Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of Aquaporin Genes and Phylogenetic Analysis
2.2. Microsynteny Relationships of Four Prunus Species
2.3. Cis-Acting Regulatory Element Analysis
2.4. Gene Structure, Characteristic Motif, Physicochemical Features, In Silico Prediction of Transmembrane Domains and Subcellular Localization
2.5. Abiotic Stress Treatments
2.6. RNA Extraction and Transcript Analysis by qRT-PCR
3. Results
3.1. Identification and Analysis of Aquaporin Genes in P. avium
3.2. Analysis of Cis-Acting Regulatory Elements of the Aquaporin Gene Family of P. avium
3.3. Analysis of Exon–Intron Structure
3.4. Structural Characteristics of P. avium Aquaporins
3.4.1. P. avium NIP Subfamily
3.4.2. P. avium PIP Subfamily
3.4.3. P. avium TIP Subfamily
3.4.4. P. avium SIP Subfamily
3.4.5. P. avium XIP Subfamily
3.5. Expression Pattern of PruavAQP Genes in Different Organs
3.6. Expression Profiles of AQPs Genes in Response to Different Abiotic Stresses
4. Discussion
4.1. Identification and In Silico Characterization of the PruavAQP Gene Family
4.2. Organ-Specific Expression
4.3. Expression Profiles of PruavAQPs under Abiotic Stresses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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SF | AQP | AA | NPA I | NPA II | ar/R | WP | PP | TDP | Mw | Ip | FR | Ka/Ks | GRAVY |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PruavNIP1;1 | 281 | NPA | NPA | WVAR | Plas | CM | 6 | 29.77 | 9.30 | FSAYI | 0.6 | 0.432 | |
PruavNIP2;1 | 291 | NPA | NPA | GSGR | Plas | CM | 6 | 30.91 | 8.64 | LTAYV | 0.63 | 0.287 | |
PruavNIP4;1 | 267 | NPA | NPA | WVAR | Plas | CM | 6 | 28.18 | 6.41 | LSAYF | 0.17 | 0.722 | |
NIP | PruavNIP4:2 | 248 | NPA | NPA | WVAR | Plas | CM | 6 | 26.06 | 6.40 | LSAYI | 0.19 | 0.732 |
PruavNIP5;1 | 298 | NPS | NPI | SIGR | Plas | CM | 6 | 31.26 | 7.64 | FTAYI | 0.11 | 0.517 | |
PruavNIP5;2 | 280 | NPS | NPV | A-GR | Vacu | CM | 5 | 29.28 | 8.85 | FTAYL | 0.58 | 0.298 | |
PruavNIP6;1 | 307 | NPS | NPV | TIAR | Plas | CM | 6 | 31.89 | 8.34 | FTAYL | 0.14 | 0.415 | |
PruavNIP7;1 | 300 | NPA | NPA | AVGR | Plas | CM | 6 | 31.99 | 5.82 | YSAYI | 0.23 | 0.535 | |
PruavPIP1;1 | 286 | NPA | NPA | FHTR | Plas | CM | 5 | 30.79 | 9.28 | ESAFW | 0.45 | 0.282 | |
PruavPIP1;2 | 290 | NPA | NPA | FIGR | Plas | CM | 6 | 30.85 | 9.20 | QSAFW | 0.36 | 0.379 | |
PruavPIP1;3 | 286 | NPA | NPA | FHTR | Plas | CM | 6 | 30.66 | 9.25 | QSAFW | 0.31 | 0.331 | |
PIP | PruavPIP2;1 | 287 | NPA | NPA | FHTR | Plas | CM | 6 | 30.52 | 8.94 | QSAFW | 0.25 | 0.511 |
PruavPIP2;2 | 281 | NPA | NPA | FHTR | Plas | CM | 6 | 30.04 | 7.00 | QSAFW | 0.38 | 0.420 | |
PruavPIP2;3 | 284 | NPA | NPA | FHTR | Plas | CM | 6 | 30.07 | 6.89 | QSAFW | 0.29 | 0.505 | |
PruavPIP2;4 | 281 | NPA | NPA | FHTR | Plas | CM | 6 | 29.83 | 9.00 | QSAFW | 0.41 | 0.415 | |
PruavSIP1;1 | 240 | NPS | NPA | AVPN | Vacu | CM.VC | 5 | 25.18 | 9.82 | MAAYW | 0.35 | 0.896 | |
