Table 3 Citrus unigenes that share homology to flowering-time genes of other plants.
Gene ID | Gene Length | Reads (MT) | Reads (WT) | Accession number | Identity (%) | E-value | Protein function (species) |
|---|---|---|---|---|---|---|---|
Photoperiod pathway | |||||||
U8650 | 1327 | 379 | 348 | XM_002523031 | 728/1003 (72%) | 5E-152 | PHYA (Ricinus communis) |
U20394 | 1643 | 233 | 275 | XM_002512550 | 1175/1500 (78%) | 0 | PHYA (Ricinus communis) |
U1862 | 4042 | 2219 | 2668 | XM_002519184 | 2759/3356 (82%) | 0 | PHYB (Ricinus communis) |
U11402 | 4270 | 748 | 829 | EU436651 | 1638/2059 (79%) | 0 | PHYC (Vitis vinifera) |
U29320 | 871 | 16 | 24 | EU436656 | 541/690 (78%) | 1E-163 | PHYE (Vitis riparia) |
U2208 | 3284 | 710 | 700 | U39787 | 2162/2958 (73%) | 0 | PHYE (Ipomoea nil) |
U8176 | 960 | 1809 | 1231 | NM_112521 | 329/460 (71%) | 4E-57 | PAP1 (Arabidopsis thaliana) |
U13637 | 1705 | 118 | 146 | XM_002275300 | 1396/1706 (81%) | 0 | PIE1 (Vitis vinifera) |
U10186 | 1611 | 49 | 92 | XM_002275300 | 1052/1475 (71%) | 0 | PIE1 (Vitis vinifera) |
U2658 | 3452 | 637 | 670 | XM_002275300 | 2232/2909 (76%) | 0 | PIE1 (Vitis vinifera) |
U12327 | 1159 | 447 | 554 | NM_179665 | 59/75 (78%) | 1E-06 | PIL5 (Arabidopsis thaliana) |
U21857 | 3019 | 1115 | 1080 | NM_102365 | 1678/2388 (70%) | 0 | PFT1 (Arabidopsis thaliana) |
U8820 | 1615 | 184 | 194 | NM_119618 | 220/271 (81%) | 5E-65 | CIB1 (Arabidopsis thaliana) |
U11824 | 2226 | 89 | 148 | NM_120506 | 463/579 (79%) | 1E-143 | ELF6 (Arabidopsis thaliana) |
U9378 | 598 | 14 | 16 | NM_148863 | 212/268 (79%) | 2E-57 | REF6 (Arabidopsis thaliana) |
U1219 | 3191 | 300 | 297 | NM_148863 | 287/371 (77%) | 6E-74 | REF6 (Arabidopsis thaliana) |
U9118 | 2795 | 3825 | 4339 | FJ882041 | 1486/1938 (76%) | 0 | CRY2 (Fragaria vesca) |
U1555 | 3639 | 439 | 401 | NM_122394 | 359/463 (77%) | 3E-97 | CRY3 (Arabidopsis thaliana) |
U9204 | 2765 | 1785 | 2109 | NM_116961 | 1364/1731 (78%) | 0 | CRY1 (Arabidopsis thaliana) |
U12873 | 3154 | 940 | 911 | XM_002268467 | 2102/2575 (81%) | 0 | FHY3 (Vitis vinifera) |
U20135 | 629 | 33 | 30 | AY830926 | 82/105 (78%) | 2E-27 | ELF4 (Pisum sativum) |
U31613 | 682 | 7 | 20 | AY830926 | 153/213 (71%) | 4E-24 | ELF4 (Pisum sativum) |
U18048 | 2019 | 507 | 568 | NM_106379 | 352/491 (71%) | 3E-62 | EFS (Arabidopsis thaliana) |
U9915 | 867 | 372 | 363 | EU916963 | 475/636 (74%) | 4E-113 | ELF4 (Citrus sinensis) |
U861 | 501 | 103 | 87 | EU916963 | 380/461 (82%) | 5E-122 | ELF4 (Citrus sinensis) |
U5852 | 687 | 497 | 341 | EU916963 | 661/669 (98%) | 0 | ELF4 (Citrus sinensis) |
