Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions
Abstract
:1. Introduction
2. Results
2.1. Identification, Alignment, Gene Structures, Distribution, and Conserved Motifs of CAT genes in Triticum durum
2.2. Identification of the 2D and 3D Structures of Catalases in Triticum durum
2.3. Phylogenetic Analysis of TdCATs
2.4. Identification of CaM Binding Domains
2.5. In Silico Localization of TdCAT Proteins
2.6. Gene Ontology (GO) Term Distribution of Triticum turgidum ssp. durum Catalase
2.7. In Silico Analysis of Cis-Elements
3. Discussion
4. Materials and Methods
4.1. Plant Materials, RNA Isolation and Data Sources
4.2. Identification and Characterization Analysis of TdCAT Genes
4.3. Phylogenetic Analysis of TdCAT Genes
4.4. Chromosomal Localization
4.5. Conserved Motifs, and Gene Structure of TdCAT Genes
4.6. The 2D and 3D Structures of Durum Wheat Catalase
4.7. Cis-Acting Element Analysis
4.8. RNA Extraction and Quantitative Real-Time Reverse Transcription PCR (QRT-PCR)
4.9. Statistical Analysis
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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Locus/Protein Id | Gene Identifier/ORF Names/Locus Tag | Chr | Strand | EMBL ID | Star/End | N° Exon | N° Intron | Orthologs | |
---|---|---|---|---|---|---|---|---|---|
TdCAT1-4B | WDD45561.1 | TRITD_4Bv1G185220 | Chr4B | - | LT934118.1 | 620612936…. | 6 | 5 | ObCATC (XP_006649332.1; 92,07%) |
TaCAT-1 (NP_001392633.1; 99.8%) | |||||||||
620616162 | TcCAT-1 (XP_037426584.1; 99.52%) | ||||||||
TmCAT- (QBZ38484.1; 98.37%) | |||||||||
TdCAT2 | VAI41949.1 | TRITD_6Av1G007920 | Chr6A | + | LT934121.1 | 19325072…. | 3 | 2 | TcCAT2 (XP_037449913.1, 96.96%) |
19327064 | HvCAT-2 (XP_044952263.1, 96.56%) | ||||||||
TaCAT-2 (XP_044407354.1; 96.56%) | |||||||||
TdCAT3 | VAI53367.1 | TRITD_6Bv1G012280 | Chr6B | - | LT934122 | 33213343… | 4 | 3 | TcCAT-2 (XP_037454937.1; 88.06%) |
33215090 | AetCAT-2 (XP_020150180.1; 87.85%) | ||||||||
TaCAT-2 (XP_044407354.1; 87.45%) | |||||||||
TdCAT4 | VAI53359.1 | TRITD_6Bv1G012280 | Chr6B | - | LT934122 | 33213343… | 4 | 3 | TcCAT-2 (XP_037454937.1; 86.84%) |
33215090 | AetCAT-2 (XP_020150180.1; 87.04%) | ||||||||
TaCAT-2 (XP_044410694.1; 86.64%) | |||||||||
TdCAT5 | VAI10245.1 | TRITD_4Bv1G185220 | Chr4B | - | LT934118.1 | 620612936…. | 7 | 6 | TaCAT-1 (XP_044376890.1 86.60%) |
620616162 | TcCAT-1 (XP_037426584.1; 87%) | ||||||||
AetCAT-1 (XP_020164896.1; 86.40%) | |||||||||
TdCAT6 | VAI53365.1 | TRITD_6Bv1G012280 | Chr6B | - | LT934122 | 33213343… | 4 | 3 | TaCAT-1 (XP_044410694.1; 95.75%) |
33215090 | TcCAT-1 (XP_037454937.1; 95.95%) | ||||||||
AetCAT-1 (XP_020150180.1; 95.75%) |
Gene Name | Locus/Protein Id | Length | Molecular Weight (MW) | Isoelectric Point (pI) | N-Glycosylation Site |
---|---|---|---|---|---|
TdCAT1 | WDD45561.1 | 492 | 56,807.99 | 6.52 | Asn-247 |
TdCAT2 | VAI41949.1 | 510 | 58,611.25 | 6.29 | Asn-247 |
TdCAT3 | VAI53367.1 | 440 | 50,447.09 | 6.39 | Asn-247 |
