Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana
Abstract
:1. Introduction
2. Results
2.1. Identification and Chromosomal Localization of U-Box Gene Family Members
2.2. Gene Structure and Phylogenetic Analysis of U-Box Gene Family Members
2.3. Analysis of MaU-Box Gene Family Conserved Motifs
2.4. Expression Profile of MaU-Box Genes in Different Organs
2.5. Expression Profile of MaU-Box Genes in Fruit Developmental Period
2.6. Differential Expression of MaU-Box Genes under Abiotic Stresses
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Treatment
4.2. Genome Identification of Banana U-Box Gene Family Members
4.3. MaU-Box Protein Conserved Motif and Phylogenetic Analysis
4.4. Gene Expression Analysis
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Gene Name | Locus ID | Chromosome Location | Gene DNA (bp) | CDS (bp) | Protein Length (aa) | Molecular Weight (kD) | Theoretical pI | Exon | Putative Localization |
---|---|---|---|---|---|---|---|---|---|
MaPUB1 | GSMUA_Achr1T12080_001 | chr1:9216255..9219037 reverse | 2783 | 1944 | 647 | 72.51 | 5.02 | 3 | Nucleus |
MaPUB2 | GSMUA_Achr1T13220_001 | chr1:10096902..10098167 forward | 1266 | 1191 | 396 | 41.13 | 7.66 | 2 | Nucleus |
MaPUB3 | GSMUA_Achr1T13730_001 | chr1:10477987..10483072 forward | 5086 | 1128 | 375 | 42.2 | 5.58 | 5 | Cytoplasm, Nucleus |
MaPUB4 | GSMUA_Achr1T16210_001 | chr1:12121706..12123412 reverse | 1707 | 1707 | 568 | 60.39 | 8.62 | 1 | Cytoplasm |
MaPUB5 | GSMUA_Achr1T22790_001 | chr1:17158846..17160507 reverse | 1662 | 1362 | 453 | 47.14 | 8.76 | 3 | Nucleus |
MaPUB6 | GSMUA_Achr1T24290_001 | chr1:18636205..18639761 reverse | 3557 | 1836 | 611 | 66.29 | 5.48 | 6 | Nucleus |
MaPUB7 | GSMUA_Achr2T08620_001 | chr2:12553612..12555419 reverse | 1808 | 1305 | 434 | 47.08 | 5.68 | 2 | Nucleus |
MaPUB8 | GSMUA_Achr2T09640_001 | chr2:13094735..13107492 forward | 12,758 | 2547 | 848 | 94.33 | 6.83 | 6 | Nucleus |
MaPUB9 | GSMUA_Achr2T11370_001 | chr2:14269037..14272568 forward | 3532 | 2301 | 766 | 84.56 | 5.85 | 4 | Nucleus |
MaPUB10 | GSMUA_Achr2T15530_001 | chr2:16801361..16803647 reverse | 2287 | 1983 | 660 | 72.39 | 9.22 | 3 | Nucleus |
MaPUB11 | GSMUA_Achr2T20690_001 | chr2:20462606..20463811 forward | 1206 | 1206 | 401 | 42.65 | 6.75 | 1 | Nucleus |
MaPUB12 | GSMUA_Achr3T00280_001 | chr3:253594..258827 forward | 5234 | 1812 | 603 | 65.43 | 5.52 | 5 | Nucleus |
MaPUB13 | GSMUA_Achr3T01110_001 | chr3:844229..845967 forward | 1739 | 1641 | 546 | 55.97 | 9.57 | 2 | Nucleus |
