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AGRP

Asteraceae Genomic Research Platform

Gene Search

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Example:

Hierarchical alignments with the Arctium lappa genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Arctium lappa as a reference, and by comparing homologous gene locus maps and Ks values between Arctium lappa and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 74×31,441 macro-matrices.


Select 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 Stre_2 Mimi_2
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00162 Sain12g00147 Ceso2g03263 Cati3g00193 Ccar2g02269 . . . . . . Pslu1g06438 Lomi1g00469 Lomi2g04148 Enbr6g01593 Ecan3g00132 Soca5g05262 . . . . . Chma7g07532 Chmo13g01219 Chmo14g01121 Chmo15g01070 Chla6g05418 Chna2g01044 Cind3g05809 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00163 Sain12g00148 Ceso2g03264 Cati3g00195 Ccar2g02268 . . . . . . Pslu1g06439 . Lomi2g04147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00164 Sain12g00150 Ceso2g03265 Cati3g00197 Ccar2g02267 . . . . . . Pslu1g06442 . Lomi2g04145 Enbr6g01591 Ecan3g00131 Soca5g05258 . . . . . Chma7g07535 Chmo13g01220 Chmo14g01122 Chmo15g01072 Chla6g05417 Chna2g01045 Cind3g05808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00165 Sain12g00153 Ceso2g03267 Cati3g00199 Ccar2g02266 . . . . . . Pslu1g06444 . Lomi2g04144 Enbr6g01588 Ecan3g00130 Soca5g05257 . . . . . . Chmo13g01222 Chmo14g01124 Chmo15g01074 Chla6g05414 Chna2g01046 Cind3g05806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00166 Sain12g00154 . . . . . . . . . Pslu1g06445 . . . Ecan3g00129 Soca5g05253 . . . . . Chma7g07536 Chmo13g01223 Chmo14g01125 Chmo15g01076 Chla6g05413 Chna2g01047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00167 Sain12g00155 . Cati3g00201 Ccar2g02265 . . . . . . Pslu1g06446 . Lomi2g04143 . Ecan3g00128 Soca5g05252 . . . . . Chma7g07537 Chmo13g01224 Chmo14g01126 . Chla6g05412 Chna2g01048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00168 Sain12g00156 Ceso2g03268 Cati3g00205 Ccar2g02263 . . . . . . Pslu1g06447 . Lomi2g04142 Enbr6g01585 Ecan3g00126 Soca5g05251 . . . . . Chma7g07538 Chmo13g01228 Chmo14g01127 Chmo15g01077 Chla6g05405 Chna2g01049 Cind3g00391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . Cati3g00206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . Cati3g00207 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 3078935 3084519 + AmiAMIRv0_Chr01g0001621 Armi1g00162 162
1 3087226 3107035 - AmiAMIRv0_Chr01g0001631 Armi1g00163 163
1 3132215 3135582 + AmiAMIRv0_Chr01g0001641 Armi1g00164 164
1 3167413 3171827 + AmiAMIRv0_Chr01g0001651 Armi1g00165 165
1 3189146 3189745 + AmiAMIRv0_Chr01g0001661 Armi1g00166 166
1 3191243 3194086 - AmiAMIRv0_Chr01g0001671 Armi1g00167 167
1 3205917 3208423 + AmiAMIRv0_Chr01g0001681 Armi1g00168 168
3 1524418 1531828 + CtAH03T0011400.1 Cati3g00193 193