SIP | PruavSIP1;2 | 244 | NPT | NPA | TVPN | Chlo | CM.VC | 6 | 25.88 | 9.52 | MAAYW | 0.22 | 0.755 |
PruavSIP2;1 | 236 | NPL | NPA | SHGS | Plas | CM | 4 | 25.80 | 9.52 | FVAYW | 0.53 | 0.538 | |
PruavTIP1;1 | 252 | NPA | NPA | HIAV | Plas | VC | 6 | 25.94 | 5.54 | TSAYW | 0.18 | 0.769 | |
PruavTIP1;2 | 252 | NPA | NPA | HIAV | Vacu | VC | 6 | 26.08 | 4.78 | TSAYW | 0.25 | 0.884 | |
PruavTIP1;3 | 252 | NPA | NPA | HIAV | Plas | VC | 6 | 26.15 | 6.12 | TSAYW | 0.41 | 0.735 | |
TIP | PruavTIP2;1 | 248 | NPA | NPA | HIGR | Plas | VC | 7 | 25.40 | 6.26 | TSAYW | 0.55 | 0.941 |
PruavTIP2;2 | 248 | NPA | NPA | HIGR | Plas | VC | 6 | 25.17 | 4.86 | TSAYW | 0.44 | 0.982 | |
PruavTIP3;1 | 256 | NPA | NPA | HIGR | Plas | VC | 6 | 27.26 | 7.11 | TAAYW | 0.58 | 0.530 | |
PruavTIP4;1 | 249 | NPA | NPA | HIAR | Vacu | VC | 7 | 26.24 | 5.54 | TSAYW | 0.54 | 0.821 | |
PruavTIP5;1 | 255 | NPA | NPA | NVGC | Plas | CM.VC | 6 | 25.84 | 6.81 | VAAYW | 0.06 | 0.842 | |
XIP | PruavXIP1;1 | 304 | SLV | SPA | VIVR | Plas | CM | 6 | 32.17 | 5.97 | MCAFW | 0.43 | 0.725 |
PruavXIP2;1 | 314 | NPV | NPA | ITVR | Plas | CM | 7 | 33.85 | 7.74 | VCAFW | 0.55 | 0.665 |
Substrate | Aquaporin | Specificity-Determining Positions | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
SDP1 | SDP2 | SDP3 | SDP4 | SDP5 | SDP6 | SDP7 | SDP8 | SDP9 | ||
Ammonia Transporter | F/T | K/L/N/V | F/T | V/L/T | A | D/S | A/H/L | E/P/S | A/R/T | |
PruavTIP2;1 | T | L | I | L | A | T | H | P | V | |
Boric Acid Transporter | T/V | I/V | H/I | P | E | I/L | I/L/T | A/T | A/G/K/P | |
PruavPIP1:1 | T | I | H | P | E | L | L | T | P | |
PruavPIP1:2 | T | I | H | P | E | L | L | T | P | |
PruavPIP1:3 | T | I | H | P | E | L | L | T | P | |
PruavPIP2;1 | T | I | H | P | E | I | L | T | P | |
PruavPIP2;2 | T | I | H | P | E | I | L | T | P | |
PruavPIP2;3 | T | I | H | P | E | I | L | T | P | |
PruavPIP2;4 | T | I | H | P | E | I | L | T | P | |
PruavNIP1;1 | V | I | H | P | E | L | M | A | P | |
PruavNIP2;1 | V | I | H | P | E | I | I | A | P | |
PruavNIP4;1 | V | I | H | P | E | I | F | A | P | |
PruavNIP4;2 | V | I | H | P | E | L | F | A | P | |
PruavNIP5;1 | V | I | H | P | E | V | L | A | P | |
PruavNIP5;2 | V | I | H | P | E | L | L | A | P | |
PruavNIP6;1 | V | I | H | P | E | L | L | A | E | |
PruavNIP7;1 | I | I | H | P | E | L | L | T | P | |
PruavXIP2;1 | T | I | H | P | E | I | T | T | V | |
CO2 Transporter | I/L/V | I | C | A | I/V | D | W | D | W | |
PruavPIP1;1 | V | I | T | A | I | D | W | D | W | |
PruavPIP1;3 | V | I | T | A | I | D | W | D | W | |
PruavPIP2;2 | V | I | S | A | V | D | W | D | W | |
H2O2 Transporter | A/S | A/G | L/V | A/F/L/T/V | I/L/V | H/I/L/Q | F/Y | A/V | P | |
PruavNIP2;1 | S | A | L | L | V | I | Y | V | P | |
PruavNIP4;1 | S | A | L | L | V | L | Y | A | P | |
PruavNIP5;1 | S | A | L | V | I | L | Y | V | P | |