MaPUB14 | GSMUA_Achr3T02030_001 | chr3:1351349..1352952 reverse | 1604 | 1260 | 419 | 45.71 | 8.64 | 3 | Nucleus |
MaPUB15 | GSMUA_Achr3T06000_001 | chr3:4040242..4042320 reverse | 2079 | 1560 | 519 | 55.21 | 7.56 | 3 | Nucleus |
MaPUB16 | GSMUA_Achr3T06160_001 | chr3:4178177..4180306 reverse | 2130 | 1704 | 567 | 61.78 | 9.34 | 2 | Cytoplasm |
MaPUB17 | GSMUA_Achr3T06320_001 | chr3:4302726..4305879 reverse | 3154 | 2805 | 934 | 103.26 | 5.67 | 5 | Nucleus |
MaPUB18 | GSMUA_Achr3T10610_001 | chr3:7831098..7835605 reverse | 4508 | 2745 | 914 | 101.97 | 6.58 | 5 | Nucleus |
MaPUB19 | GSMUA_Achr3T12370_001 | chr3:9151629..9153329 reverse | 1701 | 1701 | 566 | 59.93 | 8.64 | 1 | Cytoplasm |
MaPUB20 | GSMUA_Achr3T14620_001 | chr3:14736420..14738258 reverse | 1839 | 1677 | 558 | 59.6 | 8.58 | 1 | Cytoplasm |
MaPUB21 | GSMUA_Achr3T19660_001 | chr3:20989179..20992456 forward | 3278 | 2946 | 981 | 107.65 | 5.92 | 4 | Nucleus |
MaPUB22 | GSMUA_Achr3T25750_001 | chr3:25831272..25832624 forward | 1353 | 1290 | 429 | 46.17 | 5.38 | 2 | Nucleus |
MaPUB23 | GSMUA_Achr4T00200_001 | chr4:193350..195464 reverse | 2115 | 2115 | 704 | 75.88 | 6.39 | 1 | Nucleus |
MaPUB24 | GSMUA_Achr4T01530_001 | chr4:1265636..1274901 reverse | 9266 | 1836 | 611 | 67.06 | 5.89 | 6 | Cytoplasm, Nucleus |
MaPUB25 | GSMUA_Achr4T03430_001 | chr4:2727458..2728362 reverse | 905 | 810 | 269 | 28.36 | 8.73 | 2 | Nucleus |
MaPUB26 | GSMUA_Achr4T04900_001 | chr4:3844084..3846449 forward | 2366 | 1587 | 528 | 59.15 | 5.65 | 7 | Nucleus |
MaPUB27 | GSMUA_Achr4T05020_001 | chr4:3920776..3926784 forward | 6009 | 2853 | 950 | 105.01 | 5.91 | 5 | Cytoplasm, Nucleus |
MaPUB28 | GSMUA_Achr4T05030_001 | chr4:3927558..3929980 reverse | 2423 | 1575 | 524 | 58.48 | 5.86 | 7 | Nucleus |
MaPUB29 | GSMUA_Achr4T06990_001 | chr4:5215355..5216775 forward | 1421 | 1212 | 403 | 41.42 | 8.56 | 3 | Nucleus |
MaPUB30 | GSMUA_Achr4T07400_001 | chr4:5497755..5499122 reverse | 1368 | 1305 | 434 | 47.46 | 5.63 | 2 | Nucleus |
MaPUB31 | GSMUA_Achr4T11070_001 | chr4:7963314..7965615 reverse | 2302 | 1269 | 422 | 43.29 | 5.56 | 2 | Nucleus |
MaPUB32 | GSMUA_Achr4T14130_001 | chr4:10562237..10563578 forward | 1342 | 1044 | 347 | 37.03 | 5.72 | 2 | Nucleus |
MaPUB33 | GSMUA_Achr5T01020_001 | chr5:597533..598908 forward | 1376 | 1206 | 401 | 42.81 | 8.42 | 2 | Nucleus |
MaPUB34 | GSMUA_Achr5T05220_001 | chr5:3854463..3856370 forward | 1908 | 1458 | 485 | 51.15 | 6.23 | 3 | Nucleus |
