Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)
Abstract
:1. Introduction
2. Results
2.1. Identification of AGC Gene Family Members in Oryza Genus
2.2. Characterization and Phylogenetic Relation of OsAGC Gene Family Members in Rice
2.3. Analysis of Gene Structures and Conserved Motifs
2.4. Collinearity Analysis of AGC Genes in Oryza Genus
2.5. Gene–CDS–Haplotype (gcHap) Analysis of AGC Genes in 3010 Rice Genomes (3KRG)
2.6. Analysis of Cis-Regulatory Elements (CREs) in the Promoters of OsAGCs
2.7. Tissue-Specific Expression Analysis of OsAGC Genes
2.8. OsAGCs That May Function in Rice Photosynthesis
3. Discussion
4. Materials and Methods
4.1. Identification of AGC Genes from Rice
4.2. Characteristics, Gene Structure, Motif and Phylogenetic Relationship Analysis of AGC Gene Family
4.3. Collinearity Analysis of AGC Genes
4.4. gcHap Analysis of the AGC Genes in 3KRG
4.5. Identification of Cis-Regulatory Elements (CREs)
4.6. Expression and Interaction Analysis of OsAGC Gene Family
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 | Locus ID | Chr | Size (aa) | MW(Da) | pI | Subcellular Location |
---|---|---|---|---|---|---|
OsAGC1 | Os01g0174700 | 1 | 493 | 54,366 | 8.86 | Nucleus |
OsAGC2 | Os01g0233800 | 1 | 532 | 57,906 | 9.14 | Nucleus |
OsAGC3 | Os01g0872800 | 1 | 498 | 55,384 | 6.54 | Nucleus |
OsAGC4 | Os02g0603000 | 2 | 447 | 47,166 | 8.37 | Nucleus |
OsAGC5 | Os02g0654300 | 2 | 690 | 74,999 | 6.15 | endomembrane |
OsAGC6 | Os02g0725000 | 2 | 588 | 65,088 | 8.06 | Nucleus |
OsAGC7 | Os03g0334000 | 3 | 480 | 53,316 | 6.29 | Nucleus |
OsAGC8 | Os03g0711800 | 3 | 1267 | 138,833 | 5.94 | endomembrane |
OsAGC9 | Os04g0304200 | 4 | 771 | 86,407 | 8.46 | Nucleus |
OsAGC10 | Os04g0488700 | 4 | 462 | 49,336 | 5.65 | Nucleus |
OsAGC11 | Os04g0546300 | 4 | 695 | 75,638 | 6.38 | Nucleus |
OsAGC12 | Os05g0237400 | 5 | 574 | 61,434 | 7.00 | Nucleus |
OsAGC13 | Os06g0291600 | 6 | 589 | 64,808 | 8.38 | chloroplast |
OsAGC14 | Os07g0680900 | 7 | 419 | 46,867 | 7.87 | Nucleus |
OsAGC15 | Os08g0491200 | 8 | 594 | 65,034 | 8.74 | plasma membrane |
OsAGC16 | Os09g0258500 | 9 | 567 | 61,832 | 8.21 | Nucleus |
OsAGC17 | Os09g0478500 | 9 | 583 | 63,813 | 7.18 | Nucleus |
OsAGC18 | Os09g0486700 | 9 | 455 | 49,179 | 6.34 | plasma membrane |
OsAGC19 | Os10g0562500 | 10 | 426 | 46,678 | 9.21 | Nucleus |
OsAGC20 | Os11g0102200 | 11 | 921 | 103,437 | 8.35 | Nucleus |
OsAGC21 | Os11g0150700 | 11 | 458 | 49,130 | 6.43 | Nucleus |
OsAGC22 | Os12g0101800 | 12 | 668 | 76,000 | 8.31 | chloroplast |
OsAGC23 | Os12g0149700 | 12 | 338 | 36,565 | 6.28 | endomembrane |
