Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (Pinus koraiensis)
Abstract
:1. Introduction
2. Results
2.1. Characterization of the PkNRT Gene Family Members in Korean Pine
2.2. Phylogenetic Analysis of PkNRTs
2.3. Motifs, Conserved Domain, and Gene Structure Analysis of PkNRTs
2.4. Analysis of Chromosomal Distribution and Collinearity of PkNRTs
2.5. Characterization of CREs in the Promoter Regions of PkNRTs
2.6. Transcript Abundance Analysis for Different Tissues in PkNRTs
2.7. Effects of N Treatment on Growth of Korean Pine Seedlings
2.8. Expression Profiles of PkNRTs Under Different N Conditions
3. Discussion
4. Materials and Methods
4.1. Identification of NRT Gene Family in Korean Pine
4.2. Phylogenetic Analysis and Structural Characterization of PkNRTs
4.3. Colinearity Analysis and Calculation of Ka/Ks Values of PkNRTs
4.4. Analysis of CREs in the Promoters of PkNRTs
4.5. Transcriptome Sequencing for Tissue-Specific Abundance Analysis
4.6. Plant Materials and Treatments
4.7. Seedling Biomass and Root Morphology
4.8. Quantitative Real-Time PCR Analysis
4.9. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | No. of AA | MW (kDa) | pI | GRAVY | No. of TMs |
---|---|---|---|---|---|---|
PkNPF1.1 | Pkor04G00574 | 633 | 69.73 | 8.69 | 0.142 | 10 |
PkNPF1.2 | Pkor04G00573 | 630 | 69.28 | 8.92 | 0.141 | 9 |
PkNPF1.3 | Pkor04G00568 | 635 | 70.17 | 9.34 | 0.17 | 10 |
PkNPF1.4 | Pkor04G04403 | 639 | 70.13 | 9.25 | 0.148 | 10 |
PkNPF1.5 | Pkor04G00571 | 639 | 70.45 | 9.35 | 0.096 | 8 |
PkNPF1.6 | Pkor04G00570 | 639 | 70.33 | 9.21 | 0.088 | 8 |
PkNPF1.7 | Pkor04G00569 | 639 | 70.33 | 9.21 | 0.088 | 8 |
PkNPF2.1 | Pkor10G02120 | 661 | 73.07 | 9.21 | 0.201 | 10 |
PkNPF2.2 | Pkor10G02119 | 638 | 70.83 | 8.53 | 0.125 | 8 |
PkNPF2.3 | Pkor10G02121 | 658 | 72.67 | 7.12 | 0.159 | 10 |
PkNPF3.1 | Pkor12G01674 | 648 | 71.75 | 9.17 | 0.154 | 11 |
PkNPF4.1 | Pkor01G02841 | 564 | 63.08 | 8.82 | 0.36 | 11 |
PkNPF4.2 | Pkor01G03784 | 574 | 64.51 | 8.29 | 0.35 | 12 |
PkNPF4.3 | Pkor11G00219 | 580 | 64.53 | 8.46 | 0.3 | 11 |
PkNPF4.4 | Pkor08G03209 | 623 | 69.08 | 7.61 | 0.234 | 12 |
PkNPF4.5 | Pkor08G02109 | 607 | 66.91 | 9.02 | 0.171 | 12 |
PkNPF4.6 | Pkor08G03210 | 606 | 67.09 | 9.01 | 0.144 | 11 |
PkNPF5.1 | Pkor10G00974 | 618 | 69.15 | 9.1 | 0.255 | 10 |
PkNPF5.2 | Pkor08G01587 | 608 | 67.49 | 9.27 | 0.179 | 9 |
PkNPF5.3 | Pkor08G01589 | 598 | 66.37 | 9.14 | 0.228 | 9 |
PkNPF5.4 | Pkor02G03103 | 609 | 68.36 | 9.15 | 0.214 | 11 |
PkNPF5.5 | Pkor02G03104 | 537 | 59.25 | 9.47 | 0.277 | 10 |
PkNPF5.6 | Pkor02G01331 | 629 | 70.39 | 9.27 | 0.163 | 12 |
PkNPF5.7 | Pkor02G01336 | 623 | 69.98 | 9.09 | 0.173 | 10 |
PkNPF5.8 | Pkor02G03105 | 623 | 69.81 | 9.33 | 0.232 | 10 |
PkNPF5.9 | Pkor02G01335 | 622 | 69.88 | 9.35 | 0.2 | 10 |
PkNPF5.10 | Pkor05G02326 | 614 | 68.27 | 9.05 | 0.269 | 10 |
PkNPF5.11 | Pkor06G02154 | 614 | 68.49 | 9.02 | 0.264 | 9 |
PkNPF5.12 | Pkor06G00882 | 605 | 67.07 | 9.14 | 0.301 | 12 |
PkNPF5.13 | Pkor06G00883 | 607 | 67.27 | 8.54 | 0.382 | 12 |
PkNPF5.14 | Pkor09G01222 | 612 | 68.18 | 8.95 | 0.29 | 11 |
PkNPF5.15 | Pkor06G00884 | 606 | 67.37 | 8.89 | 0.323 | 12 |
PkNPF5.16 | Pkor06G03064 | 611 | 68.28 | 7.54 | 0.296 | 12 |
PkNPF5.17 | Pkor06G00881 | 607 | 68.42 | 9.05 | 0.254 | 12 |
PkNPF5.18 | Pkor06G03063 | 608 | 67.87 | 8.88 | 0.305 | 12 |
