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AGRP

Asteraceae Genomic Research Platform

Gene Search

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Example:

Hierarchical alignments with the Vitis vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Vitis vinifera as a reference, and by comparing homologous gene locus maps and Ks values between Vitis vinifera and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 219×23,647 macro-matrices.
Select Vivi_1 Arla_1 Armi_1 Sain_1 Ceso_1 Cati_1 Ccar_1 Cien_1 Cich_1 Lssa_1 Laca_1 Tako_1 Tamo_1 Pslu_1 Lomi_1 Lomi_2 Enbr_1 Ecan_1 Soca_1 Glco_1 Artr_1 Aary_1 Aary_2 Aann_1 Chma_1 Chmo_1 Chmo_2 Chmo_3 Chla_1 Chna_1 Cind_1 Pdy_1 Cobi_1 Hean_1 Bial_1 Bial_2 Dapi_1 Dapi_2 Hetu_1 Hetu_2 Hetu_3 Amtr_1 Smso_1 Smso_2 Taer_1 Fro_1 Fso_1 Ftr_1 Fra_1 Fli_1 Stre_1 Mimi_1 Cobi_2 Hean_2 Bial_3 Bial_4 Dapi_3 Dapi_4 Hetu_4 Hetu_5 Hetu_6 Amtr_2 Smso_3 Smso_4 Taer_2 Fro_2 Fso_2 Ftr_2 Fra_2 Fli_2
Vivi19g00894 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00895 Arla1g00395 Armi1g00484 Sain12g00439 . Cati3g00548 . Cien5g03191 Cich4g04480 Lssa7g03449 Laca7g02790 Tako4g03983 . . Lomi1g00290 Lomi2g04366 . Ecan3g02145 Soca5g02517 . . . . . Chma7g08130 Chmo13g00765 . Chmo15g00637 . Chna2g00628 . Pdy4g00501 . Hean15g03916 Bial24g02231 Bial12g02372 . . Hetu17g02532 Hetu16g02646 Hetu18g02803 Amtr02g04071 . . . . . . . . . Mimi9g01366 . . . . . . . . . . . . . . . . . .
Vivi19g00896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00897 Arla1g00397 Armi1g00487 Sain12g00442 Ceso2g01363 Cati3g00550 Ccar2g01994 Cien5g03189 Cich4g04476 Lssa7g03446 Laca7g02786 Tako4g03984 . . Lomi1g00289 Lomi2g04367 . Ecan3g02144 Soca5g02518 Glco3g01098 . . . Aann4g01150 Chma7g08131 Chmo13g00764 . Chmo15g00636 . Chna2g00613 . Pdy4g00499 . Hean15g03913 . . . . . . . . . . . . . . . . . . Cobi4g03116 Hean11g00768 . . . . . . . . . . . . . . . .
Vivi19g00898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00900 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00901 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00902 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 71864019 71872830 - chr1g0064731 Aann1g02294 2294
4 61369062 61372261 + chr4g0776741 Aann4g01150 1150
7 216272075 216274379 - Aargg7g25560.1 Aary7g02556 2556
2 81201470 81205368 - AtrifAMIRv0_Chr02g0136671 Amtr02g04071 4071
7 16980209 16983252 - AtrifAMIRv0_Chr07g0463751 Amtr07g01228 1228
1 9038816 9041231 + evm.model.000012F.502.1 Arla1g00395 395
1 9127518 9130043 + evm.model.000012F.505 Arla1g00397 397
8 7503485 7505737 + evm.model.000043F.447 Arla8g00347 347
8 7711206 7714200 + evm.model.000043F.442 Arla8g00350 350
1 9677020 9678975 + AmiAMIRv0_Chr01g0004841 Armi1g00484 484
1 9805227 9807510 + AmiAMIRv0_Chr01g0004871 Armi1g00487 487
8 92649015 92651272 - AmiAMIRv0_Chr08g0292801 Armi8g02449 2449
1 54128411 54136621 + AtridAMIRv0_Chr01g0018611 Artr1g01861 1861
