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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
Vivi19g01124 Arla1g00087 Armi1g00099 Sain12g00102 Ceso2g03217 Cati3g00135 Ccar2g02313 Cien5g03542 Cich4g04854 Lssa7g03785 Laca7g03092 Tako4g03048 . Pslu1g20722 . Lomi2g04182 . Ecan3g00197 Soca5g05356 Glco3g01571 Artr3g10750 . Aary13g03122 Aann4g00725 . . . . . . . Pdy4g00859 . . . . . . . . . . . . . . . . . . . . Cobi4g02793 Hean11g01536 Bial4g03016 Bial16g02442 Dapi7g00567 Dapi23g00586 . Hetu31g00970 Hetu33g01089 Amtr02g06557 Smso7g00502 Smso29g00653 Taer1g05930 Fro12g02156 Fso2g00465 Ftr4g03465 Fra11g02334 Fli1g00527
Vivi19g01125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01132 Arla1g00086 Armi1g00098 Sain12g00101 Ceso2g03216 Cati3g00134 Ccar2g02314 Cien5g03541 Cich4g04853 Lssa7g03784 Laca7g03091 Tako4g03047 Tamo4g02132 Pslu1g20723 . . . Ecan3g00198 Soca5g05357 Glco3g01570 Artr3g10751 . Aary13g03123 Aann4g00726 . . . . . . . Pdy4g00858 . . . . . . . . . . . . . . . . . . . . Cobi4g02794 Hean11g01537 Bial4g03017 Bial16g02443 Dapi7g00566 Dapi23g00585 . Hetu31g00969 Hetu33g01088 Amtr02g06560 . Smso29g00652 Taer1g05929 Fro12g02157 . Ftr4g03466 Fra11g02335 Fli1g00526
Vivi19g01133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 48485903 48492762 + chr4g0765201 Aann4g00725 725
4 48492764 48503635 - chr4g0765211 Aann4g00726 726
13 184891695 184903296 + Aargg13g31220.1 Aary13g03122 3122
13 184915165 184918731 - Aargg13g31230.1 Aary13g03123 3123
2 118986119 118991501 + AtrifAMIRv0_Chr02g0161531 Amtr02g06557 6557
2 118997889 119002125 - AtrifAMIRv0_Chr02g0161561 Amtr02g06560 6560
1 1570532 1575886 + evm.model.000012F.109 Arla1g00086 86
1 1579876 1585950 - evm.model.000012F.110 Arla1g00087 87
8 753724 760324 + evm.model.000077F.409_evm.model.000077F.410 Arla8g00012 12
1 1517008 1521266 + AmiAMIRv0_Chr01g0000981 Armi1g00098 98
1 1526717 1533514 - AmiAMIRv0_Chr01g0000991 Armi1g00099 99
8 99831584 99834110 - AmiAMIRv0_Chr08g0297231 Armi8g02892 2892
3 362738687 362744753 + AtridAMIRv0_Chr03g0414861 Artr3g10750 10750
3 362746076 362749752 - AtridAMIRv0_Chr03g0414871 Artr3g10751 10751
4 69100965 69105584 + g42855.t1 Bial4g03016 3016
4 69106330 69108987 - g42856.t1 Bial4g03017 3017
16 63796070 63803217 + g150140.t1 Bial16g02442 2442
16 63804046 63807522 - g150139.t1 Bial16g02443 2443
3 676343 684603 + CtAH03T0007200.1 Cati3g00134 134
3 685748 700777 - CtAH03T0007300.1 Cati3g00135 135
2 70299182 70308252 + gnl|WGS:LEKV|Ccrd_011364.mRNA.1_mrna Ccar2g02313 2313
2 70309216 70314635 - gnl|WGS:LEKV|Ccrd_011365.mRNA.1_mrna Ccar2g02314 2314
17 32572 39175 + gnl|WGS:LEKV|Ccrd_019322.mRNA.1_mrna Ccar17g00005 5
2 81076664 81083092 + >KAJ9562713.1 Ceso2g03216 3216
2 81085226 81093273 - >KAJ9562648.1 Ceso2g03217 3217
6 559819 562698 - CmaNakai_Chr06g0511721 Chma6g00023 23
24 326666735 326671158 - evm.model.scaffold_857.26 Chmo24g05751 5751
5 1881611 1884828 + Cn0259190 Chna5g00046 46
4 137328470 137330285 + KAI3753988.1 Cich4g04853 4853
4 137332702 137335166 - KAI3753989.1 Cich4g04854 4854
5 81289321 81291003 + KAI3510061.1 Cien5g03541 3541
5 81294017 81296437 - KAI3510062.1 Cien5g03542 3542
4 75510467 75514489 + h2tg000009l_1.g42486.t1 Cobi4g02793 2793
4 75515617 75518156 - h2tg000009l_1.g42485.t1 Cobi4g02794 2794
7 12055608 12060196 + h1tg000030l.g77156.t1 Dapi7g00566 566
7 12060791 12074967 - h1tg000030l.g77157.t1 Dapi7g00567 567
23 12892692 12897133 + h2tg000020l.g165114.t1 Dapi23g00585 585
23 12897731 12908189 - h2tg000020l.g165113.t1 Dapi23g00586 586
3 2217467 2222871 + XM_043765134.1 Ecan3g00197 197
3 2224949 2228323 - XM_043765133.1 Ecan3g00198 198
