Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis
Abstract
1. Introduction
2. Results
2.1. Identification and Characteristics of HSP70 and HSP90 Genes in T. septentrionalis
2.2. Phylogenetic Analysis of HSP70 and HSP90 Genes
2.3. Gene Structure and Chromosome Distribution Analysis
2.4. Motif and Conserved Domain Analysis
2.5. Protein Structure Prediction and Subcellular Localization
2.6. Signal Peptide Prediction, Transmembrane Structural Domain Prediction and Selection Test on Duplicated HSP70 and HSP90 Gene Pairs
2.7. Expression Patterns of HSP70 and HSP90 Genes in Tissues of T. septentrionalis
2.8. Expression Patterns of HSP70 and HSP90 Genes during Different Developmental Stages of T. septentrionalis
2.9. Expression Patterns of HSP70 and HSP90 Genes in Abiotic Stresses of T. septentrionalis
2.10. qPCR Validation of HSP70 and HSP90 Genes Expression Patterns under Abiotic Stresses
3. Discussion
4. Materials and Methods
4.1. Identification and Nomenclature of HSP70 and HSP90 Gene Family Members in T. septentrionalis
4.2. Physicochemical Property Analysis and Phylogenetic Analysis
4.3. Gene Structure, Chromosome Distribution Analysis, Motif, and Conserved Domain Analysis
4.4. Protein Structure and Subcellular Localization
4.5. Signal Peptides Prediction, Transmembrane Structural Domain Prediction and Selection Test of Duplicated HSP70 and HSP90 Genes
4.6. Expression Profiles of HSP70 and HSP90 Genes in Tissues of T. septentrionalis
4.7. Expression Profiles of HSP70 and HSP90 Genes during Different Developmental Stages of T. septentrionalis
4.8. Expression Profiles of HSP70 and HSP90 Genes under Abiotic Stresses
4.9. Quantitative Real-Time PCR (qPCR)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | NCBI Accession Number | Number of Amino Acid | Molecular Weight (Da) | Theoretical pI | Instability Index | Aliphatic Index | Grand Average of Hydropathicity |
---|---|---|---|---|---|---|---|
hsp70 | PP349927 | 639 | 70,266.65 | 5.44 | 36.44 | 84.98 | −0.423 |
hspa1b | PP349926 | 639 | 70,106.24 | 5.53 | 37.52 | 83.93 | −0.412 |
hspa4 | PP349928 | 846 | 95,013.44 | 5.04 | 43.03 | 72.97 | −0.628 |
hspa4a | PP349923 | 842 | 94,144.84 | 5.17 | 43.54 | 76.28 | −0.534 |
hspa4l | PP349922 | 832 | 92,954.52 | 5.46 | 41.20 | 79.68 | −0.487 |
hspa5 | PP349929 | 656 | 72,413.78 | 4.97 | 30.55 | 84.39 | −0.482 |
hspa8.1 | PP357443 | 515 | 56,702.91 | 5.90 | 36.45 | 81.98 | −0.405 |
hspa8.2 | PP349925 | 647 | 70,877.18 | 5.27 | 39.45 | 81.82 | −0.422 |
hspa9 | PP349930 | 688 | 74,170.99 | 6.24 | 45.59 | 81.79 | −0.374 |
hspa13 | PP339453 | 442 | 47,831.97 | 5.52 | 40.48 | 102.15 | 0.082 |
hspa14 | PP349924 | 506 | 54,814.52 | 5.66 | 38.49 | 94.43 | −0.052 |
hyou1 | PP349931 | 945 | 106,412.40 | 6.03 | 45.14 | 79.47 | −0.527 |
hsp90aa1 | PP349934 | 725 | 83,238.60 | 5.06 | 35.70 | 82.81 | −0.625 |
