Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (Raphanus sativus L.) Reveal Their Involvement in Clubroot Resistance
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification and Distribution of CKX and IPT Genes in Radish
2.2. Phylogenetic Analysis of RsIPT and RsCKX Gene Families
2.3. Gene Structure and Conserved Motif Analysis of the RsIPT and RsCKX Genes
2.4. Cis-Acting Elements in the Promoters of RsIPT and RsCKX Genes
2.5. Gene Duplication and Divergence of the RsIPT and RsCKX Genes
2.6. Expression Profiles of RsIPT and RsCKX Genes in Tissues and Growth Stages of Radish Root
2.7. Expression Divergences of RsIPT and RsCKX Genes after Infection with P. brassicae
2.8. Predicted Secondary Structure and 3D Structure of RsCKX Proteins
2.9. Analysis of the Interaction Networks of RsCKX Proteins
3. Discussion
4. Materials and Methods
4.1. Identifying IPT Genes and CKX Genes
4.2. Mapping IPT and CKX Genes to Chromosomes
4.3. Phylogenetic Tree Construction of RsIPT and RsCKX Gene Families
4.4. Analysis of Gene Structure and Conserved Motif
4.5. Analysis of the Promoters of RsIPT and RsCKX Genes
4.6. Analysis of Segmental Duplication, Tandem Duplication, and Collinearity between Raphanus and Arabidopsis or B. rapa
4.7. Plant Materials, Cultivation, and Treatment with P. brassicae
4.8. RNA Extraction, cDNA Synthesis, qRT-PCR, and Statistical Analysis
4.9. Expression Profile Analysis of the RsIPT and RsCKX Genes
4.10. Prediction and Analysis of Secondary Structure and 3D Structure of Proteins
4.11. Interaction Network Analysis of RsCKX Proteins
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 | Chromosome | Gene Length (bp) | Protein Length (aa) | MW (Da) | PI | Predicted Localization |
---|---|---|---|---|---|---|---|
RsIPT1 | Rsa10009818 | R07 | 1032 | 344 | 38,962.4 | 9.75 | Cytoskeleton |
RsIPT2 | Rsa10020209 | R04 | 2169 | 470 | 53,202.4 | 6.18 | Nucleus |
RsIPT3-1 | Rsa10027751 | R05 | 1312 | 333 | 37,545 | 8.27 | Chloroplast |
RsIPT3-2 | Rsa10001423 | Scaffold638 | 1151 | 218 | 25,130.6 | 7.82 | Cytoplasm |
RsIPT5-1 | Rsa10015237 | R07 | 1926 | 335 | 37,836.2 | 5.78 | Mitochondrion |
RsIPT5-2 | Rsa10023282 | R02 | 1943 | 335 | 37,872 | 5.94 | Chloroplast |
RsIPT7-1 | Rsa10028124 | R01 | 1390 | 322 | 35,774.8 | 8.57 | Chloroplast |
RsIPT7-2 | Rsa10010488 | R05 | 339 | 113 | 12,356.3 | 10.35 | Chloroplast |
RsIPT8-1 | Rsa10042487 | R05 | 1563 | 327 | 36,928.9 | 9.29 | Chloroplast |
RsIPT8-2 | Rsa10027852 | R01 | 1405 | 325 | 36,904.9 | 9.08 | Mitochondrion |
RsIPT9-1 | Rsa10023211 | R02 | 3166 | 499 | 56,375.9 | 7.18 | Chloroplast |
RsIPT9-2 | Rsa10035858 | R03 | 2755 | 467 | 52,553.9 | 8 | Chloroplast |
RsIPT10 | Rsa10008422 | R02 | 3375 | 300 | 33,134 | 5.28 | Chloroplast |
Gene Name | Gene ID | Chromosome | Gene Length (bp) | Protein Length (aa) | MW (Da) | PI | Predicted Localization |
