Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress
Abstract
:1. Introduction
2. Results
2.1. Identification and Protein Tree Construction of the PUB Gene Family in Z. japonica
2.2. Characteristics, Gene Structure and Domain Analysis of PUB Genes in Z. japonica
2.3. Cis-Acting Regulatory Element Prediction in Promoter Regions of ZjPUB Family Members
2.4. Expression Analysis of ZjPUB Genes under Salt Stress
2.5. Protein–Protein Interaction (PPI) Network Analysis of Differentially Expressed ZjPUB Members under Salt Stress
3. Discussion
4. Materials and Methods
4.1. Genome and Transcriptome Data Sources
4.2. Identification of ZjPUBs and Construction of the Protein Tree
4.3. Characteristics, Gene Structure and Domain Analysis of PUB Genes in Z. japonica
4.4. Cis-Acting Elements within the Promoter Region of ZjPUB Genes
4.5. Gene Expression Analysis of ZjPUBs under Salt Stress
4.6. PPI Network Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Transcript ID | CDS Length (bp) | Amino Acids (aa) | MW (Da) | pI | Subcellular Localization |
---|---|---|---|---|---|---|
ZjPUB1 | Zjn_sc00010.1.g02110.1.am.mkhc | 2331 | 777 | 88,914 | 5.35 | endomembrane system |
ZjPUB2 | Zjn_sc00182.1.g00060.1.sm.mkhc | 1398 | 466 | 52,315.6 | 6.02 | nucleus |
ZjPUB3 | Zjn_sc00102.1.g00610.1.sm.mkhc | 1344 | 448 | 49,809.3 | 5.03 | nucleus |
ZjPUB4 | Zjn_sc00022.1.g06260.1.sm.mk | 576 | 192 | 21,098.8 | 4.86 | nucleus |
ZjPUB5 | Zjn_sc00041.1.g00960.1.am.mk | 1200 | 400 | 44,426.1 | 7.1 | chloroplast |
ZjPUB6 | Zjn_sc00049.1.g01240.1.sm.mk | 1374 | 458 | 51,715.7 | 5.5 | nucleus |
ZjPUB7 | Zjn_sc00049.1.g00160.1.sm.mkhc | 2424 | 808 | 90,586 | 7.46 | nucleus |
ZjPUB8 | Zjn_sc00067.1.g02790.1.am.mkhc | 2208 | 736 | 82,274.4 | 7.26 | nucleus |
ZjPUB9 | Zjn_sc00066.1.g00450.1.am.mk | 2304 | 768 | 85,501.4 | 6.09 | nucleus |
ZjPUB10 | Zjn_sc00102.1.g00620.1.am.mk | 1764 | 588 | 65,486.1 | 8.06 | nucleus |
ZjPUB11 | Zjn_sc00026.1.g00430.1.sm.mkhc | 2976 | 992 | 108,074.2 | 6.65 | chloroplast |
ZjPUB12 | Zjn_sc00004.1.g08300.1.am.mkhc | 1464 | 488 | 53,820.9 | 4.55 | nucleus |
ZjPUB13 | Zjn_sc00023.1.g01280.1.sm.mkhc | 2859 | 953 | 104,355 | 6.38 | chloroplast |
ZjPUB14 | Zjn_sc00150.1.g00150.1.sm.mkhc | 825 | 275 | 31,037 | 7.17 | nucleus |
ZjPUB15 | Zjn_sc00016.1.g06570.1.sm.mkhc | 303 | 101 | 11,515.1 | 5.7 | nucleus |
ZjPUB16 | Zjn_sc00093.1.g01230.1.sm.mkhc | 3093 | 1031 | 112,713.5 | 6.61 | nucleus |
ZjPUB17 | Zjn_sc00131.1.g00970.1.sm.mkhc | 3069 | 1023 | 111,844.9 | 6.15 | nucleus |
ZjPUB18 | Zjn_sc00165.1.g00170.1.sm.mkhc | 1890 | 630 | 69,830.4 | 5.31 | plasma membrane |
