Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa
Abstract
:1. Introduction
2. Results
2.1. Identification of CDPK Family Members
2.2. Phylogenetic Analysis and Classification of CDPK Genes
2.3. Structural Characterizations and Protein Domain Conservation Analysis of PmCDPK and PmvCDPK Gene Families
2.4. Chromosome Localization of PmCDPK and PmvCDPK Gene Families
2.5. Gene Duplication and Synteny Analysis PmCDPK and PmvCDPK Gene Families
2.6. Promoter Analysis of PmCDPK and PmvCDPK Gene Families
2.7. Protein-Protein Interaction Network of PmCDPK and PmvCDPK
2.8. Expression Pattern of PmCDPKs in Different Underground and Aerial Tissues
2.9. RT-PCR of PmCDPKs under Cold Treatment
3. Discussion
4. Materials and Methods
4.1. Plants Genome Resources and Identification of CDPK Genes
4.2. Phylogenetic and Collinearity Analysis
4.3. Gene Structure, Conserved Motifs, Chromosomal Location, and Promoter Analyses
4.4. Protein Interaction Network of CDPKs
4.5. Transcriptome Data Analysis
4.6. qRT–PCR Analysis
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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Gene Name | Gene ID | Group | CDS Length (bp) | Chromosome Location | Chromosome Starting Position | Chromosome Termination Position | Protein Length (aa) | pI | Molecular Weight (kDa) | N-Myristoylation | Palmitoylation | Subcellula Localization |
---|---|---|---|---|---|---|---|---|---|---|---|---|
PmCDPK1 | Pm002913 | III | 1584 | 1 | 22,164,004 | 22,168,153 | 527 | 5.95 | 59.44 | N | Y | Cyto. |
PmCDPK2 | Pm006154 | II | 1605 | 2 | 15,149,171 | 15,152,466 | 534 | 6.07 | 60.41 | Y | Y | Chlo. |
PmCDPK3 | Pm007589 | III | 1791 | 2 | 26,332,496 | 26,337,814 | 596 | 5.49 | 67.49 | Y | Y | Plas. |
PmCDPK4 | Pm009790 | II | 1194 | 3 | 940,220 | 943,249 | 397 | 5.14 | 44.85 | ND | ND | E.R. |
PmCDPK5 | Pm011831 | II | 1638 | 3 | 14,012,305 | 14,016,582 | 545 | 6.38 | 61.19 | Y | Y | Nucl. |
PmCDPK6 | Pm012231 | II | 1605 | 3 | 17,715,387 | 17,718,099 | 534 | 5.72 | 59.76 | Y | Y | Nucl. |
PmCDPK7 | Pm012379 | III | 1602 | 3 | 19,277,893 | 19,281,650 | 533 | 5.95 | 59.92 | N | Y | Cyto. |
PmCDPK8 | Pm013203 | I | 1509 | 4 | 2,459,927 | 2,461,435 | 502 | 5.14 | 56.51 | ND | ND | Cyto. |
PmCDPK9 | Pm017091 | I | 1620 | 5 | 7,971,082 | 7,977,817 | 539 | 5.23 | 60.19 | N | N | Chlo. |
PmCDPK10 | Pm020686 | I | 1722 | 6 | 4,404,203 | 4,407,462 | 573 | 5.88 | 64.24 | N | Y | Nucl. |
PmCDPK11 | Pm022189 | I | 1494 | 6 | 14,941,879 | 14,946,305 | 497 | 5.17 | 55.77 | ND | ND | Chlo. |
PmCDPK12 | Pm025893 | III | 1317 | 8 | 6,191,749 | 6,195,770 | 438 | 6.34 | 49.38 | N | Y | Cyto. |
PmCDPK13 | Pm026064 | I | 1893 | 8 | 7,481,694 | 7,484,694 | 630 | 5.94 | 70.37 | N | Y | Chlo. |
