|---|---|---|
31369563 | CD454935.1 | TraesCS3D02G120200 | 484 | 0 | 97.9 | 3D | 75946541 | 75948546 |
25245708 | CA667105.1 | TraesCS6A02G328700 | 146 | 1.50 × 10−75 | 99.3 | 6A | 562271850 | 562272738 |
31369545 | CD454917 | TraesCS2D02G000200 | 424 | 0 | 99.5 | 2D | 39478 | 40878 |
25232126 | CA653601 | TraesCS6D02G086600 | 248 | 2.50 × 10−136 | 100 | 6D | 52285210 | 52292603 |
19959095 | BJ220896 | TraesCS6D02G260700 | 696 | 0 | 99.9 | 6D | 368305109 | 368306633 |
14320 | X52867 | TraesCSU02G154600 | 507 | 0 | 98.3 | Un | 206782100 | 206784099 |
25550165 | CA734567 | TraesCS6B02G234100 | 105 | 9.40 × 10−51 | 100 | 6B | 393072749 | 393090605 |
25270582 | CA684029 | TraesCS1D02G333000 | 118 | 1.30 × 10−58 | 96.2 | 1D | 423261565 | 423269992 |
20313737 | BQ168410 | TraesCS5A02G456300 | 224 | 6.00 × 10−122 | 100 | 5A | 636429039 | 636430690 |
20334251 | BQ172428 | TraesCS6A02G240400 | 308 | 5.40 × 10−172 | 99.4 | 6A | 451659872 | 451662196 |
25231635 | CA653110 | TraesCS7B02G243600 | 235 | 3.20 × 10−128 | 99.6 | 7B | 452150743 | 452210823 |
GO Type | Description | Negative Log10 (p Adjusted) | ID | Gene Ratio | Bg. Ratio | p Value | P Adjust | Q Value | Gene ID | Count |
---|---|---|---|---|---|---|---|---|---|---|
BP | regulation of autophagy | 2.107492695 | GO:0010506 | ¼ | 3/7682 | 0.001561 | 0.007807 | 0.001644 | 25270582 | 1 |
response to auxin | 1.683984604 | GO:0009733 | ¼ | 25/7682 | 0.012957 | 0.020702 | 0.004358 | 25245708 | 1 | |
electron transport chain | 1.683984604 | GO:0022900 | ¼ | 31/7682 | 0.016047 | 0.020702 | 0.004358 | 14320 | 1 | |
regulation of transcription from RNA polymerase II promoter | 1.683984604 | GO:0006357 | ¼ | 32/7682 | 0.016562 | 0.020702 | 0.004358 | 20334251 | 1 | |
CC | Mon1-Ccz1 complex | 3.155214539 | GO:0035658 | 1/5 | 1/7148 | 0.000699 | 0.000699 | #N/A | 25270582 | 1 |
MF | RNA polymerase II transcription factor activity, sequence-specific DNA binding | 2.290980192 | GO:0000981 | ¼ | 2/7814 | 0.001024 | 0.005117 | 0.001616 | 20334251 | 1 |
D-threo-aldose 1-dehydrogenase activity | 2.290980192 | GO:0047834 | ¼ | 2/7814 | 0.001024 | 0.005117 | 0.001616 | 31369545 | 1 | |
alditol:NADP+ 1-oxidoreductase activity | 2.290980192 | GO:0004032 | ¼ | 3/7814 | 0.001535 | 0.005117 | 0.001616 | 31369545 | 1 | |
cytochrome-c oxidase activity | 2.048275717 | GO:0004129 | ¼ | 7/7814 | 0.003579 | 0.008948 | 0.002826 | 14320 | 1 |
Drought Genes | Hit ID | Organism | Description | Score | E-Value |
---|---|---|---|---|---|
TraesCS6D02G260700 | Zmw_sc01257.1. g00130.1 | Zea mays | Zoysia matrella SBP family protein | 110 | 7.00 × 10−6 |
TraesCS6D02G260700 | AT1G53160.1 | Arabidopsis thaliana | Arabidopsis thaliana squamosa promoter-binding protein-like 4 | 278 | 3.00 × 10−29 |
TraesCS6A02G240400 | AT2G46680.2 | Arabidopsis thaliana | Arabidopsis thaliana homeobox 7 | 264 | 6.00 × 10−27 |
TraesCS2D02G000200 | 678321642 | Utricularia gibba | Utricularia gibba bHLH family protein | 138 | 3.00 × 10−8 |
TraesCS2D02G000200 | AT3G59060.4 | Arabidopsis thaliana | phytochrome interacting factor 3-like 6 | - | 3.00 × 10−18 |
TraesCS6D02G086600 | kfl00432_0070 | Klebsormidium flaccidum | Klebsormidium flaccidum C3H family protein | 709 | 2.00 × 10−78 |
TraesCS6D02G086600 | AT1G29560.2 | Arabidopsis thaliana | Arabidopsis thaliana C3H family protein | 101 | 1.00 × 10−4 |
TraesCS6B02G234100 | Medtr2g092960.1 | Medicago truncatula | Medicago truncatula Trihelix family protein | 104 | 0.001 |
TraesCS6B02G234100 | AT3G58630.1 | Arabidopsis thaliana | sequence-specific DNA binding transcription factors | - | 2.00 × 10−24 |
TraesCS6A02G328700 | AT1G70510.1 | Arabidopsis thaliana | Arabidopsis thaliana KNOTTED-like from Arabidopsis thaliana 2 | 64 | 0.04 |