ZjPUB19 | Zjn_sc00007.1.g00090.1.cf.mkhc | 903 | 301 | 34,248.6 | 4.84 | nucleus |
ZjPUB20 | Zjn_sc00010.1.g03830.1.sm.mkhc | 1266 | 422 | 46,902.2 | 5.08 | nucleus |
ZjPUB21 | Zjn_sc00006.1.g02940.1.sm.mk | 1164 | 388 | 42,146.4 | 5.02 | nucleus |
ZjPUB22 | Zjn_sc00058.1.g02220.1.sm.mk | 1113 | 371 | 39,634.4 | 8.65 | nucleus |
ZjPUB23 | Zjn_sc00020.1.g01280.1.sm.mk | 969 | 323 | 33,963.6 | 5.69 | nucleus |
ZjPUB24 | Zjn_sc00003.1.g07570.1.am.mk | 1578 | 526 | 56,312.6 | 8.25 | nucleus |
ZjPUB25 | Zjn_sc00002.1.g09550.1.am.mk | 1848 | 616 | 66,461.4 | 8.93 | chloroplast |
ZjPUB26 | Zjn_sc00012.1.g05350.1.am.mk | 1512 | 504 | 51,890.3 | 9.76 | chloroplast |
ZjPUB27 | Zjn_sc00020.1.g01450.1.am.mk | 2397 | 799 | 85,768.3 | 9.95 | nucleus |
ZjPUB28 | Zjn_sc00006.1.g03530.1.am.mk | 1911 | 637 | 67,282.2 | 9.7 | nucleus |
ZjPUB29 | Zjn_sc00002.1.g08810.1.am.mk | 1338 | 446 | 47,119.9 | 7.7 | mitochondrion |
ZjPUB30 | Zjn_sc00003.1.g06760.1.am.mk | 1332 | 444 | 47,189 | 7.88 | nucleus |
ZjPUB31 | Zjn_sc00093.1.g00320.1.am.mk | 1554 | 518 | 55,204.8 | 10.25 | nucleus |
ZjPUB32 | Zjn_sc00007.1.g05420.1.am.mk | 1488 | 496 | 53,359.2 | 8.73 | chloroplast |
ZjPUB33 | Zjn_sc00022.1.g01940.1.sm.mk | 1368 | 456 | 48,826.9 | 8.17 | nucleus |
ZjPUB34 | Zjn_sc00006.1.g06155.1.br | 432 | 144 | 14,928.8 | 6.79 | nucleus |
ZjPUB35 | Zjn_sc00004.1.g08630.1.am.mk | 1494 | 498 | 54,381.3 | 8.31 | nucleus |
ZjPUB36 | Zjn_sc00023.1.g01610.1.sm.mk | 1242 | 414 | 45,167.9 | 7.34 | nucleus |
ZjPUB37 | Zjn_sc00007.1.g08400.1.am.mk | 1449 | 483 | 52,598.4 | 5.33 | nucleus |
ZjPUB38 | Zjn_sc00022.1.g04900.1.sm.mk | 1287 | 429 | 46,311 | 4.85 | nucleus |
ZjPUB39 | Zjn_sc00028.1.g01890.1.am.mk | 933 | 311 | 33,132.5 | 6.7 | nucleus |
ZjPUB40 | Zjn_sc00034.1.g05980.1.am.mk | 1830 | 610 | 66,145.2 | 10.03 | nucleus |
ZjPUB41 | Zjn_sc00004.1.g14050.1.sm.mk | 1272 | 424 | 45,043.1 | 7.06 | nucleus |
ZjPUB42 | Zjn_sc00020.1.g01520.1.am.mk | 1545 | 515 | 55,689.2 | 9.83 | nucleus |
ZjPUB43 | Zjn_sc00006.1.g03610.1.am.mk | 1314 | 438 | 46,999.6 | 7.94 | nucleus |
ZjPUB44 | Zjn_sc00071.1.g01640.1.am.mk | 3036 | 1012 | 111,234.8 | 7.37 | chloroplast thylakoid membrane |
ZjPUB45 | Zjn_sc04324.1.g00010.1.am.mk | 678 | 226 | 23,553.7 | 7.64 | nucleus |
ZjPUB46 | Zjn_sc00018.1.g06300.1.sm.mk | 2091 | 697 | 73,597.5 | 7.31 | chloroplast |
ZjPUB47 | Zjn_sc00047.1.g02090.1.am.mk | 2241 | 747 | 81,591.7 | 5.39 | endomembrane system |
ZjPUB48 | Zjn_sc00174.1.g00010.1.sm.mk | 1965 | 655 | 70,775.8 | 6.66 | nucleus |
ZjPUB49 | Zjn_sc00012.1.g07180.1.sm.mkhc | 1923 | 641 | 68,015.4 | 7.07 | nucleus |