Circadian clock | |||||||
U10400 | 2627 | 907 | 1052 | DQ371901 | 1516/1849 (81%) | 0 | ZTL2 (Glycine max) |
U17912 | 1648 | 1194 | 1240 | AY611028 | 803/1067 (75%) | 0 | TOC1 (Castanea sativa) |
U12636 | 870 | 81 | 108 | AY611028 | 134/162 (82%) | 1E-37 | TOC1 (Castanea sativa) |
U10936 | 3030 | 753 | 1022 | NM_128153 | 94/109 (86%) | 1E-25 | ELF3 (Arabidopsis thaliana) |
U10110 | 3033 | 812 | 934 | AY371292 | 285/380 (75%) | 7E-60 | ELF3 (Mesembryanthemum) |
U33021 | 293 | 12 | 17 | NM_102715 | 84/117 (71%) | 1E-06 | RKF1 (Arabidopsis thaliana) |
U10089 | 381 | 17 | 14 | NM_102715 | 241/351 (68%) | 4E-26 | RKF1 (Arabidopsis thaliana) |
U12503 | 2363 | 229 | 258 | NM_130368 | 726/1031 (70%) | 3E-127 | RKF3 (Arabidopsis thaliana) |
U9215 | 3251 | 2563 | 2990 | XM_002524295 | 2328/2901 (80%) | 0 | GI (Ricinus communis) |
U7045 | 559 | 765 | 891 | XM_002524295 | 463/559 (82%) | 5E-161 | GI (Ricinus communis) |
U9165 | 2436 | 716 | 860 | NM_105475 | 1303/1747 (74%) | 0 | FKF1 (Arabidopsis thaliana) |
Vernalization pathway | |||||||
U9585 | 1466 | 67 | 133 | NM_111874 | 1079/1457 (74%) | 0 | FLD (Arabidopsis thaliana) |
U22618 | 1361 | 200 | 211 | NM_111874 | 367/527 (69%) | 3E-54 | FLD (Arabidopsis thaliana) |
U23858 | 458 | 5 | 2 | NM_111874 | 141/185 (76%) | 1E-28 | FLD (Arabidopsis thaliana) |
U4972 | 283 | 72 | 95 | NM_111333 | 217/281 (77%) | 8E-53 | FLK (Arabidopsis thaliana) |
U2940 | 947 | 298 | 402 | NM_111333 | 143/171 (83%) | 2E-42 | FLK (Arabidopsis thaliana) |
U8380 | 1094 | 588 | 690 | NM_111333 | 531/714 (74%) | 3E-122 | FLK (Arabidopsis thaliana) |
U15692 | 502 | 860 | 282 | EU497679 | 327/327 (100%) | 2E-165 | FLC9 (Poncirus trifoliata) |
U12215 | 691 | 377 | 180 | EU605888 | 668/671 (99%) | 0 | FLC7 (Poncirus trifoliata) |
U11512 | 2236 | 258 | 293 | XM_002511008 | 453/635 (71%) | 2E-83 | FRI (Ricinus communis) |
U2597 | 2060 | 637 | 638 | XM_002524905 | 1369/1728 (79%) | 0 | FRI (Ricinus communis) |
U11002 | 1954 | 405 | 491 | XM_002529001 | 289/452 (63%) | 8E-51 | FRI (Ricinus communis) |
U767 | 2311 | 257 | 227 | XM_002266277 | 289/452 (63%) | 8E-51 | FRI (Ricinus communis) |
U17929 | 1689 | 828 | 767 | NM_113199 | 926/1232 (75%) | 0 | LFR (Arabidopsis thaliana) |
U14324 | 3620 | 950 | 928 | XM_002520611 | 621/839 (74%) | 2E-144 | LUM (Ricinus communis) |
U12966 | 1832 | 396 | 399 | EU884426 | 937/1258 (74%) | 0 | VRN2-1 (Malus × domestica) |
U8773 | 1681 | 1784 | 1643 | EF064791 | 81/111 (72%) | 9E-05 | VIN3-1 (Arabidopsis thaliana) |