TraesCS1D02G333000 | No hits found | ||||
TraesCS5A02G456300 | Zmw_sc03344.1. g00030.1 | Zoysia matrella | Zoysia matrella ERF family protein | 160 | 1.00 × 10−11 |
TraesCS5A02G456300 | AT5G19790.1 | Arabidopsis thaliana | Arabidopsis thaliana related to AP2 11 | 229 | 4.00 × 10−22 |
TraesCS3D02G120200 | Tp57577_TGAC_v2_mRNA33215 | Trifolium pratense | Trifolium pratense bHLH family protein | 325 | 5.00 × 10−31 |
TraesCS3D02G120200 | AT2G22760.1 | Arabidopsis thaliana | bHLH family protein | - | 1.00 × 10−20 |
TraesCS7B02G243600 | Do013987.1 | Dichanthelium oligosanthes | Dichanthelium oligosanthes ERF family protein | 244 | 1.00 × 10−20 |
TraesCS7B02G243600 | AT5G19790.1 | Arabidopsis thaliana | related to AP2 11 | - | 2.00 × 10−18 |
ID | Description | Gene Ratio | Bg Ratio | p Value | P Adjust | Q Value | Gene ID | Count |
---|---|---|---|---|---|---|---|---|
PO:0003015 | primary root differentiation zone | 2/9 | 42/24102 | 0.000106 | 0.001957 | 0.000309 | TraesCS5A02G456300/TraesCS7B02G243600 | 2 |
PO:0005679 | Epidermis | 2/9 | 57/24102 | 0.000196 | 0.001957 | 0.000309 | TraesCS5A02G456300/TraesCS7B02G243600 | 2 |
PO:0000256 | root hair cell | 2/9 | 208/24102 | 0.002564 | 0.015719 | 0.002482 | TraesCS5A02G456300/TraesCS7B02G243600 | 2 |
PO:0004707 | fruit dehiscence zone | 1/9 | 11/24102 | 0.004101 | 0.015719 | 0.002482 | TraesCS3D02G120200 | 1 |
PO:0020128 | leaf margin | 1/9 | 16/24102 | 0.00596 | 0.015719 | 0.002482 | TraesCS3D02G120200 | 1 |
PO:0009064 | receptacle | 1/9 | 17/24102 | 0.006331 | 0.015719 | 0.002482 | TraesCS6A02G328700 | 1 |
PO:0000112 | shoot axis epidermis | 1/9 | 18/24102 | 0.006702 | 0.015719 | 0.002482 | TraesCS3D02G120200 | 1 |
PO:0000033 | fruit valve | 1/9 | 19/24102 | 0.007074 | 0.015719 | 0.002482 | TraesCS3D02G120200 | 1 |
PO:0004006 | mesophyll cell | 1/9 | 19/24102 | 0.007074 | 0.015719 | 0.002482 | TraesCS3D02G120200 | 1 |
PO:0006016 | leaf epidermis | 1/9 | 23/24102 | 0.008557 | 0.017114 | 0.002702 | TraesCS3D02G120200 | 1 |
PO:0009053 | Peduncle | 1/9 | 31/24102 | 0.011518 | 0.019813 | 0.003128 | TraesCS3D02G120200 | 1 |
PO:0020127 | primary root | 1/9 | 32/24102 | 0.011888 | 0.019813 | 0.003128 | TraesCS3D02G120200 | 1 |
PO:0006036 | root epidermis | 1/9 | 62/24102 | 0.022919 | 0.035259 | 0.005567 | TraesCS3D02G120200 | 1 |
PO:0006504 | leaf trichome | 1/9 | 81/24102 | 0.029848 | 0.04264 | 0.006733 | TraesCS3D02G120200 | 1 |
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Aqeel, M.; Ajmal, W.; Mujahid, Q.; Murtaza, M.; Almuqbil, M.; Ghazanfar, S.; Uzair, M.; Wadood, A.; Asdaq, S.M.B.; Abid, R.; et al. Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.). Genes 2022, 13, 1906. https://doi.org/10.3390/genes13101906
Aqeel M, Ajmal W, Mujahid Q, Murtaza M, Almuqbil M, Ghazanfar S, Uzair M, Wadood A, Asdaq SMB, Abid R, et al. Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.). Genes. 2022; 13(10):1906. https://doi.org/10.3390/genes13101906
Chicago/Turabian StyleAqeel, Muhammad, Wajya Ajmal, Quratulain Mujahid, Maryam Murtaza, Mansour Almuqbil, Shakira Ghazanfar, Muhammad Uzair, Ayesha Wadood, Syed Mohammed Basheeruddin Asdaq, Rameesha Abid, and et al. 2022. "Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.)" Genes 13, no. 10: 1906. https://doi.org/10.3390/genes13101906
APA StyleAqeel, M., Ajmal, W., Mujahid, Q., Murtaza, M., Almuqbil, M., Ghazanfar, S., Uzair, M., Wadood, A., Asdaq, S. M. B., Abid, R., Ali, G. M., & Khan, M. R. (2022). Genome-Wide Identification of Potential mRNAs in Drought Response in Wheat (Triticum aestivum L.). Genes, 13(10), 1906. https://doi.org/10.3390/genes13101906