Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Distribution and Classification of V. angularis AQPs
2.2. Phylogenetic Distribution of AQPs in V. angularis
2.3. Gene Structure, Organization, and Evolution of AQPs
2.4. Characterization of NPA Motifs, Transmembrane Domains, and Subcellular Localization of Adzuki Bean AQPs
2.5. Tertiary Structure of Aquaporin
2.6. Effect of Drought Stress on Plant Attributes and Soil Moisture Content
2.7. Expression Profiling of AQPs in V. angularis
3. Discussion
4. Materials and Methods
4.1. Genome-Wide Identification of Aquaporin Genes in Vigna angularis
4.2. Structural Attributes of Aquaporin Genes and Proteins
4.3. Multiple Sequence Alignments and Phylogenetic Analysis of Aquaporin Genes
4.4. Tertiary Protein Structure Prediction
4.5. Expression Profiling of Adzuki Bean AQPs
4.6. Plant Materials and Growth Conditions
4.7. RNA Extraction and qRT-PCR
4.8. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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AQPs | Gene Id | Len | ExpAA | First60 | Predicted Helix | Subcellular Localization | ||
---|---|---|---|---|---|---|---|---|
TMHMM | SOSUI | CELLO | WoLF PSORT | |||||
>VaTIP2-2 | XP_017407401.1 | 248 | 154.87 | 29.45 | 7 | 6 | Plasma membrane | Vacuole |
>VaPIP1-3 | XP_017408780.1 | 117 | 44.66 | 22.07 | 2 | 2 | Plasma membrane | Peroxisome |
>VaNIP3-3 | XP_017408931.1 | 284 | 135.19 | 40.11 | 6 | 8 | Plasma membrane | Plasma membrane |
>VaTIP4-1 | XP_017409180.1 | 246 | 145.75 | 33.54 | 7 | 6 | Plasma membrane | Vacuole |
>VaTIP1-3 | XP_017410025.1 | 250 | 148.13 | 26.18 | 7 | 6 | Plasma membrane | Plasma membrane |
>VaNIP1-3 | XP_017411834.1 | 272 | 113.48 | 20.39 | 5 | 6 | Plasma membrane | Plasma membrane |
>VaNIP1-2 | XP_017411847.1 | 272 | 128.31 | 20.56 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaNIP4-1 | XP_017413066.1 | 330 | 133.66 | 0.75 | 6 | 7 | Plasma membrane | Plasma membrane |
>VaNIP3-1 | XP_017413544.1 | 299 | 116.69 | 0.02 | 5 | 6 | Plasma membrane | Plasma membrane |
>VaPIP2-3 | XP_017414933.1 | 287 | 133.34 | 20.29 | 6 | 5 | Plasma membrane | Plasma membrane |
>VaTIP3-2 | XP_017415113.1 | 254 | 131.52 | 22.33 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP1-2 | XP_017415825.1 | 287 | 129.56 | 5.45 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaSIP1-1 | XP_017415827.1 | 248 | 130.84 | 33.04 | 6 | 5 | Plasma membrane | Plasma membrane |
>VaSIP2-1 | XP_017415846.1 | 236 | 114.37 | 42.85 | 5 | 3 | Plasma membrane | Vacuole |
>VaNIP2-1 | XP_017417585.1 | 288 | 114.17 | 11.98 | 5 | 6 | Plasma membrane | Vacuole |
>VaPIP1-4 | XP_017418201.1 | 87 | 45.08 | 27.3 | 2 | 2 | Plasma membrane | Peroxisome |
>VaPIP2-4 | XP_017419065.1 | 284 | 131.22 | 20.96 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP1-7 | XP_017419407.1 | 289 | 128.09 | 4.22 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaTIP1-2 | XP_017424211.1 | 252 | 143.82 | 25.7 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaNIP3-2 | XP_017424310.1 | 302 | 130.14 | 0.08 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaTIP2-1 | XP_017424763.1 | 248 | 151.49 | 29.42 | 6 | 7 | Plasma membrane | Plasma membrane |
