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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
Vivi19g01184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01189 Arla1g00071 Armi1g00082 Sain12g00085 Ceso2g03204 Cati3g00106 Ccar2g02327 Cien5g03526 Cich4g04845 Lssa7g03768 . Tako4g02940 . Pslu1g20747 Lomi1g00445 Lomi2g04199 Enbr6g03203 Ecan3g00226 Soca5g05380 Glco3g01531 . . . . Chma7g07452 Chmo13g01105 . Chmo15g00972 . Chna2g00943 Cind3g02058 Pdy4g00833 . . . . . . . . . . . . . . . . . . . . Cobi4g02813 Hean11g01557 Bial4g03035 Bial16g02464 . . . Hetu31g00947 Hetu33g01073 Amtr02g06575 Smso7g00490 Smso29g00638 Taer1g05914 Fro12g02171 Fso2g00448 Ftr4g03478 Fra11g02348 Fli1g00512
Vivi19g01190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01192 Arla1g00070 Armi1g00081 Sain12g00084 Ceso2g03203 Cati3g00105 Ccar2g02327 Cien5g03525 Cich4g04844 Lssa7g03767 . Tako4g02944 Tamo4g02114 Pslu1g20748 Lomi1g00444 Lomi2g04200 Enbr6g03204 Ecan3g00227 Soca5g05382 Glco3g01530 Artr3g10801 . . Aann4g00777 Chma7g07449 Chmo13g01099 Chmo14g01025 Chmo15g00965 Chla6g05643 Chna2g00941 Cind3g02061 Pdy4g00831 . . . . . . . . . . . . . . . . . . . . Cobi4g02814 Hean11g01558 Bial4g03036 Bial16g02465 Dapi7g00549 Dapi23g00569 . Hetu31g00946 Hetu33g01071 Amtr02g06576 Smso7g00489 Smso29g00637 Taer1g05913 Fro12g02172 Fso2g00447 Ftr4g03479 Fra11g02349 Fli1g00511
Vivi19g01193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 49945022 49947278 + chr4g0766551 Aann4g00777 777
2 119288475 119289928 - AtrifAMIRv0_Chr02g0161711 Amtr02g06575 6575
2 119295905 119298983 + AtrifAMIRv0_Chr02g0161721 Amtr02g06576 6576
1 1310971 1315656 - evm.model.000012F.90 Arla1g00070 70
1 1318963 1321785 + evm.model.000012F.91 Arla1g00071 71
1 1264586 1269174 - AmiAMIRv0_Chr01g0000811 Armi1g00081 81
1 1275850 1278018 + AmiAMIRv0_Chr01g0000821 Armi1g00082 82
3 364116552 364118342 + AtridAMIRv0_Chr03g0415371 Artr3g10801 10801
4 69473653 69476010 - g42874.t1 Bial4g03035 3035
4 69484768 69486191 + g42875.t1 Bial4g03036 3036
16 64111951 64114723 - g150118.t1 Bial16g02464 2464
16 64127425 64128892 + g150117.t1 Bial16g02465 2465
3 522667 529419 - CtAH03T0005600.1 Cati3g00105 105
3 529212 532408 + CtAH03T0005700.1 Cati3g00106 106
2 70439055 70440810 - gnl|WGS:LEKV|Ccrd_011378.mRNA.1_mrna Ccar2g02327 2327
2 80864182 80866769 - >KAJ9562977.1 Ceso2g03203 3203
2 80879540 80881382 + >KAJ9562976.1 Ceso2g03204 3204
6 223562902 223564732 + ClaG1_Chr06g0428901 Chla6g05643 5643
7 255612879 255617359 - CmaNakai_Chr07g0697511 Chma7g07449 7449
7 255653757 255656485 + CmaNakai_Chr07g0697541 Chma7g07452 7452
13 56689060 56691014 - evm.model.scaffold_1239.93 Chmo13g01099 1099
13 57003234 57006522 + evm.model.scaffold_1239.70 Chmo13g01105 1105
14 51388466 51390359 - evm.model.scaffold_490.22 Chmo14g01025 1025
15 56399460 56401973 - evm.model.scaffold_1049.120 Chmo15g00965 965
15 56530938 56533806 + evm.model.scaffold_1049.132 Chmo15g00972 972
2 71987342 71988937 - Cn1274890 Chna2g00941 941
2 72064746 72066054 + Cn1274840 Chna2g00943 943
4 137189525 137190836 - KAI3753979.1 Cich4g04844 4844
4 137193415 137194624 + KAI3753980.1 Cich4g04845 4845
5 81174180 81175855 - KAI3510045.1 Cien5g03525 3525
5 81178920 81180068 + KAI3510046.1 Cien5g03526 3526
3 311610189 311613198 - D.indicum_Contig21_G00102.t1 Cind3g02058 2058
3 311810580 311812100 + D.indicum_Contig21_G00105.t1 Cind3g02061 2061
4 75884662 75886425 - h2tg000009l_1.g42466.t1 Cobi4g02813 2813
4 75890946 75893160 + h2tg000009l_1.g42465.t1 Cobi4g02814 2814
7 11886125 11888799 - h1tg000030l.g77139.t1 Dapi7g00549 549
