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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
Vivi19g01164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01167 Arla1g00074 Armi1g00084 Sain12g00087 Ceso2g03206 Cati3g00116 Ccar2g02325 Cien5g03528 . Lssa7g03770 Laca7g03081 Tako4g03024 Tamo4g02119 Pslu1g20744 Lomi1g00448 Lomi2g04197 Enbr6g03173 Ecan3g00216 Soca5g05375 . Artr3g10786 . . Aann4g00763 Chma7g07477 Chmo13g01110 Chmo14g01030 Chmo15g00976 Chla6g05640 Chna2g00949 Cind3g02053 Pdy4g00842 . . . . . . . . . . . . . . . . . . . . Cobi4g02809 Hean11g01549 Bial4g03027 Bial16g02454 Dapi7g00553 Dapi23g00574 . Hetu31g00953 Hetu33g01077 Amtr02g06574 Smso7g00492 Smso29g00639 . . . . . .
Vivi19g01168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01170 Arla1g00072 Armi1g00083 Sain12g00086 Ceso2g03205 Cati3g00108 Ccar2g02326 Cien5g03527 Cich4g04846 Lssa7g03769 Laca7g03079 Tako4g03022 Tamo4g02117 Pslu1g20746 Lomi1g00447 Lomi2g04198 . Ecan3g00224 Soca5g05378 Glco3g01533 . . . Aann4g00769 Chma7g07457 Chmo13g01107 Chmo14g01027 Chmo15g00973 Chla6g05641 Chna2g00945 Cind3g02056 Pdy4g00834 . Hean6g02881 . . . . . . . . . Smso26g01730 . . . . . . Stre9g01544 . Cobi4g02810 Hean11g01554 Bial4g03031 Bial16g02458 . Dapi23g00571 . . . . . . . . . . . .
Vivi19g01171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01173 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 49839673 49843997 - chr4g0766371 Aann4g00763 763
4 49879906 49885704 + chr4g0766451 Aann4g00769 769
2 119216253 119219326 - AtrifAMIRv0_Chr02g0161701 Amtr02g06574 6574
1 1322119 1332426 - evm.model.000012F.92 Arla1g00072 72
1 1363259 1366135 + evm.model.000012F.94 Arla1g00074 74
8 522274 525682 - evm.model.000077F.422 Arla8g00003 3
1 1279060 1289049 - AmiAMIRv0_Chr01g0000831 Armi1g00083 83
1 1333734 1336566 + AmiAMIRv0_Chr01g0000841 Armi1g00084 84
8 100039933 100042820 + AmiAMIRv0_Chr08g0297381 Armi8g02907 2907
3 363597168 363600914 - AtridAMIRv0_Chr03g0415221 Artr3g10786 10786
4 69275607 69279413 - g42866.t1 Bial4g03027 3027
4 69360505 69366337 + g42870.t1 Bial4g03031 3031
16 63965535 63968687 - g150128.t1 Bial16g02454 2454
16 64026819 64037926 + g150124.t1 Bial16g02458 2458
3 532909 556544 - CtAH03T0005800.2 Cati3g00108 108
3 566385 572495 + CtAH03T0006100.1 Cati3g00116 116
7 72739600 72742862 + CtAH07T0261300.1 Cati7g03564 3564
2 70416754 70420220 - gnl|WGS:LEKV|Ccrd_011376.mRNA.1_mrna Ccar2g02325 2325
2 70425883 70438440 + gnl|WGS:LEKV|Ccrd_011377.mRNA.1_mrna Ccar2g02326 2326
2 80898044 80907853 - >KAJ9562689.1 Ceso2g03205 3205
2 80936826 80940601 + >KAJ9562685.1 Ceso2g03206 3206
6 223474923 223478846 - ClaG1_Chr06g0428871 Chla6g05640 5640
6 223495942 223502990 + ClaG1_Chr06g0428881 Chla6g05641 5641
7 255730982 255738621 - CmaNakai_Chr07g0697591 Chma7g07457 7457
7 257152754 257156293 + CmaNakai_Chr07g0697791 Chma7g07477 7477
13 57015389 57020410 - evm.model.scaffold_1239.68 Chmo13g01107 1107
13 57154521 57158632 + evm.model.scaffold_1239.63 Chmo13g01110 1110
14 51515262 51540251 - evm.model.scaffold_490.18.2 Chmo14g01027 1027
14 51814509 51818341 + evm.model.scaffold_490.9 Chmo14g01030 1030
15 56537167 56537925 - evm.model.scaffold_1049.134 Chmo15g00973 973
15 56780925 56784714 + evm.model.scaffold_1049.142 Chmo15g00976 976
2 72126737 72131039 - Cn1274820 Chna2g00945 945
2 72215557 72219910 + Cn1274750 Chna2g00949 949
4 137195104 137199308 - KAI3753981.1 Cich4g04846 4846
5 81180552 81184707 - KAI3510047.1 Cien5g03527 3527