U17262 | 1894 | 191 | 161 | EF064791 | 218/294 (74%) | 4E-41 | VIN3-1 (Arabidopsis thaliana) |
U11331 | 1533 | 813 | 846 | EF064792 | 665/963 (69%) | 1E-97 | VIN3-2 (Arabidopsis thaliana) |
U17602 | 1306 | 951 | 885 | NM_119129 | 713/967 (73%) | 5E-171 | VIP3 (Arabidopsis thaliana) |
U23612 | 1156 | 148 | 117 | NM_112785 | 38/47 (80%) | 1.4 | VRN1 (Arabidopsis thaliana) |
U8880 | 1600 | 512 | 515 | NM_112785 | 284/384 (73%) | 1E-59 | VRN1 (Arabidopsis thaliana) |
U7754 | 1102 | 273 | 191 | NM_112785 | 127/183 (69%) | 6E-11 | VRN1 (Arabidopsis thaliana) |
U9616 | 1943 | 550 | 469 | NM_102836 | 748/1086 (68%) | 5E-110 | SUF4 (Arabidopsis thaliana) |
U9937 | 953 | 38 | 41 | GQ177180 | 86/120 (71%) | 1E-06 | FES1 (Arabidopsis thaliana) |
U34190 | 1385 | 121 | 129 | NM_179890 | 176/259 (67%) | 2E-13 | FES1 (Arabidopsis thaliana) |
U12018 | 1939 | 288 | 248 | NM_121191 | 63/81 (77%) | 7E-07 | EMF1 (Arabidopsis thaliana) |
U11876 | 2468 | 769 | 751 | XM_002281643 | 1519/2012 (75%) | 0 | EMF2 (Vitis vinifera) |
U2303 | 1580 | 677 | 580 | NM_112965 | 784/1037 (75%) | 0 | FIE (Arabidopsis thaliana) |
Autonomous pathway | |||||||
U15708 | 416 | 21 | 23 | XM_002519206 | 146/185 (78%) | 4E-33 | FCA (Ricinus communis) |
U13760 | 1112 | 593 | 591 | XM_002519206 | 146/185 (78%) | 4E-33 | FCA (Ricinus communis) |
U9139 | 2236 | 883 | 868 | AK229352 | 75/97 (77%) | 2E-10 | FCA (Arabidopsis thaliana) |
U32661 | 983 | 8 | 8 | AK229352 | 75/97 (77%) | 2E-10 | FCA (Arabidopsis thaliana) |
U20071 | 955 | 126 | 82 | AK229352 | 75/97 (77%) | 2E-10 | FCA (Arabidopsis thaliana) |
Floral pathway integrator | |||||||
U19004 | 346 | 6 | 3 | EU032531 | 167/170 (98%) | 5E-76 | SOC1-1 (Citrus sinensis) |
U3347 | 353 | 22 | 8 | EU032532 | 343/353 (97%) | 4E-166 | SOC1- 2 (Citrus sinensis) |
U1570 | 283 | 8 | 6 | EU032532 | 244/281 (86%) | 2E-98 | SOC1-2 (Citrus sinensis) |
U27861 | 691 | 43 | 12 | AB301935 | 672/695 (96%) | 0 | CiFT (Citrus unshiu) |
U27120 | 303 | 12 | 0 | AY338974 | 298/303 (98%) | 1E-145 | AP1 (Citrus sinensis) |
U17717 | 1389 | 1066 | 1165 | DQ371898 | 340/433 (78%) | 5E-96 | CO2 (Glycine max) |
U2713 | 1871 | 799 | 962 | NM_001125127 | 279/375 (74%) | 9E-56 | CO9 (Arabidopsis thaliana) |
U17161 | 836 | 1317 | 1623 | FJ719767 | 538/716 (75%) | 4E-132 | CO (Mangifera indica) |
U8846 | 1586 | 2570 | 1905 | GQ864262 | 250/360 (69%) | 2E-32 | CO8 (Glycine max) |
U36503 | 1822 | 849 | 875 | GQ864265 | 114/140 (81%) | 4E-28 | CO (Glycine max) |
U9364 | 1051 | 128 | 123 | GQ864265 | 92/129 (71%) | 4E-07 | CO (Glycine max) |
U2300 | 1394 | 589 | 840 | GQ864263 | 116/147 (78%) | 6E-25 | CO9 (Glycine max) |