23 12638432 12641578 - h2tg000020l.g165130.t1 Dapi23g00569 569
3 2561758 2563479 - XM_043765756.1 Ecan3g00226 226
3 2564776 2569029 + XM_043765260.1 Ecan3g00227 227
6 116826672 116828340 - evm.model.ctg633.3 Enbr6g03203 3203
6 116830130 116833553 + evm.model.ctg633.4 Enbr6g03204 3204
1 10415434 10418107 - FliAMIRv0_Chr01g0005061 Fli1g00511 511
1 10421438 10433314 + FliAMIRv0_Chr01g0005071 Fli1g00512 512
11 77241864 77243857 - FraAMIRv0_Chr11g0223701 Fra11g02348 2348
11 77245385 77248274 + FraAMIRv0_Chr11g0223711 Fra11g02349 2349
12 29132532 29134816 - FroAMIRv0_Chr12g0217191 Fro12g02171 2171
12 29136115 29139242 + FroAMIRv0_Chr12g0217201 Fro12g02172 2172
2 5956292 5959325 - FsoAMIRv0_Chr02g0032661 Fso2g00447 447
2 5964401 5967098 + FsoAMIRv0_Chr02g0032671 Fso2g00448 448
4 117649790 117652069 - FtrAMIRv0_Chr04g0129121 Ftr4g03478 3478
4 117653212 117656062 + FtrAMIRv0_Chr04g0129131 Ftr4g03479 3479
3 99306213 99308469 - GcoAMIRv0_Chr03g0171591 Glco3g01530 1530
3 99325840 99328574 + GcoAMIRv0_Chr03g0171601 Glco3g01531 1531
11 47376576 47379950 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484211 Hean11g01557 1557
11 47489395 47492713 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484221 Hean11g01558 1558
31 42184758 42187536 - >Htub.h1tg002121l.g178.t1 Hetu31g00946 946
31 42266052 42268593 + >Htub.h1tg002121l.g179.t1 Hetu31g00947 947
33 44870139 44872716 - >Htub.h1tg001052l.g291.t1 Hetu33g01071 1071
33 44914758 44917455 + >Htub.h1tg001052l.g289.t1 Hetu33g01073 1073
1 4050713 4053007 - LmiAMIRv0_Chr01g0004441 Lomi1g00444 444
1 4055001 4056110 + LmiAMIRv0_Chr01g0004451 Lomi1g00445 445
2 47509818 47511789 - LmiAMIRv0_Chr02g0087321 Lomi2g04199 4199
2 47515100 47516818 + LmiAMIRv0_Chr02g0087331 Lomi2g04200 4200
7 198543764 198545612 - >KAJ0197002.1 Lssa7g03767 3767
7 198546728 198547891 + >KAJ0195514.1 Lssa7g03768 3768
4 14731582 14735201 - PdyAMIRv0_Chr04g0156381 Pdy4g00831 831
4 14760859 14762186 + PdyAMIRv0_Chr04g0156401 Pdy4g00833 833
1 149649158 149651061 - PluAMIRv0_Chr01g0206561 Pslu1g20747 20747
1 149654211 149655864 + PluAMIRv0_Chr01g0206571 Pslu1g20748 20748
12 1067630 1069898 - SinAMIRv0_Chr12g0356491 Sain12g00084 84
12 1082518 1085107 + SinAMIRv0_Chr12g0356501 Sain12g00085 85
7 8181599 8184208 - KAI3810069.1 Smso7g00489 489
7 8202211 8203947 + KAI3810070.1 Smso7g00490 490
29 9024288 9026585 - KAI3675631.1 Smso29g00637 637
29 9029457 9031181 + KAI3675632.1 Smso29g00638 638
5 74083166 74086010 - transfrag23931.t01 Soca5g05380 5380
5 74089859 74093057 + augustus35988.t02 Soca5g05382 5382
6 19976166 19978858 - Streb.6G006900.1 Stre6g00690 690
1 53359933 53361804 - >KAK1440088.1 Taer1g05913 5913
1 53362744 53364426 + >KAK1440089.1 Taer1g05914 5914
4 53740800 53742553 + TkA04G209840.1 Tako4g02940 2940
4 53779097 53784094 - TkA04G209970.1 Tako4g02944 2944
4 34360377 34362471 - TbA04G052830.1 Tamo4g02114 2114
19 23634533 23683391 + GSVIVT01036699001 Vivi19g01184 1184
19 23701986 23776140 + GSVIVT01036698001 Vivi19g01185 1185
19 23780412 23784906 - GSVIVT01036696001 Vivi19g01186 1186
19 23803974 23806961 - GSVIVT01036694001 Vivi19g01187 1187
19 23817847 23823394 + GSVIVT01036692001 Vivi19g01188 1188
19 23824657 23827974 - GSVIVT01036691001 Vivi19g01189 1189
19 23829724 23831896 + GSVIVT01036690001 Vivi19g01190 1190
19 23832465 23836195 + GSVIVT01036689001 Vivi19g01191 1191
19 23841502 23845561 + GSVIVT01036688001 Vivi19g01192 1192
19 23845782 23846168 + GSVIVT01036687001 Vivi19g01193 1193
       
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