12 54045200 54048788 + g35571.t1 Bial12g02372 2372
24 52917716 52920474 + g67897.t1 Bial24g02231 2231
3 5495508 5499314 + CtAH03T0038300.1 Cati3g00548 548
3 5533561 5536282 + CtAH03T0038400.2 Cati3g00550 550
7 68560817 68563138 + CtAH07T0235000.1 Cati7g03177 3177
2 66819775 66821956 - gnl|WGS:LEKV|Ccrd_011041.mRNA.1_mrna Ccar2g01994 1994
17 2877415 2881708 + gnl|WGS:LEKV|Ccrd_019587.mRNA.1_mrna Ccar17g00265 265
17 2936790 2938862 + gnl|WGS:LEKV|Ccrd_019589.mRNA.1_mrna Ccar17g00267 267
2 27619394 27622013 + >KAJ9560695.1 Ceso2g01363 1363
4 27901054 27906844 + >KAJ9551523.1 Ceso4g01584 1584
6 43142811 43145131 - CmaNakai_Chr06g0530711 Chma6g01922 1922
7 277249596 277257003 + CmaNakai_Chr07g0704321 Chma7g08130 8130
7 277304519 277307776 + CmaNakai_Chr07g0704331 Chma7g08131 8131
13 37582537 37584903 - evm.model.scaffold_461.83 Chmo13g00764 764
13 37646495 37655398 - evm.model.scaffold_461.86 Chmo13g00765 765
15 34861341 34864069 - evm.model.scaffold_126.108 Chmo15g00636 636
15 34952459 34955437 - evm.model.scaffold_126.102 Chmo15g00637 637
22 294407952 294409274 - evm.model.scaffold_448.483 Chmo22g04875 4875
22 294409293 294409983 - evm.model.scaffold_448.484 Chmo22g04876 4876
23 286837627 286838043 - evm.model.scaffold_1107.22 Chmo23g04823 4823
23 286891089 286893139 - evm.model.scaffold_1107.15 Chmo23g04828 4828
24 290793596 290802437 - evm.model.scaffold_421.330 Chmo24g04828 4828
24 290964615 290968904 - evm.model.scaffold_421.323 Chmo24g04830 4830
2 42906394 42909141 - Cn0067340 Chna2g00613 613
2 45899058 45902049 - Cn0653240 Chna2g00628 628
5 44230099 44232099 + Cn0367380 Chna5g00897 897
5 44423758 44425893 + Cn0367450 Chna5g00901 901
4 130727675 130729106 - KAI3753611.1 Cich4g04476 4476
4 130799094 130801035 - KAI3753615.1 Cich4g04480 4480
7 16120292 16123992 - KAI3708224.1 Cich7g00476 476
5 77197525 77198968 - KAI3509709.1 Cien5g03189 3189
5 77264001 77264786 - KAI3509711.1 Cien5g03191 3191
9 47011878 47015059 + KAI3497192.1 Cien9g02328 2328
1 360096944 360099132 - D.indicum_Contig40_G00064.t1 Cind1g03301 3301
4 80608980 80611378 + h2tg000009l_1.g42163.t1 Cobi4g03116 3116
12 95776320 95779815 - h2tg000104l.g32318.t1 Dapi12g01341 1341
3 32277310 32279707 - XM_043763425.1 Ecan3g02144 2144
3 32292039 32294866 - XM_043765493.1 Ecan3g02145 2145
5 30068563 30070465 - XM_043773695.1 Ecan5g01633 1633
4 82589844 82591804 - FliAMIRv0_Chr04g0109571 Fli4g01368 1368
8 9699836 9702675 + FraAMIRv0_Chr08g0144101 Fra8g01011 1011
9 25493448 25495152 - FroAMIRv0_Chr09g0138121 Fro9g01263 1263
11 10719070 10720582 + FsoAMIRv0_Chr11g0268781 Fso11g01050 1050
8 11229394 11231786 + FtrAMIRv0_Chr08g0229901 Ftr8g00913 913
3 66629024 66630665 + GcoAMIRv0_Chr03g0167271 Glco3g01098 1098
7 576461006 576464165 - GcoAMIRv0_Chr07g0516551 Glco7g06870 6870
3 124123970 124126401 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr03g0114031 Hean3g02248 2248