TdCAT4 | VAI53366.1 | 464 | 50,316.01 | 6.97 | Asn-198 |
TdCAT5 | VAI10245.1 | 446 | 51,475.98 | 6.47 | Asn-201 |
TdCAT6 | VAI53365.1 | 475 | 54,695.84 | 6.35 | Asn 228 |
Gene Name | Aliphatic Index | Gravy | Total Number of Negatively Charged Residues (Asp + Glu): | Total Number of Positively Charged Residues (Arg + Lys): | % of Alpha Helix | % Beta Turns | % Extended Strands | % Random Coils |
---|---|---|---|---|---|---|---|---|
TdCAT-1 | 69.15 | −0.595 | 63 | 58 | 28.46 | 5.49 | 16.87 | 49.19 |
TdCAT-2 | 69.35 | −0.483 | 69 | 62 | 26.4 | 5.69 | 15.29 | 52.55 |
TdCAT-3 | 69.52 | −0.454 | 61 | 56 | 29.55 | 6.14 | 16.59 | 47.73 |
TdCAT-4 | 68.15 | −0.552 | 60 | 59 | 27.79 | 5.24 | 13.21 | 53.76 |
TdCAT-5 | 68.21 | −0.606 | 57 | 52 | 30.72 | 5.38 | 14.13 | 49.78 |
TdCAT-6 | 66.86 | −0.518 | 65 | 59 | 27.16 | 4.00 | 14.32 | 54.53 |
Gene Name | Number of Putative CaMBDs | Typical CaMBD | Position | IQ Motif | Position |
---|---|---|---|---|---|
TdCAT-1 | 4 | 3 | 48–79; 207–229 | 1 | 296–316 |
462–486 | |||||
TdCAT-2 | 4 | 3 | 58–79; 214–229 | 1 | 296–316 |
341–315 | |||||
TdCAT-3 | 3 | 2 | 59–77; 210–227 | 1 | 296–315 |
TdCAT-4 | 3 | 2 | 59–77; 241–260 | 1 | 287–305 |
TdCAT-5 | 4 | 3 | 66–87; 161–183 | 1 | 250–269 |
417–437 | |||||
TdCAT-6 | 3 | 2 | 188–210; 322–342 | 1 | 277–296 |
Gene Name | CELLO2GO Results | LocTRee | Wolf PSORT | Pannzer2 |
---|---|---|---|---|
TdCAT-1 | Peroxisomal | Peroxisomal | Peroxisomal | Peroxisomal |
TdCAT-2 | Peroxisomal | mitochondrion | Cytoplasmic | Peroxisomal |
TdCAT-3 | Peroxisomal | mitochondrion | Cytoplasmic | Peroxisomal |
TdCAT-4 | Peroxisomal | Mitochondrion | Cytoplamsic | Peroxisomal |
TdCAT-5 | Peroxisomal | Peroxisomal | Chloroplast | Peroxisomal |
TdCAT-6 | Peroxisomal | Mitochondrion | Cytoplasm | Peroxisomal |
Gene Name | Biological Process | Molecular Function |
---|---|---|
TdCAT-1 |
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TdCAT-2 |
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TdCAT-3 |
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TdCAT-4 |
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TdCAT-5 |
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TdCAT-6 |
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Ghorbel, M.; Zribi, I.; Besbes, M.; Bouali, N.; Brini, F. Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions. Plants 2023, 12, 2720. https://doi.org/10.3390/plants12142720
Ghorbel M, Zribi I, Besbes M, Bouali N, Brini F. Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions. Plants. 2023; 12(14):2720. https://doi.org/10.3390/plants12142720
Chicago/Turabian StyleGhorbel, Mouna, Ikram Zribi, Malek Besbes, Nouha Bouali, and Faiçal Brini. 2023. "Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions" Plants 12, no. 14: 2720. https://doi.org/10.3390/plants12142720
APA StyleGhorbel, M., Zribi, I., Besbes, M., Bouali, N., & Brini, F. (2023). Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions. Plants, 12(14), 2720. https://doi.org/10.3390/plants12142720