Journal of Agricultural Science and Technology ›› 2024, Vol. 26 ›› Issue (3): 15-25.DOI: 10.13304/j.nykjdb.2023.0551
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Zhanqing WU1(), Wei CHEN1(
), Zhan ZHAO2, Hailiang XU1, Haoyuan LI1, Xingxing PENG1, Dongxu CHEN1, Mingyue ZHANG1
Received:
2023-07-17
Accepted:
2023-09-08
Online:
2024-03-15
Published:
2024-03-07
Contact:
Wei CHEN
吴占清1(), 陈威1(
), 赵展2, 许海良1, 李豪远1, 彭星星1, 陈东旭1, 张明月1
通讯作者:
陈威
作者简介:
吴占清 E-mail:13383782062@163.com;
基金资助:
CLC Number:
Zhanqing WU, Wei CHEN, Zhan ZHAO, Hailiang XU, Haoyuan LI, Xingxing PENG, Dongxu CHEN, Mingyue ZHANG. Genome-wide Identification and Bioinformatics Analysis of GRAS Gene Family in Maize[J]. Journal of Agricultural Science and Technology, 2024, 26(3): 15-25.
吴占清, 陈威, 赵展, 许海良, 李豪远, 彭星星, 陈东旭, 张明月. 玉米GRAS基因家族的全基因组鉴定及生物信息学分析[J]. 中国农业科技导报, 2024, 26(3): 15-25.
基因名称 Gene name | 基因ID Gene ID | 氨基酸长度Amino acids length/aa | 分子量Molecular weight/Da | 等电点PI | 带负电荷残基总数 Total number of negatively charged residues | 带正电荷残基总数 Total number of positively charged residues | 不稳定 指数 Instability index | 脂肪族氨基酸指数 Aliphatic index | 平均 疏水性 Grand average of hydropathicity |
---|---|---|---|---|---|---|---|---|---|
ZmGRAS1 | Zm00001eb216610 | 625 | 65 742.60 | 5.18 | 70 | 50 | 46.59 | 75.66 | -0.204 |
ZmGRAS2 | Zm00001eb107910 | 554 | 60 835.57 | 5.84 | 68 | 52 | 53.95 | 83.83 | -0.302 |
ZmGRAS3 | Zm00001eb325750 | 558 | 60 991.58 | 5.71 | 69 | 52 | 55.68 | 82.17 | -0.301 |
ZmGRAS4 | Zm00001eb106490 | 570 | 64 511.14 | 5.99 | 73 | 64 | 46.97 | 83.72 | -0.475 |
ZmGRAS5 | Zm00001eb027720 | 542 | 59 914.41 | 5.76 | 58 | 43 | 48.73 | 83.86 | -0.245 |
ZmGRAS6 | Zm00001eb170110 | 775 | 82 511.74 | 6.19 | 73 | 62 | 63.30 | 74.27 | -0.245 |
ZmGRAS7 | Zm00001eb195650 | 668 | 71 162.84 | 6.15 | 66 | 53 | 57.35 | 85.21 | -0.197 |
ZmGRAS8 | Zm00001eb288400 | 561 | 62 826.62 | 4.92 | 79 | 54 | 46.74 | 81.23 | -0.340 |
ZmGRAS9 | Zm00001eb141310 | 447 | 48 471.03 | 6.36 | 55 | 50 | 54.57 | 89.44 | -0.145 |
ZmGRAS10 | Zm00001eb093670 | 678 | 72 083.67 | 6.18 | 67 | 55 | 56.48 | 87.23 | -0.168 |
ZmGRAS11 | Zm00001eb363140 | 449 | 48 889.56 | 6.26 | 56 | 50 | 56.39 | 89.49 | -0.133 |
ZmGRAS12 | Zm00001eb148290 | 809 | 89 139.89 | 6.06 | 101 | 88 | 44.93 | 77.00 | -0.344 |
ZmGRAS13 | Zm00001eb378590 | 616 | 65 472.30 | 6.30 | 70 | 63 | 45.04 | 71.62 | -0.240 |
ZmGRAS14 | Zm00001eb136350 | 710 | 78 391.49 | 5.30 | 92 | 73 | 53.77 | 79.77 | -0.339 |
ZmGRAS15 | Zm00001eb324600 | 452 | 48 411.17 | 6.05 | 55 | 49 | 58.80 | 96.26 | -0.044 |
ZmGRAS16 | Zm00001eb164530 | 765 | 84 654.31 | 5.30 | 103 | 78 | 49.74 | 73.02 | -0.392 |
ZmGRAS17 | Zm00001eb055700 | 551 | 59 842.10 | 5.20 | 63 | 47 | 56.67 | 86.03 | -0.091 |