3 1533691 1545383 - CtAH03T0011500.2 Cati3g00195 195
3 1558945 1563499 + CtAH03T0011600.3 Cati3g00197 197
3 1584484 1592054 + CtAH03T0011700.1 Cati3g00199 199
3 1607408 1610218 - CtAH03T0011900.1 Cati3g00201 201
3 1610548 1619833 + CtAH03T0012200.2 Cati3g00205 205
3 1631461 1631850 - CtAH03T0012300.1 Cati3g00206 206
3 1638509 1640026 - CtAH03T0012400.1 Cati3g00207 207
2 69653909 69656531 - gnl|WGS:LEKV|Ccrd_011314.mRNA.1_mrna Ccar2g02263 2263
2 69663059 69665938 + gnl|WGS:LEKV|Ccrd_011316.mRNA.1_mrna Ccar2g02265 2265
2 69673110 69677526 - gnl|WGS:LEKV|Ccrd_011317.mRNA.1_mrna Ccar2g02266 2266
2 69699755 69704285 - gnl|WGS:LEKV|Ccrd_011318.mRNA.1_mrna Ccar2g02267 2267
2 69709936 69737195 + gnl|WGS:LEKV|Ccrd_011319.mRNA.1_mrna Ccar2g02268 2268
2 69740032 69746572 - gnl|WGS:LEKV|Ccrd_011320.mRNA.1_mrna Ccar2g02269 2269
2 81830873 81836442 + >KAJ9562750.1 Ceso2g03263 3263
2 81841520 81851348 - >KAJ9562751.1 Ceso2g03264 3264
2 81860784 81864530 + >KAJ9562749.1 Ceso2g03265 3265
2 81898551 81903049 + >KAJ9562700.1 Ceso2g03267 3267
2 81922332 81925276 + >KAJ9562699.1 Ceso2g03268 3268
6 212792747 212796819 - ClaG1_Chr06g0426521 Chla6g05405 5405
6 212890540 212894017 + ClaG1_Chr06g0426591 Chla6g05412 5412
6 212894403 212895516 - ClaG1_Chr06g0426601 Chla6g05413 5413
6 213061834 213066374 - ClaG1_Chr06g0426611 Chla6g05414 5414
6 213295483 213299742 - ClaG1_Chr06g0426641 Chla6g05417 5417
6 213313132 213316269 - ClaG1_Chr06g0426651 Chla6g05418 5418
7 258862056 258865215 + CmaNakai_Chr07g0698341 Chma7g07532 7532
7 259117425 259119283 - CmaNakai_Chr07g0698371 Chma7g07535 7535
7 259237342 259237881 + CmaNakai_Chr07g0698381 Chma7g07536 7536
7 259239072 259241875 - CmaNakai_Chr07g0698391 Chma7g07537 7537
7 259270564 259273946 + CmaNakai_Chr07g0698401 Chma7g07538 7538
13 64320482 64323629 + evm.model.scaffold_4060.73 Chmo13g01219 1219
13 64360824 64365764 + evm.model.scaffold_4060.72 Chmo13g01220 1220
13 64523722 64529284 + evm.model.scaffold_4060.61 Chmo13g01222 1222
13 64592003 64593164 + evm.model.scaffold_4060.57 Chmo13g01223 1223
13 64593549 64597112 - evm.model.scaffold_4060.56 Chmo13g01224 1224
13 64814781 64819367 + evm.model.scaffold_4060.42 Chmo13g01228 1228
14 59325929 59330365 + evm.model.scaffold_948.101 Chmo14g01121 1121
14 59350058 59354982 + evm.model.scaffold_948.102 Chmo14g01122 1122
14 59495791 59501341 + evm.model.scaffold_948.109 Chmo14g01124 1124
14 59586566 59587726 + evm.model.scaffold_948.112 Chmo14g01125 1125
14 59588113 59591676 - evm.model.scaffold_948.113 Chmo14g01126 1126
14 60007083 60010032 + evm.model.scaffold_948.131 Chmo14g01127 1127
15 61621195 61623698 + evm.model.scaffold_1478.40 Chmo15g01070 1070
15 61752041 61756825 + evm.model.scaffold_1478.49 Chmo15g01072 1072
15 62048540 62052704 + evm.model.scaffold_1478.73 Chmo15g01074 1074
15 62153464 62154006 + evm.model.scaffold_1478.77 Chmo15g01076 1076
