Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium
Abstract
:1. Introduction
2. Results
2.1. Concept and Components of Knowledge-Based Identification of Pathway Enzymes (KIPEs)
2.1.1. General Concept
2.1.2. Three Modes
2.1.3. Final Filtering
2.2. Technical Validation of KIPEs
2.3. The Flavonoid Biosynthesis Enzymes in Croton tiglium
2.4. Transcriptional Regulators of the Flavonoid Biosynthesis in Croton tiglium
3. Discussion
4. Materials and Methods
4.1. Retrieval of Bait and Reference Sequences
4.2. Collection of Information about Important Amino Acid Residues
4.3. Implementation and Availability of KIPEs
4.4. Phylogenetic Analysis
4.5. Transcript Abundance Quantification
4.6. Application of KIPEs for the Identification of Transcription Factors
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sequence ID | Function | Leaf | Stem | Inflorescence | Root | Seed |
---|---|---|---|---|---|---|
DN23351_c0_g1_i2 | CtPALa | 18 | 10 | 0 | 1 | 29 |
DN32981_c5_g1_i1 | CtPALb | 0 | 0 | 0 | 0 | 0 |
DN32981_c5_g1_i16 | CtPALc | 4 | 3 | 0 | 0 | 0 |
DN32981_c5_g1_i9 | CtPALd | 0 | 0 | 0 | 0 | 0 |
DN32981_c5_g1_i17 | CtPALe | 0 | 25 | 0 | 5 | 10 |
DN32981_c5_g1_i12 | CtPALf | 5 | 233 | 0 | 18 | 48 |
DN32981_c5_g1_i5 | CtPALg | 0 | 318 | 0 | 3 | 3 |
DN32981_c5_g1_i13 | CtPALh | 0 | 3 | 0 | 0 | 0 |
DN32981_c5_g1_i14 | CtPALi | 0 | 0 | 0 | 0 | 0 |
DN23351_c0_g2_i1 | CtPALj | 18 | 1 | 0 | 9 | 12 |
DN32464_c6_g3_i2 | CtC4Ha | 122 | 110 | 2 | 77 | 233 |
DN15593_c0_g1_i1 | CtC4Hb | 0 | 0 | 0 | 0 | 3 |
DN32164_c5_g1_i2 | Ct4CLa | 46 | 19 | 1 | 2 | 113 |
DN50385_c0_g1_i1 | CtCHSa | 3 | 6 | 0 | 1 | 588 |
DN27125_c0_g1_i1 | CtCHI Ia | 11 | 2 | 19 | 3 | 88 |
DN33424_c3_g3_i1 | CtF3Ha | 4 | 21 | 1 | 2 | 342 |
DN33407_c7_g7_i2 1 | CtFNS IIa | 1 | 7 | 0 | 95 | 1 |
DN33407_c7_g7_i1 1 | CtFNS IIb | 0 | 3 | 1 | 4 | 2 |
DN27999_c0_g1_i2 1 | CtFNS IIc | 0 | 2 | 0 | 75 | 0 |
DN33407_c7_g6_i4 1 | CtFNS IId | 0 | 0 | 0 | 22 | 0 |
DN252_c0_g1_i1 | CtF3′Ha | 111 | 62 | 0 | 9 | 165 |
DN32466_c16_g7_i1 | CtF3′5′Ha | 0 | 0 | 0 | 7 | 266 |
DN32466_c16_g7_i3 | CtF3′5′Hb | 0 | 0 | 0 | 0 | 3 |
DN25915_c0_g1_i3 | CtFLSa | 18 | 19 | 0 | 0 | 84 |
DN25915_c0_g2_i1 | CtFLSb | 0 | 1 | 0 | 1 | 2 |
DN27402_c0_g1_i3 | CtDFRa | 0 | 0 | 0 | 0 | 51 |
DN32893_c8_g1_i1 | CtANSa | 0 | 0 | 0 | 0 | 25 |
DN33042_c3_g1_i3 | CtLARa | 3 | 2 | 0 | 1 | 101 |