ZmGRAS18 | Zm00001eb215870 | 569 | 61 233.71 | 5.08 | 63 | 44 | 57.67 | 85.59 | -0.056 |
ZmGRAS19 | Zm00001eb344400 | 508 | 56 088.05 | 5.91 | 55 | 43 | 35.75 | 90.08 | -0.105 |
ZmGRAS20 | Zm00001eb164480 | 642 | 71 250.62 | 6.67 | 84 | 80 | 52.59 | 79.63 | -0.405 |
ZmGRAS21 | Zm00001eb164490 | 666 | 73 486.54 | 5.51 | 93 | 76 | 51.16 | 74.25 | -0.425 |
ZmGRAS22 | Zm00001eb326020 | 592 | 63 904.56 | 5.67 | 64 | 50 | 58.88 | 68.06 | -0.370 |
ZmGRAS23 | Zm00001eb108250 | 456 | 49 134.09 | 5.32 | 50 | 35 | 40.45 | 90.99 | 0.057 |
ZmGRAS24 | Zm00001eb011560 | 564 | 59 835.16 | 5.12 | 65 | 44 | 43.97 | 75.30 | -0.152 |
ZmGRAS25 | Zm00001eb326210 | 456 | 49 478.48 | 5.38 | 51 | 36 | 39.36 | 89.06 | 0.011 |
ZmGRAS26 | Zm00001eb108090 | 586 | 63 755.58 | 5.49 | 66 | 53 | 59.45 | 70.56 | -0.343 |
ZmGRAS27 | Zm00001eb081760 | 607 | 66 678.45 | 6.04 | 77 | 67 | 47.34 | 80.97 | -0.287 |
ZmGRAS28 | Zm00001eb020850 | 630 | 67 547.26 | 6.15 | 65 | 53 | 66.00 | 63.40 | -0.416 |
ZmGRAS29 | Zm00001eb073130 | 623 | 65 570.98 | 6.15 | 60 | 54 | 52.23 | 87.26 | -0.116 |
ZmGRAS30 | Zm00001eb187310 | 607 | 63 032.09 | 8.75 | 54 | 59 | 46.96 | 84.93 | -0.109 |
ZmGRAS31 | Zm00001eb428430 | 623 | 65 303.67 | 6.34 | 58 | 54 | 48.36 | 84.11 | -0.137 |
ZmGRAS32 | Zm00001eb164470 | 645 | 72 101.21 | 6.37 | 78 | 70 | 47.76 | 80.96 | -0.356 |
ZmGRAS33 | Zm00001eb165340 | 639 | 72 513.56 | 6.09 | 85 | 75 | 45.77 | 81.61 | -0.384 |
ZmGRAS34 | Zm00001eb236120 | 416 | 43 484.86 | 5.43 | 48 | 35 | 32.57 | 88.92 | -0.042 |
ZmGRAS35 | Zm00001eb291030 | 497 | 52 002.72 | 5.80 | 51 | 38 | 46.41 | 82.39 | -0.007 |
ZmGRAS36 | Zm00001eb291930 | 426 | 45 514.68 | 6.09 | 48 | 43 | 47.88 | 87.37 | -0.100 |
ZmGRAS37 | Zm00001eb115950 | 599 | 67 026.72 | 6.12 | 76 | 68 | 50.16 | 74.89 | -0.375 |
ZmGRAS38 | Zm00001eb074460 | 721 | 75 225.55 | 5.74 | 62 | 46 | 47.98 | 82.98 | -0.050 |
ZmGRAS39 | Zm00001eb429450 | 718 | 75 350.35 | 5.72 | 64 | 47 | 50.61 | 81.82 | -0.081 |
ZmGRAS40 | Zm00001eb186770 | 708 | 73 942.10 | 5.63 | 65 | 48 | 45.89 | 87.67 | 0.004 |
ZmGRAS41 | Zm00001eb000470 | 481 | 51 254.82 | 6.10 | 48 | 37 | 41.79 | 95.88 | 0.099 |
ZmGRAS42 | Zm00001eb196430 | 487 | 51 456.32 | 6.18 | 59 | 53 | 54.58 | 89.08 | -0.151 |
ZmGRAS43 | Zm00001eb249840 | 706 | 73 961.86 | 5.47 | 66 | 44 | 45.87 | 85.55 | 0.001 |
ZmGRAS44 | Zm00001eb202270 | 473 | 51 700.38 | 4.73 | 62 | 32 | 52.48 | 88.12 | 0.013 |
ZmGRAS45 | Zm00001eb326550 | 306 | 33 520.48 | 6.05 | 30 | 25 | 33.94 | 97.32 | 0.086 |
ZmGRAS46 | Zm00001eb139470 | 492 | 52 614.47 | 5.15 | 58 | 39 | 47.00 | 87.11 | -0.015 |
ZmGRAS47 | Zm00001eb019640 | 526 | 54 677.28 | 6.72 | 53 | 51 | 51.38 | 76.24 | -0.189 |