MaPUB35 | GSMUA_Achr5T07140_001 | chr5:5158762..5162462 forward | 3701 | 1887 | 628 | 69.15 | 5.75 | 7 | Nucleus |
MaPUB36 | GSMUA_Achr5T08500_001 | chr5:6179256..6185540 reverse | 6285 | 3129 | 1042 | 114.11 | 5.84 | 5 | Nucleus |
MaPUB37 | GSMUA_Achr5T11040_001 | chr5:7966157..7968849 reverse | 2693 | 2094 | 697 | 76.13 | 5.74 | 4 | Nucleus |
MaPUB38 | GSMUA_Achr5T12380_001 | chr5:8892024..8899046 forward | 7023 | 2403 | 800 | 90.49 | 6.39 | 12 | Nucleus |
MaPUB39 | GSMUA_Achr5T13700_001 | chr5:9859570..9861021 forward | 1452 | 1365 | 454 | 48.23 | 8.75 | 1 | Cytoplasm |
MaPUB40 | GSMUA_Achr5T21060_001 | chr5:22947743..22958748 reverse | 11,006 | 2412 | 803 | 90.01 | 5.48 | 9 | Nucleus |
MaPUB41 | GSMUA_Achr5T21360_001 | chr5:23436476..23440174 forward | 3699 | 2280 | 759 | 83.62 | 6.06 | 4 | Cytoplasm, Nucleus |
MaPUB42 | GSMUA_Achr5T28670_001 | chr5:28750592..28755063 reverse | 4472 | 1713 | 570 | 62.66 | 5.75 | 6 | Nucleus |
MaPUB43 | GSMUA_Achr6T02470_001 | chr6:1615103..1616422 reverse | 1320 | 1143 | 380 | 40.98 | 8.69 | 3 | Nucleus |
MaPUB44 | GSMUA_Achr6T06560_001 | chr6:4418997..4420524 forward | 1528 | 1122 | 373 | 40.57 | 7.67 | 2 | Nucleus |
MaPUB45 | GSMUA_Achr6T10990_001 | chr6:7323129..7324847 reverse | 1719 | 1719 | 572 | 59.6 | 8.22 | 1 | Cytoplasm, Nucleus |
MaPUB46 | GSMUA_Achr6T11310_001 | chr6:7517739..7519221 reverse | 1483 | 1143 | 380 | 41.25 | 6.73 | 3 | Nucleus |
MaPUB47 | GSMUA_Achr6T18140_001 | chr6:12201719..12203017 reverse | 1299 | 1230 | 409 | 43.26 | 5.84 | 2 | Nucleus |
MaPUB48 | GSMUA_Achr6T22980_001 | chr6:22176387..22181121 reverse | 4735 | 1884 | 627 | 69.88 | 8.57 | 10 | Nucleus |
MaPUB49 | GSMUA_Achr6T25390_001 | chr6:26469894..26479975 reverse | 10,082 | 5637 | 1878 | 202.19 | 5.28 | 7 | Cytoplasm, Nucleus |
MaPUB50 | GSMUA_Achr6T25670_001 | chr6:26728664..26729950 forward | 1287 | 1287 | 428 | 44.86 | 8.66 | 1 | Nucleus |
MaPUB51 | GSMUA_Achr6T28500_001 | chr6:28868630..28876365 forward | 7736 | 1833 | 610 | 67.96 | 8.79 | 9 | Nucleus |
MaPUB52 | GSMUA_Achr6T36530_001 | chr6:34466958..34471270 reverse | 4313 | 1983 | 660 | 72.48 | 6.42 | 6 | Nucleus |
MaPUB53 | GSMUA_Achr7T04450_001 | chr7:3366660..3370421 forward | 3762 | 2349 | 798 | 88.28 | 7.88 | 11 | Nucleus |
MaPUB54 | GSMUA_Achr7T05890_001 | chr7:4367855..4369228 forward | 1374 | 1374 | 457 | 48.06 | 9.35 | 1 | Cytoplasm |
MaPUB55 | GSMUA_Achr7T09440_001 | chr7:7719776..7722069 forward | 2294 | 1917 | 638 | 70.34 | 8.95 | 4 | Nucleus |