>VaPIP2-5 | XP_017425377.1 | 287 | 127.98 | 19.9 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaTIP2-3 | XP_017426514.1 | 249 | 140.66 | 29.25 | 6 | 7 | Plasma membrane | Vacuole |
>VaNIP1-5 | XP_017428564.1 | 215 | 98.39 | 22.42 | 5 | 4 | Plasma membrane | Plasma membrane |
>VaTIP1-1 | XP_017429504.1 | 252 | 135.74 | 25.28 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP1-6 | XP_017430460.1 | 289 | 127.03 | 3.53 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaXIP1-1 | XP_017431397.1 | 307 | 129.32 | 17.19 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP2-7 | XP_017432054.1 | 257 | 109.36 | 22.17 | 5 | 5 | Plasma membrane | Plasma membrane |
>VaXIP2-1 | XP_017432779.1 | 270 | 130.44 | 43.24 | 6 | 7 | Plasma membrane | Plasma membrane |
>VaTIP5-1 | XP_017432819.1 | 254 | 141.01 | 26.33 | 7 | 7 | Plasma membrane | Plasma membrane |
>VaPIP2-8 | XP_017433605.1 | 282 | 129.84 | 22.14 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP2-6 | XP_017433699.1 | 285 | 130.67 | 20.66 | 6 | 5 | Plasma membrane | Plasma membrane |
>VaNIP1-4 | XP_017434552.1 | 242 | 127.5 | 24.19 | 5 | 6 | Plasma membrane | Plasma membrane |
>VaNIP1-1 | XP_017435093.1 | 273 | 129.06 | 17.44 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaSIP1-2 | XP_017438952.1 | 247 | 133.45 | 29.6 | 6 | 6 | Plasma membrane | Vacuole |
>VaPIP2-1 | XP_017439936.1 | 285 | 136.52 | 22.37 | 6 | 5 | Plasma membrane | Plasma membrane |
>VaTIP3-1 | XP_017439967.1 | 256 | 135.76 | 22.58 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP2-2 | XP_017440026.1 | 285 | 136.52 | 22.37 | 6 | 5 | Plasma membrane | Plasma membrane |
>VaPIP1-1 | XP_017442272.1 | 287 | 129.23 | 4.75 | 6 | 6 | Plasma membrane | Plasma membrane |
>VaPIP1-5 | XP_017442471.1 | 287 | 129.46 | 7.26 | 6 | 6 | Plasma membrane | Plasma membrane |
ar/R Filter | Froger’s Residues | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene ID | Length | NPA (LB) | NPA (LE) | NPA-NPA | H2 | H5 | LE1 | LE2 | P1 | P2 | P3 | P4 | P5 | Mitani’s Residue |
VaTIP2-2 | 248 | NPA | NPA | 111 | H | I | G | R | T | S | A | Y | W | P |
VaPIP1-3 | 117 | NPA | - | - | I | - | - | R | I | D | A | M | E | S |
VaNIP3-3 | 284 | NPV | - | - | T | - | - | I | Y | G | L | V | Y | F |
VaTIP4-1 | 246 | NPA | NPA | 111 | A | I | A | R | S | S | A | Y | W | P |
VaTIP1-3 | 250 | NPA | NPA | 110 | H | I | A | V | T | T | A | Y | W | P |
VaNIP1-3 | 272 | NPA | NPV | 109 | W | V | A | R | F | S | A | F | I | P |
VaNIP1-2 | 272 | NPA | NPA | 109 | W | V | A | R | F | S | A | Y | L | P |
VaNIP4-1 | 330 | NPA | NPA | 108 | A | V | G | R | Y | S | A | Y | M | P |
VaNIP3-1 | 299 | NPS | NPV | 108 | A | I | G | R | Y | T | A | Y | L | P |
VaPIP2-3 | 287 | NPA | NPA | 118 | F | H | T | R | Q | S | A | H | W | W |
VaTIP3-2 | 254 | NPA | NPA | 111 | H | I | A | R | T | A | A | F | W | P |
VaPIP1-2 | 287 | NPA | NPA | 118 | F | H | T | R | Q | S | A | H | W | W |