Other flowering genes | |||||||
U5505 | 430 | 23 | 13 | U78949 | 331/396 (83%) | 2E-114 | MADS3 (Malus domestica) |
U13903 | 870 | 147 | 137 | DQ500880 | 470/617 (76%) | 4E-126 | MADS3 (Populus tomentosa) |
U1579 | 1210 | 152 | 93 | XM_002301057 | 526/669 (78%) | 2E-156 | MADS9 (Populus tomentosa) |
U6983 | 545 | 908 | 706 | AB218613 | 543/545 (99%) | 0 | CitMADS6 (Citrus unshiu) |
U34186 | 773 | 14 | 35 | AB218614 | 440/551 (79%) | 2E-136 | CitMADS8 (Citrus unshiu) |
U24167 | 336 | 9 | 5 | AB218611 | 286/336 (85%) | 0 | CitMADS3 (Citrus unshiu) |
U12163 | 996 | 276 | 85 | AB218612 | 677/686 (98%) | 0 | CitMADS5 (Citrus unshiu) |
U217 | 490 | 22 | 31 | NM_001084836 | 78/96 (81%) | 1E-15 | AGL16 (Arabidopsis thaliana) |
U9295 | 1938 | 2427 | 2378 | NM_101733 | 308/390 (78%) | 9E-88 | AGL65 (Arabidopsis thaliana) |
U8625 | 2045 | 400 | 316 | NM_105623 | 343/487 (70%) | 1E-55 | AGL94 (Arabidopsis thaliana) |
U20726 | 1826 | 257 | 166 | XM_002326128 | 450/604 (74%) | 7E-102 | AP2 (Populus trichocarpa) |
U12861 | 1107 | 443 | 679 | FJ809943 | 818/820 (99%) | 0 | AP2 (Poncirus trifoliata) |
U23896 | 275 | 11 | 3 | AY256859 | 210/277 (75%) | 3E-45 | AP1 (Vitis vinifera) |
U24321 | 344 | 14 | 5 | GU357461 | 218/335 (65%) | 2E-11 | SEP1 (Euptelea pleiosperma) |
U4356 | 1096 | 319 | 190 | AB218614 | 627/636 (98%) | 0 | CitMADS8 (Citrus unshiu) |
U3656 | 2411 | 1156 | 1400 | NM_180137 | 534/715 (74%) | 5E-130 | SPL1 (Arabidopsis thaliana) |
U12668 | 2514 | 1897 | 1917 | AJ011628.1 | 437/609 (71%) | 0 | SPL1(Arabidopsis thaliana) |
U9906 | 4081 | 1684 | 1828 | NM_101951 | 1803/2671 (67%) | 0 | SPL14 (Arabidopsis thaliana) |
U3220 | 3148 | 854 | 790 | NM_180519 | 1221/1790 (68%) | 2E-168 | SPL7 (Arabidopsis thaliana) |
U11760 | 1435 | 168 | 143 | HM018601 | 335/469 (71%) | 8E-62 | SPL10 (Vitis vinifera) |
U17573 | 1158 | 162 | 161 | XM_002517836 | 319/400 (79%) | 5E-95 | SPL (Ricinus communis) |
U31888 | 713 | 50 | 41 | FJ502237 | 595/639 (93%) | 0 | SPL9 (Poncirus trifoliata) |
U23754 | 732 | 15 | 11 | FJ502238 | 563/576 (97%) | 0 | SPL13 (Poncirus trifoliata) |
U12575 | 1329 | 71 | 81 | FJ502238 | 1272/1326 (95%) | 0 | SPL13 (Poncirus trifoliata) |
U8652 | 1325 | 1020 | 1130 | NM_180137 | 734/1115 (65%) | 9E-86 | SPL1 (Arabidopsis thaliana) |
U9909 | 2323 | 99 | 162 | NM_105584 | 176/240 (73%) | 1E-30 | SPL6 (Arabidopsis thaliana) |
U12495 | 1047 | 460 | 397 | FJ373211 | 428/435 (98%) | 0 | SVP (Poncirus trifoliata) |
U10522 | 1710 | 454 | 450 | AB290727 | 719/1066 (67%) | 8E-88 | TFL2 (Malus × domestica) |