hsp90ab1 | PP349932 | 724 | 83,206.20 | 4.87 | 39.91 | 82.56 | −0.640 |
hsp90b1 | PP349933 | 801 | 91,991.32 | 4.74 | 38.96 | 79.38 | −0.693 |
trap1 | PP349935 | 719 | 81,840.08 | 5.99 | 45.54 | 83.99 | −0.440 |
Gene Name | α Helix | Extended Strand | β Turn | Random Coil | Subcellular Location | Three-Dimensional Structural Quality Parameters |
---|---|---|---|---|---|---|
hsp70 | 42.10% | 18.47% | 5.95% | 33.49% | Nucleus | 94.0% |
hspa1b | 42.57% | 18.94% | 7.20% | 31.30% | Cytosol | 94.5% |
hspa4 | 42.55% | 14.18% | 3.07% | 40.19% | Cytosol | 90.6% |
hspa4a | 43.11% | 14.01% | 3.09% | 39.79% | Cytosol | 92.2% |
hspa4l | 43.63% | 14.06% | 3.25% | 39.06% | Cytosol | 91.9% |
hspa5 | 43.75% | 18.60% | 6.71% | 30.95% | Endoplasmic reticulum | 93.6% |
hspa8.1 | 33.79% | 23.30% | 8.54% | 34.37% | Cytosol | 93.2% |
hspa8.2 | 41.58% | 17.77% | 6.96% | 33.69% | Cytosol | 93.8% |
hspa9 | 43.75% | 19.77% | 8.14% | 28.34% | mitochondrion | 92.9% |
hspa13 | 40.27% | 21.27% | 5.66% | 32.81% | Endoplasmic reticulum | 93.7% |
hspa14 | 34.78% | 24.90% | 5.14% | 35.18% | Cytosol | 93.6% |
hyou1 | 48.99% | 13.23% | 3.28% | 34.50% | Endoplasmic reticulum | 89.9% |
hsp90aa1 | 52.55% | 13.66% | 5.38% | 28.41% | Cytosol | 89.5% |
hsp90ab1 | 50.14% | 13.54% | 4.56% | 31.77% | Cytosol | 90.4% |
hsp90b1 | 54.68% | 12.36% | 3.75% | 29.21% | Endoplasmic reticulum | 88.2% |
trap1 | 45.20% | 13.77% | 5.70% | 35.33% | mitochondrion | 88.8% |
Gene Pair | Ka | Ks | Ka/Ks |
---|---|---|---|
hsp70-hspa1b | 0.104125523 | 0.918427 | 0.113374 |
hspa4-hspa4a | 0.175276849 | 1.508566 | 0.116188 |
hspa4-hspa4l | 0.307067194 | 1.683617 | 0.182385 |
hspa4a-hspa4l | 0.285118286 | 1.702043 | 0.167515 |
hspa8.1-hspa8.2 | 0.06700074 | 1.461276 | 0.045851 |
hsp90aa1-hsp90ab1 | 0.116635393 | 1.012976 | 0.115141 |
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Chen, Y.; Chang, Q.; Fang, Q.; Zhang, Z.; Wu, D.; Bian, L.; Chen, S. Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis. Int. J. Mol. Sci. 2024, 25, 5706. https://doi.org/10.3390/ijms25115706
Chen Y, Chang Q, Fang Q, Zhang Z, Wu D, Bian L, Chen S. Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis. International Journal of Molecular Sciences. 2024; 25(11):5706. https://doi.org/10.3390/ijms25115706
Chicago/Turabian StyleChen, Ying, Qing Chang, Qinmei Fang, Ziyang Zhang, Dan Wu, Li Bian, and Siqing Chen. 2024. "Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis" International Journal of Molecular Sciences 25, no. 11: 5706. https://doi.org/10.3390/ijms25115706
APA StyleChen, Y., Chang, Q., Fang, Q., Zhang, Z., Wu, D., Bian, L., & Chen, S. (2024). Genome-Wide Identification, Molecular Characterization, and Expression Analysis of the HSP70 and HSP90 Gene Families in Thamnaconus septentrionalis. International Journal of Molecular Sciences, 25(11), 5706. https://doi.org/10.3390/ijms25115706