VaSIP1-1 | 248 | NPT | NPA | 112 | V | V | P | N | E | A | A | L | Y | W |
VaSIP2-1 | 236 | NPL | NPA | 108 | S | H | G | S | D | V | A | F | F | W |
VaNIP2-1 | 288 | NPA | NPA | 108 | A | S | G | R | F | T | A | Y | F | P |
VaPIP1-4 | 87 | NPV | - | - | I | - | - | P | I | S | S | V | F | H |
VaPIP2-4 | 284 | NPA | NPA | 118 | F | H | T | R | Q | S | A | Q | W | W |
VaPIP1-7 | 289 | NPA | NPA | 119 | F | H | T | R | E | S | A | H | W | W |
VaTIP1-2 | 252 | NPA | NPA | 111 | H | I | A | V | T | S | A | Y | W | P |
VaNIP3-2 | 302 | NPA | NPV | 108 | T | I | G | R | Y | T | A | Y | L | P |
VaTIP2-1 | 248 | NPA | NPA | 110 | H | I | G | R | T | S | A | Y | W | P |
VaPIP2-5 | 287 | NPA | NPA | 118 | F | H | T | R | Q | S | A | Q | W | W |
VaTIP2-3 | 249 | NPA | NPA | 110 | H | I | G | R | T | S | A | Y | W | P |
VaNIP1-5 | 215 | NPA | - | - | W | - | - | S | L | M | F | H | C | N |
VaTIP1-1 | 252 | NPA | NPA | 111 | H | I | A | V | T | S | A | Y | W | P |
VaPIP1-6 | 289 | NPA | NPA | 119 | F | H | T | R | E | S | A | H | W | W |
VaXIP1-1 | 307 | NPK | NPA | 158 | G | V | A | R | G | C | A | W | I | V |
VaPIP2-7 | 257 | NPA | NPA | 118 | F | H | T | R | Q | S | A | Q | W | W |
VaXIP2-1 | 270 | SPV | NPA | 129 | V | V | V | R | I | C | A | W | V | L |
VaTIP5-1 | 254 | NPA | NPA | 110 | S | V | G | C | V | A | A | Y | W | P |
VaPIP2-8 | 282 | NPA | NPA | 118 | F | H | T | R | Q | S | A | Q | W | W |
VaPIP2-6 | 285 | NPA | NPA | 118 | F | H | T | R | Q | S | A | Q | W | W |
VaNIP1-4 | 242 | NPG | NPA | 110 | W | V | A | R | F | S | A | Y | I | P |
VaNIP1-1 | 273 | NPA | NPA | 109 | W | V | A | R | F | S | A | Y | L | T |
VaSIP1-2 | 247 | NPT | NPA | 112 | I | I | P | F | E | A | A | F | Y | W |
VaPIP2-1 | 285 | NPA | NPA | 118 | F | H | T | R | Q | S | A | H | W | W |
VaTIP3-1 | 256 | NPA | NPA | 111 | H | I | A | L | T | A | S | F | W | P |
VaPIP2-2 | 285 | NPA | NPA | 118 | F | H | T | R | Q | S | A | H | W | W |
VaPIP1-1 | 287 | NPA | NPA | 118 | F | H | T | R | Q | S | A | H | W | W |
VaPIP1-5 | 287 | NPA | NPA | 119 | F | H | T | R | E | S | A | Q | W | W |
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Tayade, R.; Rana, V.; Shafiqul, M.; Nabi, R.B.S.; Raturi, G.; Dhar, H.; Thakral, V.; Kim, Y. Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress. Int. J. Mol. Sci. 2022, 23, 16189. https://doi.org/10.3390/ijms232416189
Tayade R, Rana V, Shafiqul M, Nabi RBS, Raturi G, Dhar H, Thakral V, Kim Y. Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress. International Journal of Molecular Sciences. 2022; 23(24):16189. https://doi.org/10.3390/ijms232416189
Chicago/Turabian StyleTayade, Rupesh, Varnika Rana, Mohammad Shafiqul, Rizwana Begum Syed Nabi, Gaurav Raturi, Hena Dhar, Vandana Thakral, and Yoonha Kim. 2022. "Genome-Wide Identification of Aquaporin Genes in Adzuki Bean (Vigna angularis) and Expression Analysis under Drought Stress" International Journal of Molecular Sciences 23, no. 24: 16189. https://doi.org/10.3390/ijms232416189