ZjPUB50 | Zjn_sc00025.1.g05030.1.am.mk | 2376 | 792 | 84,931.1 | 10.13 | endomembrane system |
ZjPUB51 | Zjn_sc00009.1.g08070.1.sm.mk | 2055 | 685 | 73,004.8 | 6.71 | chloroplast |
ZjPUB52 | Zjn_sc00040.1.g03750.1.am.mk | 2061 | 687 | 73,448.3 | 6.24 | nucleus |
ZjPUB53 | Zjn_sc00090.1.g01510.1.am.mk | 2430 | 810 | 87,041.7 | 6.28 | nucleus |
ZjPUB54 | Zjn_sc00006.1.g06160.1.sm.mk | 1368 | 456 | 49,690 | 5.01 | nucleus |
ZjPUB55 | Zjn_sc00020.1.g03330.1.sm.mkhc | 1377 | 459 | 49,914.2 | 5.94 | nucleus |
ZjPUB56 | Zjn_sc00015.1.g04170.1.am.mk | 1914 | 638 | 70,795.3 | 7.92 | nucleus |
ZjPUB57 | Zjn_sc00022.1.g02290.1.sm.mkhc | 1569 | 523 | 57,066.2 | 5.52 | nucleus |
ZjPUB58 | Zjn_sc00184.1.g00310.1.sm.mkhc | 2367 | 789 | 85,448.1 | 7.41 | nucleus |
ZjPUB59 | Zjn_sc00002.1.g06310.1.sm.mkhc | 2118 | 706 | 76,646.2 | 8.2 | nucleus |
ZjPUB60 | Zjn_sc00038.1.g02650.1.sm.mkhc | 1971 | 657 | 71,535.9 | 5.22 | nucleus |
ZjPUB61 | Zjn_sc00093.1.g00050.1.sm.mk | 1416 | 472 | 49,182.2 | 6.32 | chloroplast outer membrane |
ZjPUB62 | Zjn_sc00018.1.g06490.1.sm.mk | 1365 | 455 | 47,388.5 | 7.28 | chloroplast |
ZjPUB63 | Zjn_sc00091.1.g00910.1.am.mk | 2031 | 677 | 70,993.7 | 8.76 | nucleus |
ZjPUB64 | Zjn_sc00039.1.g04330.1.am.mk | 480 | 160 | 16,782.6 | 7.09 | chloroplast |
ZjPUB65 | Zjn_sc00039.1.g04340.1.am.mk | 651 | 217 | 23,010.2 | 5.02 | chloroplast |
ZjPUB66 | Zjn_sc00008.1.g00320.1.sm.mk | 1272 | 424 | 46,803.7 | 6.76 | nucleus |
ZjPUB67 | Zjn_sc00071.1.g00460.1.am.mkhc | 2496 | 832 | 90,311.8 | 5.76 | nucleus |
ZjPUB68 | Zjn_sc00007.1.g07460.1.sm.mkhc | 2319 | 773 | 86,679.4 | 5.64 | nucleus |
ZjPUB69 | Zjn_sc00022.1.g03900.1.sm.mkhc | 1884 | 628 | 69,200 | 6.42 | nucleus |
ZjPUB70 | Zjn_sc00056.1.g00870.1.am.mkhc | 1470 | 490 | 54,562.6 | 4.82 | nucleus |
ZjPUB71 | Zjn_sc00009.1.g03620.1.am.mkhc | 2373 | 791 | 86,729.6 | 6.14 | nucleus |
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Share and Cite
Sun, D.; Xu, J.; Wang, H.; Guo, H.; Chen, Y.; Zhang, L.; Li, J.; Hao, D.; Yao, X.; Li, X. Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress. Plants 2024, 13, 788. https://doi.org/10.3390/plants13060788
Sun D, Xu J, Wang H, Guo H, Chen Y, Zhang L, Li J, Hao D, Yao X, Li X. Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress. Plants. 2024; 13(6):788. https://doi.org/10.3390/plants13060788
Chicago/Turabian StyleSun, Daojin, Jingya Xu, Haoran Wang, Hailin Guo, Yu Chen, Ling Zhang, Jianjian Li, Dongli Hao, Xiang Yao, and Xiaohui Li. 2024. "Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress" Plants 13, no. 6: 788. https://doi.org/10.3390/plants13060788