5 33626177 33629265 - XM_043775030.1 Ecan5g02023 2023
8 109326389 109329189 + evm.model.ctg51.18 Enbr8g03405 3405
1 10728200 10733187 + FliAMIRv0_Chr01g0005211 Fli1g00526 526
1 10735132 10745178 - FliAMIRv0_Chr01g0005221 Fli1g00527 527
11 77120891 77128591 + FraAMIRv0_Chr11g0223561 Fra11g02334 2334
11 77129984 77133151 - FraAMIRv0_Chr11g0223571 Fra11g02335 2335
12 29023839 29028979 + FroAMIRv0_Chr12g0217041 Fro12g02156 2156
12 29030386 29033640 - FroAMIRv0_Chr12g0217051 Fro12g02157 2157
2 6098113 6104392 - FsoAMIRv0_Chr02g0032841 Fso2g00465 465
4 117531609 117542421 + FtrAMIRv0_Chr04g0128991 Ftr4g03465 3465
4 117543617 117546808 - FtrAMIRv0_Chr04g0129001 Ftr4g03466 3466
3 101127172 101130281 + GcoAMIRv0_Chr03g0171991 Glco3g01570 1570
3 101131395 101137164 - GcoAMIRv0_Chr03g0172001 Glco3g01571 1571
11 46883357 46890837 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483991 Hean11g01536 1536
11 46892239 46896722 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484001 Hean11g01537 1537
31 43036845 43041111 + >Htub.h1tg002121l.g201.t1 Hetu31g00969 969
31 43043345 43049327 - >Htub.h1tg002121l.g202.t1 Hetu31g00970 970
33 45453990 45458109 + >Htub.h1tg001052l.g274.t1 Hetu33g01088 1088
33 45464942 45477421 - >Htub.h1tg001052l.g273.t1 Hetu33g01089 1089
7 145698756 145701327 + CAI9295291.1 Laca7g03091 3091
7 145701684 145705738 - CAI9295292.1 Laca7g03092 3092
2 47403982 47409075 + LmiAMIRv0_Chr02g0087151 Lomi2g04182 4182
5 30045230 30048484 + LmiAMIRv0_Chr05g0175121 Lomi5g01863 1863
11 26324564 26327636 + LmiAMIRv0_Chr11g0337711 Lomi11g01800 1800
7 198757704 198760183 + >KAJ0197352.1 Lssa7g03784 3784
7 198761071 198764538 - >KAJ0198243.1 Lssa7g03785 3785
17 44073004 44076840 + KAD3067127.1 Mimi17g00805 805
17 44107298 44120507 - KAD3067128.1 Mimi17g00806 806
4 15615211 15618892 + PdyAMIRv0_Chr04g0156651 Pdy4g00858 858
4 15622781 15635092 - PdyAMIRv0_Chr04g0156661 Pdy4g00859 859
1 149489401 149496305 + PluAMIRv0_Chr01g0206311 Pslu1g20722 20722
1 149497577 149499769 - PluAMIRv0_Chr01g0206321 Pslu1g20723 20723
3 114397980 114401192 + PluAMIRv0_Chr03g0557281 Pslu3g15901 15901
12 1290212 1295803 + SinAMIRv0_Chr12g0356661 Sain12g00101 101
12 1299696 1307600 - SinAMIRv0_Chr12g0356671 Sain12g00102 102
13 139409135 139411635 - SinAMIRv0_Chr13g0402661 Sain13g02710 2710
7 8337107 8342111 - KAI3810082.1 Smso7g00502 502
29 9209529 9215322 + KAI3675646.1 Smso29g00652 652
29 9216623 9222002 - KAI3675647.1 Smso29g00653 653
2 91382960 91389916 - transfrag28212.t01 Soca2g04669 4669
5 73749691 73755394 + transfrag23904.t01 Soca5g05356 5356
5 73756508 73760215 - transfrag23905.t01 Soca5g05357 5357
6 20814749 20820865 + Streb.6G007130.1 Stre6g00713 713
6 20821622 20827379 - Streb.6G007140.1 Stre6g00714 714
1 53450984 53454136 + >KAK1440104.1 Taer1g05929 5929
1 53454883 53459217 - >KAK1440105.1 Taer1g05930 5930
4 58990624 58994091 + TkA04G232380.1 Tako4g03047 3047
4 58994207 58997959 - TkA04G232390.1 Tako4g03048 3048
4 34786258 34789874 + TbA04G052440.1 Tamo4g02132 2132
19 22558794 22573951 + GSVIVT01036786001 Vivi19g01124 1124
19 22575606 22581761 + GSVIVT01036785001 Vivi19g01125 1125
19 22654525 22657736 + GSVIVT01036782001 Vivi19g01126 1126
19 22662521 22670040 - GSVIVT01036780001 Vivi19g01127 1127
19 22672340 22673080 - GSVIVT01036779001 Vivi19g01128 1128
19 22673124 22674794 + GSVIVT01036778001 Vivi19g01129 1129
19 22678798 22680489 + GSVIVT01036777001 Vivi19g01130 1130
19 22688699 22717134 + GSVIVT01036776001 Vivi19g01131 1131
19 22721760 22727850 - GSVIVT01036775001 Vivi19g01132 1132
19 22741010 22745951 - GSVIVT01036773001 Vivi19g01133 1133
       
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