Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume
Abstract
:1. Introduction
2. Results
2.1. Identification of MPK and MKK Gene Family Members
2.2. MPK and MKK Genes’ Phylogenetic Analysis and Classification
2.3. Conserved Motif, Domain, and Gene Structure of MPK and MKK Proteins in P. mume and P. mume var. tortuosa
2.4. Chromosomal Distribution and Gene Duplication Analysis
2.5. Interspecies Collinearity Analysis of the MPK and MKK Gene Family
2.6. Cis-Acting Elements in MPK and MKK Gene Promoter Prediction Analysis
2.7. Expression Pattern Analysis of MPKs and MKKs in P. mume
2.8. PmMPK and PmMKK Expression Patterns in Response to Cold Treatment
3. Discussion
4. Materials and Methods
4.1. Plant Genomic Resources
4.2. Identification of MPK and MKK Gene Family Members
4.3. Phylogenetic Analysis
4.4. Conserved Motif, Conserved Domain, and Gene Structure of MPK and MKK Proteins in P. mume and P. mume var. tortuosa
4.5. Chromosome Location, Duplication, and Synteny Analysis
4.6. Cis-Acting Element Analysis of P. mume and P. mume var. tortuosa MPK and MKK Gene Promoter Regions
4.7. PmMPK and PmMKK Gene Expression Analysis
4.8. qRT–PCR Analysis of PmMPK and PmMKK Genes
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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Species/ Gene Family | Name | Gene ID | Clade | CDS (bp) | No. of Amino Acids | Molecular Weight (kDa) | pI | Locus | Subcellular Location |
---|---|---|---|---|---|---|---|---|---|
P. mume | PmMPK1 | Pm005869 | C | 1141 | 372 | 42.71 | 6.47 | Pm2:13426673:13428592 | Nucleus |
Q. | |||||||||
MAPK | PmMPK3 | Pm000966 | A | 1135 | 370 | 42.61 | 5.62 | Pm1:5929065:5930985 | Nucleus |
PmMPK4 | Pm018234 | B | 1144 | 373 | 42.91 | 6.08 | Pm5:17007404:17011789 | Nucleus | |
PmMPK5 | Pm023935 | B | 1153 | 376 | 43.11 | 6.01 | Pm7:9355221:9358805 | Nucleus | |
PmMPK6 | Pm027774 | A | 1248 | 407 | 46.44 | 5.8 | Pm8:16998106:17001298 | Nucleus | |
PmMPK7 | Pm026678 | C | 1129 | 368 | 42.39 | 8.46 | Pm8:11162132:11163561 | Nucleus | |
PmMPK8 | Pm025094 | D | 2506 | 818 | 92.92 | 8.32 | Pm7:15979218:15985644 | Nucleus | |
PmMPK13 | Pm000736 | B | 1135 | 370 | 42.58 | 5.18 | Pm1:4461784:4464553 | Nucleus | |
PmMPK16 | Pm008036 | D | 1710 | 558 | 63.28 | 8.45 | Pm2:30424089:30427599 | Nucleus | |
PmMPK19 | Pm011269 | D | 1829 | 597 | 67.75 | 9.31 | Pm3:9959653:9963198 | Nucleus | |
PmMPK20 | Pm014593 | D | 1857 | 606 | 69.09 | 9.11 | Pm4:14063001:14066620 | Nucleus | |
P. mume var. tortuosa | PmvMPK1 | PmuVar_Chr2_1968 | C | 1141 | 372 | 42.71 | 6.47 | Chr2:14262930:14264849 | Nucleus |
PmvMPK3 | PmuVar_Chr1_3496 | A | 1135 | 370 | 42.61 | 5.62 | Chr1:26706111:26708031 | Nucleus | |
MAPK | PmvMPK4 | PmuVar_Chr5_2162 | B | 1159 | 378 | 43.56 | 6.08 | Chr5:21784736:21789120 | Nucleus |
PmvMPK6 | PmuVar_Chr8_0208 | A | 1248 | 407 | 46.42 | 5.8 | Chr8:1295418:1298610 | Nucleus | |