ZmGRAS48 | Zm00001eb405080 | 235 | 25 649.61 | 6.55 | 27 | 25 | 48.23 | 99.66 | 0.063 |
ZmGRAS49 | Zm00001eb002990 | 313 | 33 288.60 | 9.66 | 25 | 36 | 54.58 | 86.77 | 0.034 |
Table 1 Physicochemical properties of proteins encoded by the GRAS gene family in maize
基因名称 Gene name | 基因ID Gene ID | 氨基酸长度Amino acids length/aa | 分子量Molecular weight/Da | 等电点PI | 带负电荷残基总数 Total number of negatively charged residues | 带正电荷残基总数 Total number of positively charged residues | 不稳定 指数 Instability index | 脂肪族氨基酸指数 Aliphatic index | 平均 疏水性 Grand average of hydropathicity |
---|---|---|---|---|---|---|---|---|---|
ZmGRAS1 | Zm00001eb216610 | 625 | 65 742.60 | 5.18 | 70 | 50 | 46.59 | 75.66 | -0.204 |
ZmGRAS2 | Zm00001eb107910 | 554 | 60 835.57 | 5.84 | 68 | 52 | 53.95 | 83.83 | -0.302 |
ZmGRAS3 | Zm00001eb325750 | 558 | 60 991.58 | 5.71 | 69 | 52 | 55.68 | 82.17 | -0.301 |
ZmGRAS4 | Zm00001eb106490 | 570 | 64 511.14 | 5.99 | 73 | 64 | 46.97 | 83.72 | -0.475 |
ZmGRAS5 | Zm00001eb027720 | 542 | 59 914.41 | 5.76 | 58 | 43 | 48.73 | 83.86 | -0.245 |
ZmGRAS6 | Zm00001eb170110 | 775 | 82 511.74 | 6.19 | 73 | 62 | 63.30 | 74.27 | -0.245 |
ZmGRAS7 | Zm00001eb195650 | 668 | 71 162.84 | 6.15 | 66 | 53 | 57.35 | 85.21 | -0.197 |
ZmGRAS8 | Zm00001eb288400 | 561 | 62 826.62 | 4.92 | 79 | 54 | 46.74 | 81.23 | -0.340 |
ZmGRAS9 | Zm00001eb141310 | 447 | 48 471.03 | 6.36 | 55 | 50 | 54.57 | 89.44 | -0.145 |
ZmGRAS10 | Zm00001eb093670 | 678 | 72 083.67 | 6.18 | 67 | 55 | 56.48 | 87.23 | -0.168 |
ZmGRAS11 | Zm00001eb363140 | 449 | 48 889.56 | 6.26 | 56 | 50 | 56.39 | 89.49 | -0.133 |
ZmGRAS12 | Zm00001eb148290 | 809 | 89 139.89 | 6.06 | 101 | 88 | 44.93 | 77.00 | -0.344 |
ZmGRAS13 | Zm00001eb378590 | 616 | 65 472.30 | 6.30 | 70 | 63 | 45.04 | 71.62 | -0.240 |
ZmGRAS14 | Zm00001eb136350 | 710 | 78 391.49 | 5.30 | 92 | 73 | 53.77 | 79.77 | -0.339 |
ZmGRAS15 | Zm00001eb324600 | 452 | 48 411.17 | 6.05 | 55 | 49 | 58.80 | 96.26 | -0.044 |
ZmGRAS16 | Zm00001eb164530 | 765 | 84 654.31 | 5.30 | 103 | 78 | 49.74 | 73.02 | -0.392 |
ZmGRAS17 | Zm00001eb055700 | 551 | 59 842.10 | 5.20 | 63 | 47 | 56.67 | 86.03 | -0.091 |
ZmGRAS18 | Zm00001eb215870 | 569 | 61 233.71 | 5.08 | 63 | 44 | 57.67 | 85.59 | -0.056 |
ZmGRAS19 | Zm00001eb344400 | 508 | 56 088.05 | 5.91 | 55 | 43 | 35.75 | 90.08 | -0.105 |
ZmGRAS20 | Zm00001eb164480 | 642 | 71 250.62 | 6.67 | 84 | 80 | 52.59 | 79.63 | -0.405 |
ZmGRAS21 | Zm00001eb164490 | 666 | 73 486.54 | 5.51 | 93 | 76 | 51.16 | 74.25 | -0.425 |
ZmGRAS22 | Zm00001eb326020 | 592 | 63 904.56 | 5.67 | 64 | 50 | 58.88 | 68.06 | -0.370 |
ZmGRAS23 | Zm00001eb108250 | 456 | 49 134.09 | 5.32 | 50 | 35 | 40.45 | 90.99 | 0.057 |