---|---|---|---|---|---|---|---|
RsCKX1-1 | Rsa10025968 | R03 | 1709 | 432 | 48,162.5 | 7.75 | Mitochondrion |
RsCKX1-2 | Rsa10039146 | R01 | 1409 | 387 | 43,085.8 | 8.39 | Mitochondrion |
RsCKX1-3 | Rsa10011234 | R04 | 2028 | 440 | 48,832.3 | 9.22 | Mitochondrion |
RsCKX2-1 | Rsa10025912 | R09 | 4169 | 508 | 56,240.3 | 6.61 | Plasma Membrane |
RsCKX2-2 | Rsa10031296 | R01 | 8890 | 506 | 56,077 | 6.02 | Chloroplast |
RsCKX3-1 | Rsa10019391 | R02 | 2619 | 424 | 47,506.6 | 6.87 | Extracell |
RsCKX3-2 | Rsa10023843 | R09 | 2391 | 425 | 47,456.9 | 7.67 | Vacuole |
RsCKX4 | Rsa10036909 | R04 | 3204 | 469 | 51,700.7 | 6.6 | Extracell |
RsCKX5 | Rsa10034185 | R07 | 1994 | 407 | 45,073.9 | 6.06 | Chloroplast |
RsCKX6 | Rsa10027735 | R05 | 2192 | 430 | 48,062.9 | 8.48 | Mitochondrion |
RsCKX7-1 | Rsa10021101 | R07 | 3676 | 526 | 57,887.1 | 4.82 | Cytoplasm |
RsCKX7-2 | Rsa10013210 | R02 | 2058 | 421 | 45,749.1 | 4.38 | Cytoplasm |
Orthologous Pairs | Ka | Ks | Ka/Ks | MYA a | Paralogous Pairs | Ka | Ks | Ka/Ks | MYA a |
---|---|---|---|---|---|---|---|---|---|
AtIPT1/RsIPT1 | 0.15 | 0.59 | 0.26 | 19.57 | RsIPT3-1/RsIPT3-2 | 0.07 | 0.43 | 0.16 | 14.31 |
AtIPT2/RsIPT2 | 0.11 | 0.44 | 0.25 | 14.53 | RsIPT5-1/RsIPT5-2 | 0.07 | 0.47 | 0.16 | 15.66 |
AtIPT3/RsIPT3-1 | 0.08 | 0.56 | 0.14 | 18.77 | RsIPT7-1/RsIPT7-2 | 0.03 | 0.19 | 0.15 | 6.20 |
AtIPT3/RsIPT3-2 | 0.09 | 0.62 | 0.14 | 20.78 | RsIPT8-1/RsIPT8-2 | 0.12 | 0.38 | 0.30 | 12.68 |
AtIPT5/RsIPT5-1 | 0.07 | 0.54 | 0.12 | 18.13 | RsIPT9-1/RsIPT9-2 | 0.06 | 0.43 | 0.14 | 14.43 |
AtIPT5/RsIPT5-2 | 0.08 | 0.45 | 0.18 | 15.03 | RsCKX1-1/RsCKX1-2 | 0.10 | 0.44 | 0.23 | 14.72 |
AtIPT7/RsIPT7-1 | 0.07 | 0.44 | 0.15 | 14.68 | RsCKX1-1/RsCKX1-3 | 0.07 | 0.46 | 0.15 | 15.47 |
AtIPT7/RsIPT7-2 | 0.07 | 0.45 | 0.15 | 14.97 | RsCKX1-2/RsCKX1-3 | 0.09 | 0.58 | 0.16 | 19.26 |
AtIPT8/RsIPT8-1 | 0.14 | 0.61 | 0.24 | 20.17 | RsCKX2-1/RsCKX2-2 | 0.10 | 0.37 | 0.27 | 12.24 |
AtIPT8/RsIPT8-2 | 0.18 | 0.51 | 0.34 | 17.11 | RsCKX3-1/RsCKX3-2 | 0.05 | 0.34 | 0.15 | 11.47 |
AtIPT9/RsIPT9-1 | 0.10 | 0.39 | 0.26 | 12.83 | RsCKX7-1/RsCKX7-2 | 0.05 | 0.39 | 0.12 | 12.86 |
AtIPT9/RsIPT9-2 | 0.09 | 0.42 | 0.22 | 14.01 | |||||
AtCKX1/RsCKX1-1 | 0.07 | 0.38 | 0.18 | 12.73 | |||||
AtCKX1/RsCKX1-2 | 0.10 | 0.44 | 0.24 | 14.75 | |||||
AtCKX1/RsCKX1-3 | 0.07 | 0.46 | 0.15 | 15.43 | |||||
AtCKX2/RsCKX2-1 | 0.10 | 0.50 | 0.21 | 16.57 | |||||
AtCKX2/RsCKX2-2 | 0.09 | 0.49 | 0.19 | 16.42 | |||||
AtCKX3/RsCKX3-1 | 0.07 | 0.32 | 0.22 | 10.69 | |||||
AtCKX3/RsCKX3-2 | 0.07 | 0.37 | 0.18 | 12.44 | |||||
AtCKX4/RsCKX4 | 0.09 | 0.44 | 0.20 | 14.73 | |||||
AtCKX5/RsCKX5 | 0.03 | 0.48 | 0.07 | 16.10 | |||||
AtCKX6/RsCKX6 | 0.06 | 0.46 | 0.14 | 15.42 | |||||
AtCKX7/RsCKX7-1 | 0.05 | 0.53 | 0.09 | 17.56 | |||||
AtCKX7/RsCKX7-2 | 0.05 | 0.52 | 0.10 | 17.47 |
