Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Collection
2.2. Sequence Alignment and Phylogenetic Reconstruction
2.3. Identification of Conserved Synteny
2.4. Detection of Differences between TPH Protein Sequences
2.5. Prediction of Tertiary Structures of TPH Proteins
2.6. Identification of Putative Positively Selected Sites
3. Results
3.1. Variation of tph Copy Number in Vertebrates
3.2. Phylogenetic Relationships among the tph Genes in Vertebrates
3.3. Synteny Data
3.4. Sequence Variations and Secondary Structures of the tph Genes
3.5. Predicted Three-Dimensional (3D) Structures of the TPH Proteins
3.6. Detection of Putative Positively Selected Sites in the TPH Family
4. Discussion
4.1. Possible Reasons for Variation of tph Copy Number in Vertebrates
4.2. Adaptive Evolution of TPHs in Vertebrates and Impact on Human Health
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
References
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Sample Availability: Not available. |
Class | Species Number | tph1 (tph1a) | tph1b | tph2 |
---|---|---|---|---|
Mammals | 11 | 11 | 0 | 11 |
Birds | 18 | 18 | 0 | 18 |
Reptiles | 9 | 9 | 0 | 9 |
Amphibians | 3 | 4 | 0 | 4 |
Actinopterygii | 29 | 37 | 26 | 37 |
Total | 70 | 79 | 26 | 79 |
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Xu, J.; Li, Y.; Lv, Y.; Bian, C.; You, X.; Endoh, D.; Teraoka, H.; Shi, Q. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes 2019, 10, 203. https://doi.org/10.3390/genes10030203
Xu J, Li Y, Lv Y, Bian C, You X, Endoh D, Teraoka H, Shi Q. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes. 2019; 10(3):203. https://doi.org/10.3390/genes10030203
Chicago/Turabian StyleXu, Junmin, Yanping Li, Yunyun Lv, Chao Bian, Xinxin You, Daiji Endoh, Hiroki Teraoka, and Qiong Shi. 2019. "Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey" Genes 10, no. 3: 203. https://doi.org/10.3390/genes10030203
APA StyleXu, J., Li, Y., Lv, Y., Bian, C., You, X., Endoh, D., Teraoka, H., & Shi, Q. (2019). Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes, 10(3), 203. https://doi.org/10.3390/genes10030203