ZmGRAS24 | Zm00001eb011560 | 564 | 59 835.16 | 5.12 | 65 | 44 | 43.97 | 75.30 | -0.152 |
ZmGRAS25 | Zm00001eb326210 | 456 | 49 478.48 | 5.38 | 51 | 36 | 39.36 | 89.06 | 0.011 |
ZmGRAS26 | Zm00001eb108090 | 586 | 63 755.58 | 5.49 | 66 | 53 | 59.45 | 70.56 | -0.343 |
ZmGRAS27 | Zm00001eb081760 | 607 | 66 678.45 | 6.04 | 77 | 67 | 47.34 | 80.97 | -0.287 |
ZmGRAS28 | Zm00001eb020850 | 630 | 67 547.26 | 6.15 | 65 | 53 | 66.00 | 63.40 | -0.416 |
ZmGRAS29 | Zm00001eb073130 | 623 | 65 570.98 | 6.15 | 60 | 54 | 52.23 | 87.26 | -0.116 |
ZmGRAS30 | Zm00001eb187310 | 607 | 63 032.09 | 8.75 | 54 | 59 | 46.96 | 84.93 | -0.109 |
ZmGRAS31 | Zm00001eb428430 | 623 | 65 303.67 | 6.34 | 58 | 54 | 48.36 | 84.11 | -0.137 |
ZmGRAS32 | Zm00001eb164470 | 645 | 72 101.21 | 6.37 | 78 | 70 | 47.76 | 80.96 | -0.356 |
ZmGRAS33 | Zm00001eb165340 | 639 | 72 513.56 | 6.09 | 85 | 75 | 45.77 | 81.61 | -0.384 |
ZmGRAS34 | Zm00001eb236120 | 416 | 43 484.86 | 5.43 | 48 | 35 | 32.57 | 88.92 | -0.042 |
ZmGRAS35 | Zm00001eb291030 | 497 | 52 002.72 | 5.80 | 51 | 38 | 46.41 | 82.39 | -0.007 |
ZmGRAS36 | Zm00001eb291930 | 426 | 45 514.68 | 6.09 | 48 | 43 | 47.88 | 87.37 | -0.100 |
ZmGRAS37 | Zm00001eb115950 | 599 | 67 026.72 | 6.12 | 76 | 68 | 50.16 | 74.89 | -0.375 |
ZmGRAS38 | Zm00001eb074460 | 721 | 75 225.55 | 5.74 | 62 | 46 | 47.98 | 82.98 | -0.050 |
ZmGRAS39 | Zm00001eb429450 | 718 | 75 350.35 | 5.72 | 64 | 47 | 50.61 | 81.82 | -0.081 |
ZmGRAS40 | Zm00001eb186770 | 708 | 73 942.10 | 5.63 | 65 | 48 | 45.89 | 87.67 | 0.004 |
ZmGRAS41 | Zm00001eb000470 | 481 | 51 254.82 | 6.10 | 48 | 37 | 41.79 | 95.88 | 0.099 |
ZmGRAS42 | Zm00001eb196430 | 487 | 51 456.32 | 6.18 | 59 | 53 | 54.58 | 89.08 | -0.151 |
ZmGRAS43 | Zm00001eb249840 | 706 | 73 961.86 | 5.47 | 66 | 44 | 45.87 | 85.55 | 0.001 |
ZmGRAS44 | Zm00001eb202270 | 473 | 51 700.38 | 4.73 | 62 | 32 | 52.48 | 88.12 | 0.013 |
ZmGRAS45 | Zm00001eb326550 | 306 | 33 520.48 | 6.05 | 30 | 25 | 33.94 | 97.32 | 0.086 |
ZmGRAS46 | Zm00001eb139470 | 492 | 52 614.47 | 5.15 | 58 | 39 | 47.00 | 87.11 | -0.015 |
ZmGRAS47 | Zm00001eb019640 | 526 | 54 677.28 | 6.72 | 53 | 51 | 51.38 | 76.24 | -0.189 |
ZmGRAS48 | Zm00001eb405080 | 235 | 25 649.61 | 6.55 | 27 | 25 | 48.23 | 99.66 | 0.063 |
ZmGRAS49 | Zm00001eb002990 | 313 | 33 288.60 | 9.66 | 25 | 36 | 54.58 | 86.77 | 0.034 |
Fig. 2 Phylogenetic tree analysis of GRAS gene family in different speciesNote: Os—Oryza sativa; Zm—Zea mays; TresCS—Triticum aestivum Chinese Spring; At—Arabidopsis thaliana; Solyc—Solanum lycopersicum.
Fig. 5 Collinearity analysis of GRAS gene family members in maizeNote: The yellow-to-red scale bar on the right indicates the number of SNPs within 1 Mb domain.
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