PmvMPK7 | PmuVar_Chr8_1256 | C | 3096 | 1011 | 115.17 | 8.99 | Chr8:7245293:7253723 | Cell membrane | |
PmvMPK8 | PmuVar_Chr7_1503 | D | 2561 | 836 | 94.75 | 8.51 | Chr7:10372791:10379229 | Nucleus | |
PmvMPK12 | PmuVar_Chr7_0255 | B | 1153 | 376 | 43.13 | 6.21 | Chr7:2387026:2390606 | Nucleus | |
PmvMPK13 | PmuVar_Chr1_3483 | B | 1135 | 370 | 42.58 | 5.18 | Chr1:26582862:26585626 | Nucleus | |
PmvMPK16 | PmuVar_Chr2_5103 | D | 1698 | 554 | 62.88 | 8.56 | Chr2:37239461:37242972 | Nucleus | |
PmvMPK17 | PmuVar_Chr2_2455 | D | 1799 | 587 | 66.31 | 6.86 | Chr2:17306082:17310386 | Nucleus | |
PmvMPK19 | PmuVar_Chr3_1670 | D | 1866 | 609 | 69.19 | 9.29 | Chr3:11546774:11551157 | Nucleus | |
PmvMPK20 | PmuVar_Chr4_3258 | D | 1878 | 613 | 69.95 | 9.06 | Chr4:25471101:25474741 | Nucleus | |
P. mume | PmMKK2 | Pm027015 | A | 1040 | 339 | 37.84 | 5.36 | Pm8:13011712:13014449 | Nucleus |
MAPKK | PmMKK3 | Pm015648 | B | 1588 | 518 | 57.79 | 5.53 | Pm4:20729768:20732555 | Nucleus |
PmMKK6 | Pm027289 | A | 1119 | 365 | 40.96 | 5.69 | Pm8:14478577:14481234 | Nucleus | |
PmMKK9-1 | Pm025044 | D | 994 | 324 | 36.17 | 7.58 | Pm7:15725552:15726526 | Nucleus | |
PmMKK9-2 | Pm007435 | D | 997 | 325 | 36.21 | 8.04 | Pm2:24735502:24736479 | Nucleus | |
PmMKK9-3 | Pm008654 | D | 1022 | 333 | 37.36 | 7.12 | Pm2:34893630:34894631 | Nucleus | |
PmMKK10 | Pm023176 | D | 1055 | 344 | 38.42 | 5.9 | Pm7:2872242:2873276 | Nucleus | |
P. mume var. tortuosa | PmvMKK2 | PmuVar_Chr8_0833 | A | 1086 | 354 | 39.50 | 5.51 | Chr8:4732675:4735395 | Nucleus |
PmvMKK3 | PmuVar_Chr4_2126 | B | 1588 | 518 | 57.77 | 5.51 | Chr4:17988174:17990962 | Nucleus | |
MAPKK | PmvMKK6 | PmuVar_Chr8_0700 | A | 1092 | 356 | 39.90 | 5.59 | Chr8:3908415:3911074 | Nucleus |
PmvMKK9−1 | PmuVar_Chr2_4435 | D | 985 | 321 | 35.95 | 7.12 | Chr2:32122931:32123896 | Nucleus | |
PmvMKK9−2 | PmuVar_Chr7_1550 | D | 994 | 324 | 36.17 | 7.58 | Chr7:10632062:10633036 | Nucleus | |
PmvMKK9−3 | PmuVar_Chr2_5667 | D | 997 | 325 | 36.08 | 7.14 | Chr2:43816380:43817357 | Nucleus | |
PmvMKK10 | PmuVar_Chr7_1991 | D | 1055 | 344 | 38.41 | 5.86 | Chr7:14554221:14555255 | Nucleus |
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Wen, Z.; Li, M.; Meng, J.; Miao, R.; Liu, X.; Fan, D.; Lv, W.; Cheng, T.; Zhang, Q.; Sun, L. Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume. Int. J. Mol. Sci. 2023, 24, 8829. https://doi.org/10.3390/ijms24108829
Wen Z, Li M, Meng J, Miao R, Liu X, Fan D, Lv W, Cheng T, Zhang Q, Sun L. Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume. International Journal of Molecular Sciences. 2023; 24(10):8829. https://doi.org/10.3390/ijms24108829
Chicago/Turabian StyleWen, Zhenying, Mingyu Li, Juan Meng, Runtian Miao, Xu Liu, Dongqing Fan, Wenjuan Lv, Tangren Cheng, Qixiang Zhang, and Lidan Sun. 2023. "Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume" International Journal of Molecular Sciences 24, no. 10: 8829. https://doi.org/10.3390/ijms24108829