11 17436435 17440221 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474921 Hean11g00768 768
15 148920708 148923554 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0716211 Hean15g03913 3913
15 149476867 149479824 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0716251 Hean15g03916 3916
7 71676863 71677198 + >Htub.h1tg000735l.g139.t1 Hetu7g01731 1731
8 66803827 66804213 + >Htub.h1tg003382l.g359.t1 Hetu8g01560 1560
16 141262062 141264512 + >Htub.h1tg002434l.g136.t1 Hetu16g02646 2646
17 133432758 133435208 + >Htub.h1tg000886l.g443.t1 Hetu17g02532 2532
18 141260294 141262744 + >Htub.h1tg002759l.g169.t1 Hetu18g02803 2803
7 133996466 133998451 - CAI9294974.1 Laca7g02786 2786
7 134385475 134387732 - CAI9294978.1 Laca7g02790 2790
9 132975709 132977610 + CAI9303860.1 Laca9g03267 3267
1 2487292 2488872 - LmiAMIRv0_Chr01g0002891 Lomi1g00289 289
1 2495361 2497653 - LmiAMIRv0_Chr01g0002901 Lomi1g00290 290
2 48998387 49000667 + LmiAMIRv0_Chr02g0088991 Lomi2g04366 4366
2 49008242 49009963 + LmiAMIRv0_Chr02g0089001 Lomi2g04367 4367
5 31893323 31895474 - LmiAMIRv0_Chr05g0177741 Lomi5g02125 2125
11 27920008 27920530 - LmiAMIRv0_Chr11g0339221 Lomi11g01951 1951
7 182217360 182219073 - >KAJ0197778.1 Lssa7g03446 3446
7 182736145 182738478 - >KAJ0197204.1 Lssa7g03449 3449
9 183824754 183826285 + >KAJ0188686.1 Lssa9g03704 3704
9 41446276 41456641 - KAD5318101.1 Mimi9g01366 1366
14 21258260 21263445 + KAD4179015.1 Mimi14g01078 1078
4 9352144 9353737 - PdyAMIRv0_Chr04g0153061 Pdy4g00499 499
4 9426180 9428151 - PdyAMIRv0_Chr04g0153081 Pdy4g00501 501
9 41729411 41731244 - PdyAMIRv0_Chr09g0346491 Pdy9g01842 1842
12 9208471 9210573 + SinAMIRv0_Chr12g0360031 Sain12g00439 439
12 9254059 9256146 + SinAMIRv0_Chr12g0360061 Sain12g00442 442
13 131859587 131862556 - SinAMIRv0_Chr13g0398941 Sain13g02338 2338
9 15616748 15619308 + KAI3804871.1 Smso9g00677 677
18 73840941 73842876 - KAI3755704.1 Smso18g01579 1579
5 27191950 27194880 + transfrag11148.t01 Soca5g02517 2517
5 27223662 27225747 + transfrag11149.t01 Soca5g02518 2518
3 80168579 80170039 + >KAK1431066.1 Taer3g03098 3098
4 89645797 89648230 + TkA04G355490.1 Tako4g03983 3983
4 89697753 89699580 + TkA04G355690.1 Tako4g03984 3984
19 15309713 15310119 + GSVIVT01000679001 Vivi19g00894 894
19 15403004 15406647 + GSVIVT01000682001 Vivi19g00895 895
19 15466461 15470255 - GSVIVT01000684001 Vivi19g00896 896
19 15497729 15499650 + GSVIVT01000687001 Vivi19g00897 897
19 15603207 15604930 + GSVIVT01000689001 Vivi19g00898 898
19 15646369 15646734 + GSVIVT01000691001 Vivi19g00899 899
19 15663551 15663916 + GSVIVT01000692001 Vivi19g00900 900
19 15754698 15779104 + GSVIVT01000696001 Vivi19g00901 901
19 15779470 15780216 - GSVIVT01000697001 Vivi19g00902 902
19 15810821 15811240 + GSVIVT01000700001 Vivi19g00903 903
       
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