15 62194635 62197573 + evm.model.scaffold_1478.83 Chmo15g01077 1077
2 83110352 83113637 + Cn0815610 Chna2g01044 1044
2 83153928 83155448 + Cn0815620 Chna2g01045 1045
2 83406566 83410432 + Cn0815630 Chna2g01046 1046
2 83621669 83622211 + Cn0815640 Chna2g01047 1047
2 83623221 83626175 - Cn0815650 Chna2g01048 1048
2 83869557 83873844 - Cn0815660 Chna2g01049 1049
3 303827331 303830906 - D.indicum_Contig13_G00002.t1 Cind3g00391 391
3 304353652 304357476 - D.indicum_Contig902_G00001.t1 Cind3g05806 5806
3 304582144 304586401 - D.indicum_Contig902_G00003.t1 Cind3g05808 5808
3 304724619 304727683 - D.indicum_Contig902_G00004.t1 Cind3g05809 5809
3 1015812 1018192 - XM_043763849.1 Ecan3g00126 126
3 1028216 1031295 + XM_043762916.1 Ecan3g00128 128
3 1032175 1032800 - XM_043762803.1 Ecan3g00129 129
3 1078060 1083612 - XM_043763105.1 Ecan3g00130 130
3 1093512 1099316 - XM_043765467.1 Ecan3g00131 131
3 1134731 1140311 - XM_043763117.1 Ecan3g00132 132
6 55058789 55063532 - evm.model.ctg2307.18 Enbr6g01585 1585
6 55157878 55161759 - evm.model.ctg2307.13 Enbr6g01588 1588
6 55205153 55207331 - evm.model.ctg2307.10 Enbr6g01591 1591
6 55221548 55226284 - evm.model.ctg2307.8 Enbr6g01593 1593
1 4299592 4304184 - LmiAMIRv0_Chr01g0004691 Lomi1g00469 469
2 47037908 47039792 - LmiAMIRv0_Chr02g0086751 Lomi2g04142 4142
2 47042679 47045657 + LmiAMIRv0_Chr02g0086761 Lomi2g04143 4143
2 47051695 47055473 - LmiAMIRv0_Chr02g0086771 Lomi2g04144 4144
2 47075342 47078548 - LmiAMIRv0_Chr02g0086781 Lomi2g04145 4145
2 47087488 47091647 + LmiAMIRv0_Chr02g0086801 Lomi2g04147 4147
2 47095259 47100800 - LmiAMIRv0_Chr02g0086811 Lomi2g04148 4148
1 44180310 44184936 + PluAMIRv0_Chr01g0064141 Pslu1g06438 6438
1 44186400 44190606 - PluAMIRv0_Chr01g0064151 Pslu1g06439 6439
1 44199121 44202330 + PluAMIRv0_Chr01g0064181 Pslu1g06442 6442
1 44249298 44253050 + PluAMIRv0_Chr01g0064201 Pslu1g06444 6444
1 44257862 44258440 + PluAMIRv0_Chr01g0064211 Pslu1g06445 6445
1 44259079 44262042 - PluAMIRv0_Chr01g0064221 Pslu1g06446 6446
1 44269643 44271524 + PluAMIRv0_Chr01g0064231 Pslu1g06447 6447
12 2671113 2675866 + SinAMIRv0_Chr12g0357121 Sain12g00147 147
12 2677777 2697570 - SinAMIRv0_Chr12g0357131 Sain12g00148 148
12 2704782 2708175 + SinAMIRv0_Chr12g0357151 Sain12g00150 150
12 2793291 2798429 + SinAMIRv0_Chr12g0357181 Sain12g00153 153
12 2834484 2835080 + SinAMIRv0_Chr12g0357191 Sain12g00154 154
12 2836250 2839123 - SinAMIRv0_Chr12g0357201 Sain12g00155 155
12 2879046 2881199 + SinAMIRv0_Chr12g0357211 Sain12g00156 156
5 71353203 71355744 - transfrag23805.t01 Soca5g05251 5251
5 71366731 71370024 + asmbl_4215.p1 Soca5g05252 5252
5 71372605 71373249 - transfrag23808.t01 Soca5g05253 5253
5 71440141 71445667 - transfrag23815.t01 Soca5g05257 5257
5 71486425 71491288 - asmbl_4228.p1 Soca5g05258 5258
5 71518058 71522898 - transfrag23818.t01 Soca5g05262 5262
       
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