MaPUB56 | GSMUA_Achr7T09650_001 | chr7:7847312..7851814 reverse | 4503 | 2208 | 735 | 82.73 | 8.7 | 10 | Cell membrane, Chloroplast, Cytoplasm, Nucleus |
MaPUB57 | GSMUA_Achr7T17740_001 | chr7:20510968..20523478 reverse | 12,511 | 6279 | 2092 | 223.93 | 5.63 | 9 | Cytoplasm, Nucleus |
MaPUB58 | GSMUA_Achr7T18640_001 | chr7:21413794..21415228 forward | 1435 | 1140 | 379 | 41.34 | 6.41 | 3 | Cell membrane, Nucleus |
MaPUB59 | GSMUA_Achr7T19940_001 | chr7:22941467..22943503 reverse | 2037 | 1590 | 529 | 55.7 | 8.55 | 3 | Nucleus |
MaPUB60 | GSMUA_Achr7T22130_001 | chr7:24687902..24690206 reverse | 2305 | 1902 | 633 | 68.33 | 6.17 | 3 | Nucleus |
MaPUB61 | GSMUA_Achr7T23310_001 | chr7:25579820..25581016 forward | 1197 | 1197 | 398 | 43.4 | 8.95 | 1 | Nucleus |
MaPUB62 | GSMUA_Achr8T01360_001 | chr8:1146290..1151389 forward | 5100 | 1731 | 576 | 63.53 | 8.57 | 8 | Nucleus |
MaPUB63 | GSMUA_Achr8T04940_001 | chr8:3264288..3266015 forward | 1728 | 1299 | 432 | 46.78 | 5.51 | 2 | Nucleus |
MaPUB64 | GSMUA_Achr8T09590_001 | chr8:6746141..6747127 forward | 987 | 987 | 328 | 33.95 | 5.91 | 1 | Nucleus |
MaPUB65 | GSMUA_Achr8T11510_001 | chr8:8320562..8327700 forward | 7139 | 2552 | 850 | 95.41 | 6.12 | 11 | Nucleus |
MaPUB66 | GSMUA_Achr8T12630_001 | chr8:9406796..9419285 forward | 12,490 | 1571 | 526 | 57.29 | 6.33 | 18 | Nucleus |
MaPUB67 | GSMUA_Achr8T25140_001 | chr8:29062381..29066399 reverse | 4019 | 1263 | 420 | 44.9 | 7.71 | 4 | Nucleus |
MaPUB68 | GSMUA_Achr8T30420_001 | chr8:32504280..32505566 forward | 1287 | 822 | 273 | 29.04 | 8.75 | 3 | Nucleus |
MaPUB69 | GSMUA_Achr9T00690_001 | chr9:540580..541705 forward | 1126 | 660 | 219 | 23.38 | 9.33 | 2 | Cytoplasm, Nucleus |
MaPUB70 | GSMUA_Achr9T01670_001 | chr9:1306678..1309170 forward | 2493 | 1401 | 466 | 50.56 | 8.52 | 2 | Nucleus |
MaPUB71 | GSMUA_Achr9T08750_001 | chr9:5638998..5640625 forward | 1628 | 1038 | 345 | 36.08 | 8.47 | 3 | Nucleus |
MaPUB72 | GSMUA_Achr9T12570_001 | chr9:8175348..8180293 reverse | 4946 | 903 | 300 | 31.91 | 6.01 | 2 | Nucleus |
MaPUB73 | GSMUA_Achr9T14450_001 | chr9:9395076..9397076 reverse | 2001 | 1398 | 465 | 49.29 | 8.95 | 5 | Nucleus |
MaPUB74 | GSMUA_Achr9T14560_001 | chr9:9502271..9504578 reverse | 2308 | 1758 | 585 | 63.11 | 8.67 | 3 | Nucleus |
MaPUB75 | GSMUA_Achr9T15600_001 | chr9:10315534..10319034 forward | 3501 | 2031 | 676 | 75.01 | 6.85 | 7 | Nucleus |
MaPUB76 | GSMUA_Achr9T28820_001 | chr9:32677125..32679340 reverse | 2216 | 1800 | 599 | 64.89 | 9.09 | 4 | Nucleus |