5 81190069 81192688 + KAI3510048.1 Cien5g03528 3528
3 311318418 311322312 - D.indicum_Contig21_G00097.t1 Cind3g02053 2053
3 311402623 311406241 + D.indicum_Contig21_G00100.t1 Cind3g02056 2056
4 75739550 75742952 - h2tg000009l_1.g42470.t1 Cobi4g02809 2809
4 75764094 75771266 + h2tg000009l_1.g42469.t1 Cobi4g02810 2810
7 11930070 11932865 + h1tg000030l.g77143.t1 Dapi7g00553 553
23 12671678 12673207 - h2tg000020l.g165128.t1 Dapi23g00571 571
23 12735482 12738244 + h2tg000020l.g165125.t1 Dapi23g00574 574
3 2369037 2371839 - XM_043766490.1 Ecan3g00216 216
3 2547936 2554540 + XM_043763424.1 Ecan3g00224 224
5 33692606 33695751 - XM_043771880.1 Ecan5g02032 2032
6 115942588 115944970 - evm.model.ctg1851.25 Enbr6g03173 3173
8 109206282 109210521 + evm.model.ctg51.8 Enbr8g03397 3397
3 99343507 99347082 - GcoAMIRv0_Chr03g0171621 Glco3g01533 1533
6 103317101 103320856 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0271251 Hean6g02881 2881
11 47188263 47193032 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484131 Hean11g01549 1549
11 47358455 47365028 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0484181 Hean11g01554 1554
31 42637701 42641607 + >Htub.h1tg002121l.g185.t1 Hetu31g00953 953
33 45132692 45135564 + >Htub.h1tg001052l.g285.t1 Hetu33g01077 1077
7 145527924 145532288 - CAI9295279.1 Laca7g03079 3079
7 145549846 145554561 + CAI9295281.1 Laca7g03081 3081
1 4066615 4067444 - LmiAMIRv0_Chr01g0004471 Lomi1g00447 447
1 4071189 4073493 + LmiAMIRv0_Chr01g0004481 Lomi1g00448 448
2 47485494 47487837 - LmiAMIRv0_Chr02g0087301 Lomi2g04197 4197
2 47498282 47504265 + LmiAMIRv0_Chr02g0087311 Lomi2g04198 4198
7 198547936 198552555 - >KAJ0198019.1 Lssa7g03769 3769
7 198590181 198595413 + >KAJ0196395.1 Lssa7g03770 3770
4 14762696 14768863 - PdyAMIRv0_Chr04g0156411 Pdy4g00834 834
4 14912437 14914971 + PdyAMIRv0_Chr04g0156491 Pdy4g00842 842
1 149612868 149615259 - PluAMIRv0_Chr01g0206531 Pslu1g20744 20744
1 149644416 149648847 + PluAMIRv0_Chr01g0206551 Pslu1g20746 20746
3 114321728 114324016 + PluAMIRv0_Chr03g0557121 Pslu3g15885 15885
12 1086346 1093618 - SinAMIRv0_Chr12g0356511 Sain12g00086 86
12 1126253 1128924 + SinAMIRv0_Chr12g0356521 Sain12g00087 87
7 8223735 8226614 + KAI3810072.1 Smso7g00492 492
26 29406956 29412802 - KAI3695215.1 Smso26g01730 1730
29 9041472 9044516 + KAI3675633.1 Smso29g00639 639
2 91512270 91531614 - augustus42305.t01 Soca2g04679 4679
5 73970752 73974412 - transfrag23926.t01 Soca5g05375 5375
5 74069141 74077266 + asmbl_4253.p1 Soca5g05378 5378
6 20210364 20214968 + Streb.6G006940.1 Stre6g00694 694
9 27102795 27108539 - Streb.9G015440.1 Stre9g01544 1544
4 58582161 58588598 - TkA04G230650.2 Tako4g03022 3022
4 58609514 58612932 + TkA04G230740.1 Tako4g03024 3024
4 34393758 34400733 - TbA04G052760.1 Tamo4g02117 2117
4 34419973 34423698 + TbA04G052740.1 Tamo4g02119 2119
19 23279325 23283793 + GSVIVT01036725001 Vivi19g01164 1164
19 23284514 23291080 - GSVIVT01036724001 Vivi19g01165 1165
19 23305998 23313302 + GSVIVT01036723001 Vivi19g01166 1166
19 23313349 23318736 - GSVIVT01036722001 Vivi19g01167 1167
19 23319003 23339683 + GSVIVT01036721001 Vivi19g01168 1168
19 23341372 23351231 + GSVIVT01036720001 Vivi19g01169 1169
19 23353908 23383396 + GSVIVT01036719001 Vivi19g01170 1170
19 23388000 23390312 + GSVIVT01036717001 Vivi19g01171 1171
19 23399297 23401496 - GSVIVT01036716001 Vivi19g01172 1172
19 23412509 23437714 + GSVIVT01036714001 Vivi19g01173 1173
       
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