Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples
Abstract
:1. Introduction
2. Results
2.1. Identification and Characterization of ALMT Gene Family in Apples
2.2. Chromosome Distribution and Duplication of MdALMT Genes
2.3. Phylogenetic Analysis, Gene Duplication, and Gene Loss in Four Rosaceae Species
2.4. Positive Selection Analysis of ALMT Genes in Four Rosaceae Species
2.5. Estimation of Functional Divergence
2.6. Different Expression Patterns and Subcellular Positions of ALMT Genes
3. Discussion
4. Materials and Methods
4.1. Identification of ALMT Genes and Phylogenetic Analyses
4.2. Gene Structure and Conserved Motif Analysis of ALMTs
4.3. Syntenic Analysis of ALMTs in Apple
4.4. Gene Duplication and Gene-Loss Estimations
4.5. Detection of Positive Selection
4.6. Detection of Functional Divergence after Gene Duplication
4.7. RNA Isolation and Quantitative RT-PCR (qRT-PCR) Analysis
4.8. Subcellular Localization of Apple ALMTs in Arabidopsis Protoplasts
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene ID | Animo Acids | MW (kDa) | pI | GRAVY | Instability Index | Aliphatic Index | TMD |
---|---|---|---|---|---|---|---|
MD13G1044200 | 521 | 58.60 | 8.30 | 0.066 | 26.07 | 91.71 | 6 |
MD07G1153600 | 498 | 54.52 | 7.93 | 0.135 | 28.12 | 101.43 | 6 |
MD13G1044400 | 284 | 31.61 | 8.86 | 0.357 | 25.08 | 104.01 | 6 |
MD14G1116200 | 546 | 61.23 | 6.69 | −0.125 | 40.61 | 91.43 | 6 |
MD06G1096000 | 719 | 80.62 | 7.18 | −0.106 | 33.56 | 86.51 | 7 |
MD14G1135700 | 497 | 54.36 | 7.09 | 0.158 | 27.06 | 96.20 | 7 |
MD06G1114500 | 488 | 53.70 | 7.88 | 0.148 | 31.09 | 95.16 | 7 |
MD03G1155400 | 484 | 53.33 | 8.83 | 0.048 | 41.05 | 94.50 | 6 |
MD11G1173000 | 485 | 53.83 | 9.39 | 0.041 | 36.04 | 95.32 | 6 |
MD03G1155200 | 812 | 90.91 | 9.55 | −0.174 | 43.50 | 92.60 | 6 |
MD14G1039500 | 494 | 53.86 | 8.75 | 0.221 | 34.37 | 107.19 | 6 |
MD12G1040500 | 532 | 57.95 | 8.76 | 0.164 | 32.81 | 104.10 | 6 |
MD03G1155500 | 467 | 51.96 | 8.39 | 0.046 | 35.46 | 96.30 | 6 |
MD16G1045200 | 568 | 63.85 | 5.97 | 0.012 | 36.38 | 93.19 | 7 |
MD16G1045000 | 600 | 66.51 | 6.64 | 0.131 | 28.26 | 94.12 | 7 |
MD06G1214800 | 603 | 67.64 | 7.92 | −0.095 | 43.33 | 89.40 | 6 |
MD14G1225700 | 597 | 66.89 | 7.55 | −0.080 | 38.72 | 89.82 | 6 |
MD06G1032000 | 541 | 60.31 | 8.17 | 0.057 | 34.71 | 98.61 | 6 |
MD16G1276700 | 522 | 58.68 | 7.99 | −0.007 | 34.82 | 98.30 | 6 |
MD14G1135900 | 496 | 54.49 | 8.22 | 0.183 | 30.68 | 99.33 | 7 |
MD03G1266500 | 423 | 46.88 | 8.09 | 0.145 | 39.44 | 106.71 | 6 |
MD11G1287000 | 433 | 48.22 | 8.31 | 0.164 | 39.89 | 106.03 | 6 |
MD11G1287100 | 430 | 47.61 | 6.56 | 0.224 | 36.35 | 107.91 | 6 |
MD00G1017600 | 472 | 51.81 | 8.21 | 0.151 | 43.26 | 97.52 | 6 |
MD00G1049200 | 485 | 53.69 | 9.28 | 0.066 | 36.40 | 97.94 | 6 |
Subgroup | Null Hypothesis | Alternative Hypothesis | LRT | ||||
---|---|---|---|---|---|---|---|
-In L | ω | -In L | ω1 | ω2 | Statistic | p | |
I + II | 8024.95 | 0.27 | 8024.38 | 0.25 | 0.29 | 1.14 | >0.05 |
(I + II) + III | 7860.32 | 0.28 | 7860.08 | 0.28 | 0.30 | 0.48 | >0.05 |
(I + II + III) + VI | 9497.94 | 0.25 | 9496.27 | 0.26 | 0.21 | 3.34 | >0.05 |
VI + VII | 3210.45 | 0.22 | 3210.00 | 0.21 | 0.25 | 0.90 | >0.05 |
(VI + VII) + V | 4121.21 | 0.20 | 4114.04 | 0.22 | 0.08 | 14.34 | <0.01 |
Subgroup A | Subgroup B | θ-II Value |
---|---|---|
I | II | 0.22 ± 0.05 |
III | −0.28 ± 0.16 | |
IV | 0.21 ± 0.13 | |
V | 0.62 ± 0.04 | |
VI | 0.51 ± 0.05 | |
VII | 0.87 ± 0.30 | |
II | III | −0.25 ± 0.11 |
IV | 0.43 ± 0.04 | |
V | 0.53 ± 0.07 | |
VI | 0.65 ± 0.03 | |
VII | 0.52 ± 0.06 | |
III | IV | 0.13 ± 0.10 |
V | 0.46 ± 0.07 | |
VI | 0.25 ± 0.12 | |
VII | 0.24 ± 0.11 | |
IV | V | 0.57 ± 0.03 |
VI | 0.55 ± 0.04 | |
VII | 0.21 ± 0.11 | |
V | VI | 0.52 ± 0.05 |
VII | 0.45 ± 0.05 | |
VI | VII | 0.26 ±0.06 |
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Ma, B.; Yuan, Y.; Gao, M.; Qi, T.; Li, M.; Ma, F. Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples. Int. J. Mol. Sci. 2018, 19, 2807. https://doi.org/10.3390/ijms19092807
Ma B, Yuan Y, Gao M, Qi T, Li M, Ma F. Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples. International Journal of Molecular Sciences. 2018; 19(9):2807. https://doi.org/10.3390/ijms19092807
Chicago/Turabian StyleMa, Baiquan, Yangyang Yuan, Meng Gao, Tonghui Qi, Mingjun Li, and Fengwang Ma. 2018. "Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples" International Journal of Molecular Sciences 19, no. 9: 2807. https://doi.org/10.3390/ijms19092807