MaPUB77 | GSMUA_Achr9T29420_001 | chr9:33126026..33130242 reverse | 4217 | 1836 | 611 | 68.18 | 6.64 | 9 | Nucleus |
MaPUB78 | GSMUA_Achr10T04850_001 | chr10:14480133..14481503 forward | 1371 | 735 | 244 | 26.1 | 4.96 | 2 | Nucleus |
MaPUB79 | GSMUA_Achr10T09450_001 | chr10:19291616..19292842 forward | 1227 | 1155 | 384 | 40.37 | 8.41 | 2 | Nucleus |
MaPUB80 | GSMUA_Achr10T11310_001 | chr10:20821803..20823180 forward | 1378 | 1119 | 372 | 39.55 | 6.28 | 3 | Nucleus |
MaPUB81 | GSMUA_Achr10T17120_001 | chr10:24446918..24449504 reverse | 2587 | 1125 | 374 | 40.87 | 6.14 | 2 | Nucleus |
MaPUB82 | GSMUA_Achr10T17900_001 | chr10:24916493..24917809 forward | 1317 | 1131 | 376 | 40.82 | 8.25 | 3 | Nucleus |
MaPUB83 | GSMUA_Achr10T22180_001 | chr10:27439361..27448280 reverse | 8920 | 4041 | 1346 | 148.98 | 5.49 | 14 | Nucleus |
MaPUB84 | GSMUA_Achr10T22750_001 | chr10:27801994..27810019 forward | 8026 | 2631 | 876 | 98.61 | 6.12 | 11 | Cell membrane, Nucleus |
MaPUB85 | GSMUA_Achr10T22780_001 | chr10:27821009..27830243 forward | 9235 | 2595 | 864 | 96.02 | 8.5 | 14 | Nucleus |
MaPUB86 | GSMUA_Achr10T27710_001 | chr10:30760030..30761828 reverse | 1799 | 1359 | 452 | 50.07 | 5.87 | 5 | Nucleus |
MaPUB87 | GSMUA_Achr11T02530_001 | chr11:1736304..1752382 reverse | 16,079 | 1581 | 526 | 57.22 | 6.41 | 18 | Nucleus |
MaPUB88 | GSMUA_Achr11T06020_001 | chr11:4516270..4520590 reverse | 4321 | 2040 | 679 | 73.94 | 7.63 | 3 | Nucleus |
MaPUB89 | GSMUA_Achr11T09460_001 | chr11:7338409..7341969 forward | 3561 | 1278 | 425 | 45.72 | 8.17 | 3 | Nucleus |
MaPUB90 | GSMUA_Achr11T20980_001 | chr11:21780963..21789676 reverse | 8714 | 2400 | 799 | 89.46 | 5.71 | 9 | Nucleus |
MaPUB91 | GSMUA_AchrUn_randomT07480_001 | chrUn_random:32367065..32372845 forward | 5781 | 2403 | 800 | 90.95 | 6.37 | 11 | Nucleus |
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Hu, H.; Dong, C.; Sun, D.; Hu, Y.; Xie, J. Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana. Int. J. Mol. Sci. 2018, 19, 3874. https://doi.org/10.3390/ijms19123874
Hu H, Dong C, Sun D, Hu Y, Xie J. Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana. International Journal of Molecular Sciences. 2018; 19(12):3874. https://doi.org/10.3390/ijms19123874
Chicago/Turabian StyleHu, Huigang, Chen Dong, Dequan Sun, Yulin Hu, and Jianghui Xie. 2018. "Genome-Wide Identification and Analysis of U-Box E3 Ubiquitin-Protein Ligase Gene Family in Banana" International Journal of Molecular Sciences 19, no. 12: 3874. https://doi.org/10.3390/ijms19123874