OsAGC24 | Os12g0480200 | 12 | 430 | 48,355 | 6.39 | Nucleus |
OsAGC25 | Os12g0614600 | 12 | 484 | 51,769 | 9.50 | chloroplast outer membrane |
OsAGC26 | Os12g0621500 | 12 | 1021 | 113,490 | 5.32 | Nucleus |
Oryza Species | Gene Pairs | Ka | Ks | Ka/Ks | Date (Mya) | Type of Selection | Type of Duplication |
---|---|---|---|---|---|---|---|
O. sativa, japonica | OsAGC2/OsAGC12 | 0.23 | 0.66 | 0.35 | 36.26 | Purifying | Segmental/WGD |
OsAGC4/OsAGC10 | 0.21 | 0.46 | 0.45 | 25.44 | Purifying | Segmental/WGD | |
OsAGC5/OsAGC11 | 0.12 | 1.08 | 0.11 | 59.56 | Purifying | Segmental/WGD | |
OsAGC15/OsAGC17 | 0.10 | 0.96 | 0.10 | 52.91 | Purifying | Segmental/WGD | |
OsAGC21/OsAGC23 | 0.05 | 0.17 | 0.27 | 9.34 | Purifying | Segmental/WGD | |
O. sativa, indica | BGIOSGA003082/BGIOSGA019454 | 0.23 | 0.65 | 0.34 | 35.93 | Purifying | Segmental/WGD |
BGIOSGA034806/BGIOSGA036995 | 0.08 | 0.20 | 0.40 | 10.93 | Purifying | Segmental/WGD | |
BGIOSGA006096/BGIOSGA014831 | 0.21 | 0.46 | 0.45 | 25.44 | Purifying | Segmental/WGD | |
BGIOSGA010794/BGIOSGA026398 | 0.14 | 1.13 | 0.12 | 62.25 | Purifying | Segmental/WGD | |
BGIOSGA028896/BGIOSGA030968 | 0.09 | 0.97 | 0.09 | 53.19 | Purifying | Segmental/WGD | |
O. nivara | ONIVA01G18870/ONIVA12G02630 | 0.05 | 0.22 | 0.25 | 12.25 | Purifying | Segmental/WGD |
ONIVA01G10990/ONIVA05G08820 | 0.22 | 0.64 | 0.34 | 35.39 | Purifying | Segmental/WGD | |
ONIVA02G28770/ONIVA04G18870 | 0.12 | 1.08 | 0.11 | 59.34 | Purifying | Segmental/WGD | |
ONIVA03G17320/ONIVA07G26170 | 0.11 | 1.06 | 0.10 | 58.30 | Purifying | Segmental/WGD | |
ONIVA08G20900/ONIVA09G14540 | 0.09 | 0.97 | 0.10 | 53.08 | Purifying | Segmental/WGD | |
O. rufipogon | ORUFI01G09210/ORUFI05G08910 | 0.23 | 0.63 | 0.37 | 34.56 | Purifying | Segmental/WGD |
ORUFI11G03140/ORUFI12G03440 | 0.05 | 0.24 | 0.22 | 13.35 | Purifying | Segmental/WGD | |
ORUFI02G24600/ORUFI04G18310 | 0.21 | 0.46 | 0.44 | 25.44 | Purifying | Segmental/WGD | |
ORUFI02G27780/ORUFI04G22190 | 0.12 | 1.08 | 0.11 | 59.45 | Purifying | Segmental/WGD | |
ORUFI03G16890/ORUFI07G27470 | 0.11 | 1.04 | 0.10 | 57.20 | Purifying | Segmental/WGD | |
ORUFI08G21130/ORUFI09G15010 | 0.10 | 0.97 | 0.10 | 53.24 | Purifying | Segmental/WGD | |
O. glaberrima | ORGLA11G0030200/ORGLA12G0028500 | 0.06 | 0.23 | 0.28 | 12.63 | Purifying | Segmental/WGD |
ORGLA02G0226100/ORGLA04G0176700 | 0.12 | 1.08 | 0.11 | 59.09 | Purifying | Segmental/WGD | |
ORGLA02G0199900/ORGLA04G0139500 | 0.20 | 0.47 | 0.43 | 25.72 | Purifying | Segmental/WGD | |
ORGLA02G0263300/ORGLA06G0106100 | 0.13 | 1.34 | 0.10 | 73.37 | Purifying | Segmental/WGD | |