DN30161_c9_g1_i2 | CtANRa | 0 | 1 | 0 | 1 | 375 |
DN30161_c9_g1_i3 | CtANRb | 0 | 0 | 0 | 0 | 3 |
Sequence ID | Group | Leaf | Stem | Inflorescence | Root | Seed |
---|---|---|---|---|---|---|
DN30455_c10_g1_i1 | Subgroup 7 | 0 | 1 | 0 | 0 | 4 |
DN21046_c0_g1_i3 | Subgroup 7 | 0 | 0 | 0 | 0 | 0 |
DN21046_c0_g1_i2 | Subgroup 7 | 0 | 1 | 0 | 0 | 9 |
DN28041_c1_g1_i4 | Subgroup 6 | 0 | 0 | 0 | 0 | 7 |
DN28041_c1_g1_i2 | Subgroup 6 | 0 | 0 | 0 | 0 | 0 |
DN33356_c3_g1_i2 | Subgroup 6 | 0 | 0 | 0 | 0 | 4 |
DN31144_c5_g1_i2 | MYB123 | 0 | 0 | 0 | 10 | 29 |
DN33314_c5_g2_i2 | MYB123 | 3 | 8 | 0 | 1 | 14 |
DN33314_c5_g2_i3 | MYB123 | 0 | 0 | 0 | 0 | 1 |
DN33314_c5_g2_i4 | MYB123 | 1 | 2 | 0 | 0 | 6 |
DN31260_c4_g2_i2 | MYB123 | 0 | 0 | 0 | 0 | 5 |
DN30681_c1_g1_i1 | bHLH2 | 0 | 0 | 0 | 0 | 0 |
DN30681_c1_g1_i2 | bHLH2 | 0 | 2 | 0 | 2 | 4 |
DN30681_c1_g1_i3 | bHLH2 | 0 | 0 | 0 | 0 | 0 |
DN30681_c1_g1_i6 | bHLH2 | 0 | 0 | 0 | 0 | 0 |
DN30681_c1_g1_i7 | bHLH2 | 2 | 13 | 0 | 16 | 16 |
DN30681_c1_g1_i8 | bHLH2 | 2 | 9 | 0 | 20 | 18 |
DN30681_c1_g1_i9 | bHLH2 | 0 | 0 | 0 | 0 | 0 |
DN32219_c4_g2_i2 | bHLH42 | 0 | 0 | 0 | 0 | 0 |
DN32219_c4_g2_i5 | bHLH42 | 0 | 0 | 0 | 0 | 2 |
DN32219_c4_g2_i12 | bHLH42 | 0 | 0 | 0 | 0 | 2 |
DN32219_c4_g2_i11 | bHLH42 | 0 | 0 | 0 | 0 | 3 |
DN32219_c4_g2_i4 | bHLH42 | 0 | 1 | 0 | 0 | 25 |
DN32219_c4_g2_i7 | bHLH42 | 0 | 0 | 0 | 0 | 4 |
DN32219_c4_g2_i8 | bHLH42 | 0 | 0 | 0 | 0 | 5 |
DN32272_c1_g1_i1 | TTG1 | 0 | 0 | 0 | 0 | 0 |
DN32272_c1_g2_i2 | TTG1 | 12 | 8 | 4 | 10 | 9 |
DN32604_c4_g1_i2 | TTG1 | 0 | 1 | 0 | 1 | 1 |
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Pucker, B.; Reiher, F.; Schilbert, H.M. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. Plants 2020, 9, 1103. https://doi.org/10.3390/plants9091103
Pucker B, Reiher F, Schilbert HM. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. Plants. 2020; 9(9):1103. https://doi.org/10.3390/plants9091103
Chicago/Turabian StylePucker, Boas, Franziska Reiher, and Hanna Marie Schilbert. 2020. "Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium" Plants 9, no. 9: 1103. https://doi.org/10.3390/plants9091103
APA StylePucker, B., Reiher, F., & Schilbert, H. M. (2020). Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. Plants, 9(9), 1103. https://doi.org/10.3390/plants9091103