Group Type | Gene ID | Secondary Structure (%) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Hh | Gg | Ti | Bb | Ee | Tt | Ss | Cc | Ambiguous States | Other States | ||
Group I | RsCKX1-1 | 33.4 | 0 | 0 | 0 | 19.72 | 7.19 | 0 | 39.68 | 0 | 0 |
RsCKX1-2 | 28.24 | 0 | 0 | 0 | 22.28 | 7.25 | 0 | 42.23 | 0 | 0 | |
RsCKX1-3 | 30.07 | 0 | 0 | 0 | 20.5 | 6.15 | 0 | 43.28 | 0 | 0 | |
RsCKX6 | 35.2 | 0 | 0 | 0 | 18.18 | 5.83 | 0 | 40.79 | 0 | 0 | |
Group II | RsCKX2-1 | 34.12 | 0 | 0 | 0 | 18.54 | 6.71 | 0 | 40.63 | 0 | 0 |
RsCKX2-2 | 37.23 | 0 | 0 | 0 | 19.21 | 6.14 | 0 | 37.43 | 0 | 0 | |
RsCKX3-1 | 36.4 | 0 | 0 | 0 | 18.44 | 6.15 | 0 | 39.01 | 0 | 0 | |
RsCKX3-2 | 33.25 | 0 | 0 | 0 | 19.81 | 5.19 | 0 | 41.75 | 0 | 0 | |
RsCKX4 | 33.76 | 0 | 0 | 0 | 18.38 | 6.41 | 0 | 41.45 | 0 | 0 | |
Group III | RsCKX5 | 33.5 | 0 | 0 | 0 | 19.21 | 4.93 | 0 | 42.36 | 0 | 0 |
Group IV | RsCKX7-1 | 32.95 | 0 | 0 | 0 | 17.9 | 6.29 | 0 | 42.86 | 0 | 0 |
RsCKX7-2 | 31.67 | 0 | 0 | 0 | 17.38 | 6.43 | 0 | 44.52 | 0 | 0 |
RsCKX1-1 | RsCKX1-2 | RsCKX1-3 | RsCKX2-1 | RsCKX2-2 | RsCKX3-1 | RsCKX3-2 | RsCKX4 | RsCKX5 | RsCKX6 | RsCKX7-1 | RsCKX7-2 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
RsCKX1-1 | 0 | 0.017 | 0.014 | 0.532 | 0.543 | 0.541 | 0.534 | 0.529 | 0.12 | 0.085 | 0.667 | 0.662 |
RsCKX1-2 | 0 | 0.023 | 0.459 | 0.457 | 0.472 | 0.477 | 0.493 | 0.129 | 0.095 | 0.519 | 0.509 | |
RsCKX1-3 | 0 | 0.529 | 0.539 | 0.54 | 0.528 | 0.528 | 0.118 | 0.089 | 0.66 | 0.671 | ||
RsCKX2-1 | 0 | 0.075 | 0.131 | 0.134 | 0.118 | 0.518 | 0.54 | 0.833 | 0.798 | |||
RsCKX2-2 | 0 | 0.139 | 0.146 | 0.111 | 0.517 | 0.546 | 0.825 | 0.467 | ||||
RsCKX3-1 | 0 | 0.079 | 0.135 | 0.526 | 0.536 | 0.813 | 0.817 | |||||
RsCKX3-2 | 0 | 0.157 | 0.517 | 0.534 | 0.842 | 0.831 | ||||||
RsCKX4 | 0 | 0.524 | 0.529 | 0.835 | 0.774 | |||||||
RsCKX5 | 0 | 0.103 | 0.702 | 0.689 | ||||||||
RsCKX6 | 0 | 0.627 | 0.629 | |||||||||
RsCKX7-1 | 0 | 0.025 | ||||||||||
RsCKX7-2 | 0 |
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Yang, H.; Wei, X.; Lei, W.; Su, H.; Zhao, Y.; Yuan, Y.; Zhang, X.; Li, X. Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (Raphanus sativus L.) Reveal Their Involvement in Clubroot Resistance. Int. J. Mol. Sci. 2024, 25, 8974. https://doi.org/10.3390/ijms25168974
Yang H, Wei X, Lei W, Su H, Zhao Y, Yuan Y, Zhang X, Li X. Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (Raphanus sativus L.) Reveal Their Involvement in Clubroot Resistance. International Journal of Molecular Sciences. 2024; 25(16):8974. https://doi.org/10.3390/ijms25168974
Chicago/Turabian StyleYang, Haohui, Xiaochun Wei, Weiwei Lei, Henan Su, Yanyan Zhao, Yuxiang Yuan, Xiaowei Zhang, and Xixiang Li. 2024. "Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (Raphanus sativus L.) Reveal Their Involvement in Clubroot Resistance" International Journal of Molecular Sciences 25, no. 16: 8974. https://doi.org/10.3390/ijms25168974