PruavPIP1;1 | A | G | V | F | I | H | F | V | P | |
PruavPIP1;2 | A | G | V | F | I | H | F | V | P | |
PruavPIP1;3 | A | G | V | F | I | H | F | V | P | |
PruavPIP2;1 | A | G | V | F | I | Q | F | V | P | |
PruavPIP2;2 | A | G | V | F | I | Q | F | L | P | |
PruavPIP2;3 | A | G | V | F | I | Q | F | V | P | |
PruavPIP2;4 | A | G | V | I | I | Q | F | V | P | |
PruavTIP1;1 | S | A | L | A | I | H | Y | A | P | |
PruavTIP1;3 | A | A | L | V | I | H | Y | V | P | |
PruavTIP2;1 | A | A | L | V | I | N | Y | V | P | |
PruavTIP2;2 | S | A | L | V | I | N | Y | V | P | |
PruavTIP3;1 | A | A | L | V | I | H | Y | V | P | |
PruavTIP5;1 | S | A | L | T | I | Q | Y | V | P | |
PruavXIP2;1 | A | G | L | V | V | H | F | V | P | |
Silicic acid Transporter | C/S | F/Y | A/E/L | H/R/Y | G | K/N/T | R | E/S/T | A/K/P/T | |
PruavNIP2;1 | S | F | V | H | G | N | R | S | N | |
Urea Transporter | H | P | F/I/L/T | A/C/F/L | L/M | A/G/P | G/S | G/S | N | |
PruavNIP1;1 | H | P | I | A | L | P | G | S | N | |
PruavNIP2;1 | H | P | L | A | M | P | G | S | N | |
PruavNIP5;1 | H | P | I | A | L | P | G | S | N | |
PruavNIP5;2 | H | P | I | A | L | P | G | S | N | |
PruavPIP1;1 | H | P | F | F | L | P | G | G | N | |
PruavPIP1;2 | H | P | F | F | L | P | G | G | N | |
PruavPIP1;3 | H | P | F | F | L | P | G | G | N | |
PruavPIP2;1 | H | P | F | F | L | P | G | G | N | |
PruavPIP2;2 | H | P | F | F | L | P | G | G | N | |
PruavPIP2;3 | H | P | F | F | L | P | G | G | N | |
PruavPIP2;4 | H | P | F | F | L | P | G | G | N | |
PruavTIP1;1 | H | P | F | F | L | A | G | S | N | |
PruavTIP1;2 | H | P | F | F | L | A | G | S | N | |
PruavTIP1;3 | H | P | F | A | L | P | G | S | N | |
PruavTIP2;1 | H | P | F | A | L | P | G | S | N | |
PruavTIP2;2 | H | P | L | A | L | P | G | S | N | |
PruavTIP3;1 | H | P | F | L | L | P | G | S | N | |
PruavTIP4;1 | H | P | L | L | L | A | G | S | N | |
PruavTIP5;1 | H | P | F | A | L | P | G | S | N | |
PruavXIP1;1 | H | L | F | A | V | G | G | G | N |
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Salvatierra, A.; Mateluna, P.; Toro, G.; Solís, S.; Pimentel, P. Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses. Genes 2023, 14, 940. https://doi.org/10.3390/genes14040940
Salvatierra A, Mateluna P, Toro G, Solís S, Pimentel P. Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses. Genes. 2023; 14(4):940. https://doi.org/10.3390/genes14040940
Chicago/Turabian StyleSalvatierra, Ariel, Patricio Mateluna, Guillermo Toro, Simón Solís, and Paula Pimentel. 2023. "Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses" Genes 14, no. 4: 940. https://doi.org/10.3390/genes14040940
APA StyleSalvatierra, A., Mateluna, P., Toro, G., Solís, S., & Pimentel, P. (2023). Genome-Wide Identification and Gene Expression Analysis of Sweet Cherry Aquaporins (Prunus avium L.) under Abiotic Stresses. Genes, 14(4), 940. https://doi.org/10.3390/genes14040940