Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of the Vacuolar Iron Transporter Genes from 14 Plant Species
2.2. Estimation of Vacuolar Iron Transporter Gene Gain and Loss in 14 Plant Species
2.3. Phylogeny, Gene Organization, and Conserved Motif Analysis of the Vacuolar Iron Transporter Gene Family
2.4. Estimation of Vacuolar Iron Transporter Gene Duplication Pattern in Tomato and Soybean
2.5. Site-Specific Selection Assessment and Prediction of Protein Secondary Structure
2.6. Expression Analysis of the Soybean Vacuolar Iron Transporter Gene Family based on RNA-Seq Data
2.7. Soybean Sample Preparation, RNA Isolation, Quantitative Real-Time PCR (qRT-PCR)
2.8. Network Assembly
3. Results
3.1. Identification and Distribution of Vacuolar Iron Transporter Genes in Plants
3.2. Phylogenetic Analysis, Gene Organization, and Conserved Motifs Distribution
3.3. Duplication Events of the Vacuolar Iron Transporter Genes
3.4. Selective Pressure Analysis among Different Amino Acid Sites
3.5. Divergent Expression Profiles of the Soybean Vacuolar Iron Transporter Genes in Different Tissues and under Iron Stress
3.6. Network Analysis of the Soybean Vacuolar Iron Transporter Members
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Motif | Width | Sites | E-Value | Sequences |
---|---|---|---|---|
1 | 26 | 110 | 1.5e-1588 | DSKAMJLAGFAGLVAGACSMAIGEFV |
2 | 35 | 66 | 2.1e-1225 | VSLALAVFGGLGAVLGKAPVVRSCLRVLIGGWLAM |
3 | 15 | 102 | 3.3e-987 | QWLRAAVLGANDGLV |
4 | 21 | 104 | 1.9e-1023 | NPLQAAAASALAFSVGALVPL |
5 | 21 | 98 | 2.8e-873 | SVYSQYDIEVAZMKREQEEID |
6 | 50 | 23 | 3.8e-863 | PDTEAAEVAEILSQYGJEPHEYGPVVNALRKNPQAWLDFMMKFELGLEKP |
7 | 50 | 30 | 1.5e-674 | VLASVVVTLLALLIFGYAKGRFTGNRPFLSAVQTALIGAJASAAAYGMAK |
8 | 11 | 75 | 1.5e-423 | STASLMMGVGA |
Species | Gene 1 | Gene 2 | Ks | Divergence Time (Mya) | Duplication Types |
---|---|---|---|---|---|
Solanum lycopersicum | Solyc01g1047802 | Solyc01g1048302 | 0.78947 | 26.32 | tandem duplication |
Solyc01g1048302 | Solyc01g1048202 | 0.61314 | 20.44 | tandem duplication | |
Solyc01g1048202 | Solyc01g1048102 | 0.52749 | 17.58 | tandem duplication | |
Solyc01g1048102 | Solyc01g1048002 | 0.34785 | 11.59 | tandem duplication | |
Solyc01g0918502 | Solyc04g0080602 | 0.87754 | 29.25 | transposition | |
Glycine max | Glyma.08G075900 | Glyma.08G076300 | 1.25353 | 41.78 | tandem duplication |
Glyma.08G075900 | Glyma.08G076100 | 0.65802 | 21.93 | tandem duplication | |
Glyma.08G076300 | Glyma.08G076200 | 0.16939 | 5.65 | tandem duplication | |
Glyma.08G076100 | Glyma.08G076000 | 0.18062 | 6.02 | tandem duplication | |
Glyma.08G076300 | Glyma.05G121600 | 0.14334 | 4.78 | segmental duplication | |
Glyma.08G076200 | Glyma.05G121500 | 0.08789 | 2.93 | segmental duplication | |
Glyma.08G076100 | Glyma.05G121400 | 0.16184 | 5.39 | segmental duplication | |
Glyma.08G076000 | Glyma.05G121300 | 0.1751 | 5.84 | segmental duplication | |
Glyma.08G075900 | Glyma.05G121200 | 0.19831 | 6.61 | segmental duplication | |
Glyma.08G047500 | Glyma.05G240600 | 0.10616 | 3.54 | transposition | |
Glyma.08G181900 | Glyma.15G050400 | 0.34178 | 11.39 | transposition | |
Glyma.20G166100 | Glyma.10G225900 | 0.12651 | 4.22 | transposition | |
Glyma.16G168200 | Glyma.02G082500 | 0.09795 | 3.27 | transposition |
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Cao, J. Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species. Genes 2019, 10, 144. https://doi.org/10.3390/genes10020144
Cao J. Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species. Genes. 2019; 10(2):144. https://doi.org/10.3390/genes10020144
Chicago/Turabian StyleCao, Jun. 2019. "Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species" Genes 10, no. 2: 144. https://doi.org/10.3390/genes10020144
APA StyleCao, J. (2019). Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species. Genes, 10(2), 144. https://doi.org/10.3390/genes10020144