PkNPF5.19 | Pkor06G03062 | 608 | 67.78 | 8.59 | 0.318 | 12 |
PkNPF5.20 | Pkor12G00815 | 559 | 61.88 | 5.83 | 0.393 | 10 |
PkNPF5.21 | Pkor12G01382 | 605 | 67.84 | 5.92 | 0.248 | 12 |
PkNPF5.22 | Pkor07G00455 | 578 | 64.67 | 5.86 | 0.274 | 9 |
PkNPF5.23 | Pkor07G00456 | 579 | 64.83 | 6.32 | 0.364 | 10 |
PkNPF5.24 | Pkor07G02566 | 547 | 61.45 | 5.71 | 0.277 | 8 |
PkNPF5.25 | Pkor07G02567 | 606 | 68.19 | 8.79 | 0.227 | 9 |
PkNPF5.26 | Pkor07G00457 | 590 | 66.15 | 8.82 | 0.253 | 9 |
PkNPF5.27 | Pkor07G00460 | 592 | 66.1 | 8.12 | 0.338 | 10 |
PkNPF5.28 | Pkor07G00458 | 595 | 66.58 | 7.53 | 0.33 | 10 |
PkNPF5.29 | Pkor07G00459 | 595 | 66.58 | 6.86 | 0.335 | 10 |
PkNPF5.30 | Pkor07G00461 | 578 | 64.18 | 7.91 | 0.304 | 10 |
PkNPF5.31 | Pkor07G02568 | 576 | 63.74 | 8.44 | 0.325 | 10 |
PkNPF5.32 | Pkor07G00462 | 576 | 63.83 | 8.27 | 0.335 | 10 |
PkNPF6.1 | Pkor12G01587 | 610 | 66.98 | 8.43 | 0.243 | 11 |
PkNPF6.2 | Pkor11G00350 | 601 | 66.65 | 8.96 | 0.242 | 11 |
PkNPF6.3 | Pkor11G02733 | 597 | 66.53 | 8.28 | 0.209 | 11 |
PkNPF7.1 | Pkor11G02681 | 598 | 65.67 | 7.96 | 0.301 | 12 |
PkNPF7.2 | Pkor11G00148 | 626 | 69.15 | 8.52 | 0.208 | 12 |
PkNPF7.3 | Pkor09G02450 | 630 | 70.58 | 8.2 | 0.082 | 11 |
PkNPF7.4 | Pkor09G02643 | 622 | 69.64 | 6.07 | 0.134 | 12 |
PkNPF8.1 | Pkor09G00733 | 589 | 65.58 | 8.97 | 0.111 | 9 |
PkNPF8.2 | Pkor09G00732 | 571 | 63.61 | 8.22 | 0.136 | 10 |
PkNPF8.3 | Pkor05G01620 | 596 | 66.25 | 5.48 | 0.212 | 10 |
PkNPF8.4 | Pkor05G01614 | 596 | 66.17 | 5.25 | 0.237 | 10 |
PkNPF8.5 | Pkor05G01606 | 594 | 65.59 | 6.28 | 0.204 | 11 |
PkNPF8.6 | Pkor05G01605 | 594 | 65.97 | 6.15 | 0.258 | 11 |
PkNPF8.7 | Pkor01G04179 | 566 | 63.29 | 8.23 | 0.258 | 10 |
PkNPF8.8 | Pkor09G00734 | 616 | 68.79 | 8.53 | 0.069 | 10 |
PkNPF8.9 | Pkor09G00735 | 589 | 66.21 | 8.86 | 0.128 | 9 |
PkNPF8.10 | Pkor09G00737 | 589 | 66.15 | 8.74 | 0.117 | 10 |
PkNRT2.1 | Pkor08G00516 | 533 | 58 | 8.69 | 0.3 | 10 |
PkNRT2.2 | Pkor12G01755 | 533 | 58 | 8.69 | 0.3 | 10 |
PkNRT2.3 | Pkor12G02554 | 533 | 58 | 8.69 | 0.3 | 10 |
PkNRT2.4 | Pkor12G02553 | 533 | 57.87 | 8.39 | 0.297 | 10 |
PkNRT2.5 | Pkor12G01756 | 533 | 57.95 | 8.14 | 0.333 | 10 |
PkNRT2.6 | Pkor09G01906 | 548 | 58.63 | 8.17 | 0.353 | 10 |
PkNRT3.1 | Pkor09G03181 | 268 | 29.26 | 9.18 | 0.018 | 1 |
PkNRT3.2 | Pkor09G01715 | 207 | 22.58 | 9.73 | 0.173 | 1 |
PkNRT3.3 | Pkor09G01713 | 214 | 23.98 | 9.25 | 0.012 | 1 |
PkNRT3.4 | Pkor09G01714 | 214 | 23.49 | 9.64 | −0.037 | 1 |
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Zhao, X.; Wu, H.; Li, B.; Wang, P.; Zhang, P.; Shen, H.; Yang, J. Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (Pinus koraiensis). Plants 2025, 14, 238. https://doi.org/10.3390/plants14020238
Zhao X, Wu H, Li B, Wang P, Zhang P, Shen H, Yang J. Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (Pinus koraiensis). Plants. 2025; 14(2):238. https://doi.org/10.3390/plants14020238
Chicago/Turabian StyleZhao, Xinyu, Haibo Wu, Boyang Li, Pengyang Wang, Peng Zhang, Hailong Shen, and Jianfei Yang. 2025. "Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (Pinus koraiensis)" Plants 14, no. 2: 238. https://doi.org/10.3390/plants14020238
APA StyleZhao, X., Wu, H., Li, B., Wang, P., Zhang, P., Shen, H., & Yang, J. (2025). Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (Pinus koraiensis). Plants, 14(2), 238. https://doi.org/10.3390/plants14020238