ORGLA02G0263300/ORGLA08G0165200 | 0.18 | 2.50 | 0.07 | 137.23 | Purifying | Segmental/WGD | |
O. meridionalis | OMERI02G25720/OMERI04G17080 | 0.12 | 1.07 | 0.12 | 58.74 | Purifying | Segmental/WGD |
OMERI02G22720/OMERI04G14220 | 0.22 | 0.48 | 0.46 | 26.52 | Purifying | Segmental/WGD | |
OMERI03G14610/OMERI07G23080 | 0.11 | 1.01 | 0.11 | 55.25 | Purifying | Segmental/WGD | |
OMERI08G14970/OMERI09G10760 | 0.092 | 0.97 | 0.09 | 53.40 | Purifying | Segmental/WGD | |
O. barthii | OBART01G08380/OBART05G08270 | 0.30 | 0.72 | 0.41 | 39.31 | Purifying | Segmental/WGD |
OBART11G03270/OBART12G03020 | 0.09 | 0.23 | 0.38 | 12.69 | Purifying | Segmental/WGD | |
OBART02G23190/OBART04G16870 | 0.35 | 0.51 | 0.70 | 27.86 | Purifying | Segmental/WGD | |
OBART02G26390/OBART04G20600 | 0.12 | 1.08 | 0.11 | 59.09 | Purifying | Segmental/WGD | |
OBART03G16340/OBART07G26460 | 0.11 | 1.06 | 0.10 | 58.29 | Purifying | Segmental/WGD | |
OBART08G18980/OBART09G13970 | 0.09 | 0.96 | 0.10 | 53.02 | Purifying | Segmental/WGD | |
OBART08G19720/OBART09G14570 | 0.20 | 0.47 | 0.44 | 25.11 | Purifying | Segmental/WGD | |
O. glumaepatula | OGLUM01G09650/OGLUM05G08690 | 0.22 | 0.62 | 0.35 | 34.34 | Purifying | Segmental/WGD |
OGLUM11G02870/OGLUM12G03660 | 0.06 | 0.22 | 0.26 | 12.23 | Purifying | Segmental/WGD | |
OGLUM12G20420/OGLUM03G27960 | 0.20 | 0.54 | 0.38 | 29.76 | Purifying | Segmental/WGD | |
OGLUM02G23570/OGLUM04G16890 | 0.20 | 0.46 | 0.44 | 25.18 | Purifying | Segmental/WGD | |
OGLUM02G26790/OGLUM04G20570 | 0.12 | 1.08 | 0.11 | 59.49 | Purifying | Segmental/WGD | |
OGLUM03G16700/OGLUM07G26500 | 0.11 | 1.07 | 0.10 | 59.05 | Purifying | Segmental/WGD | |
OGLUM08G19930/OGLUM09G14610 | 0.10 | 0.96 | 0.10 | 52.78 | Purifying | Segmental/WGD | |
OGLUM08G20880/OGLUM09G15220 | 0.21 | 0.42 | 0.50 | 23.32 | Purifying | Segmental/WGD |
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Jiang, Y.; Liu, X.; Zhou, M.; Yang, J.; Ke, S.; Li, Y. Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa). Int. J. Mol. Sci. 2022, 23, 12557. https://doi.org/10.3390/ijms232012557
Jiang Y, Liu X, Zhou M, Yang J, Ke S, Li Y. Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa). International Journal of Molecular Sciences. 2022; 23(20):12557. https://doi.org/10.3390/ijms232012557
Chicago/Turabian StyleJiang, Yifei, Xuhui Liu, Mingao Zhou, Jian Yang, Simin Ke, and Yangsheng Li. 2022. "Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)" International Journal of Molecular Sciences 23, no. 20: 12557. https://doi.org/10.3390/ijms232012557