PmCDPK14 | Pm026757 | IV | 1674 | 8 | 11,588,959 | 11,592,896 | 557 | 9.15 | 62.91 | Y | Y | Chlo. |
PmvCDPK1 | PmuVar_Chr1_1688 | III | 1584 | 1 | 15,005,082 | 15,009,232 | 527 | 5.95 | 59.44 | N | Y | Cyto. |
PmvCDPK2 | PmuVar_Chr2_2118 | II | 1605 | 2 | 15,091,603 | 15,094,609 | 534 | 6.07 | 60.39 | Y | Y | Chlo. |
PmvCDPK3 | PmuVar_Chr2_5629 | III | 1632 | 2 | 43,536,639 | 43,539,536 | 543 | 5.58 | 61.67 | Y | Y | Cyto. |
PmvCDPK4 | PmuVar_Chr2_5639 | III | 1620 | 2 | 43,605,806 | 43,610,614 | 539 | 5.67 | 61.23 | Y | Y | Cyto. |
PmvCDPK5 | PmuVar_Chr3_0208 | II | 1671 | 3 | 1,179,360 | 1,182,876 | 556 | 6.24 | 62.26 | Y | Y | Chlo. |
PmvCDPK6 | PmuVar_Chr3_2251 | II | 1638 | 3 | 16,612,214 | 16,616,505 | 545 | 6.38 | 61.19 | Y | Y | Nucl. |
PmvCDPK7 | PmuVar_Chr3_2694 | III | 1515 | 3 | 20,764,473 | 20,768,229 | 504 | 5.80 | 56.54 | N | Y | Cyto. |
PmvCDPK8 | PmuVar_Chr3_2937 | II | 1605 | 3 | 23,712,812 | 23,715,522 | 534 | 5.72 | 59.76 | Y | Y | Nucl. |
PmvCDPK9 | PmuVar_Chr4_1515 | I | 1509 | 4 | 13,779,495 | 13,781,003 | 502 | 5.21 | 56.50 | ND | ND | Chlo. |
PmvCDPK10 | PmuVar_Chr5_0743 | IV | 1575 | 5 | 7,977,018 | 7,979,900 | 524 | 5.58 | 58.21 | N | N | Cyto. |
PmvCDPK11 | PmuVar_Chr5_1007 | I | 1704 | 5 | 11,205,040 | 11,211,809 | 567 | 5.34 | 63.22 | N | N | Chlo. |
PmvCDPK12 | PmuVar_Chr6_1581 | I | 1722 | 6 | 11,753,785 | 11,756,996 | 573 | 5.88 | 64.24 | N | Y | Nucl. |
PmvCDPK13 | PmuVar_Chr6_3038 | I | 1494 | 6 | 23,843,556 | 23,847,980 | 497 | 5.17 | 55.77 | N | N | Chlo. |
PmvCDPK14 | PmuVar_Chr7_1057 | III | 1647 | 7 | 7,607,280 | 7,610,805 | 548 | 6.71 | 62.18 | N | Y | Cyto. |
PmvCDPK15 | PmuVar_Chr8_1181 | IV | 1674 | 8 | 6,815,631 | 6,819,563 | 557 | 9.21 | 62.90 | Y | Y | Chlo. |
PmvCDPK16 | PmuVar_Chr8_1868 | I | 1797 | 8 | 11,437,704 | 11,440,698 | 598 | 5.75 | 66.62 | N | Y | Chlo. |
PmvCDPK17 | PmuVar_Chr8_2100 | III | 1596 | 8 | 13,491,294 | 13,495,563 | 531 | 6.25 | 60.12 | N | Y | Cyto. |
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Miao, R.; Li, M.; Wen, Z.; Meng, J.; Liu, X.; Fan, D.; Lv, W.; Cheng, T.; Zhang, Q.; Sun, L. Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa. Plants 2023, 12, 2548. https://doi.org/10.3390/plants12132548
Miao R, Li M, Wen Z, Meng J, Liu X, Fan D, Lv W, Cheng T, Zhang Q, Sun L. Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa. Plants. 2023; 12(13):2548. https://doi.org/10.3390/plants12132548
Chicago/Turabian StyleMiao, Runtian, Mingyu Li, Zhenying Wen, Juan Meng, Xu Liu, Dongqing Fan, Wenjuan Lv, Tangren Cheng, Qixiang Zhang, and Lidan Sun. 2023. "Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa" Plants 12, no. 13: 2548. https://doi.org/10.3390/plants12132548