AGRP Logo

AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
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.


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
Armi1g01078 Sain12g00863 Ceso2g01696 Cati3g01099 . . Cich4g03977 Lssa7g02949 Laca7g02399 Tako4g04659 Tamo4g03387 Pslu1g21948 Lomi1g00054 Lomi2g04601 Enbr6g01889 Ecan3g01774 . Glco3g00578 Artr3g13091 Aary5g03153 Aary13g03647 Aann4g01730 Chma7g09366 Chmo13g00134 Chmo14g00190 Chmo15g00156 Chla6g06971 Chna2g00051 Cind3g03214 Pdy4g00077 . . . . . . . . . . . . . . . . . . . . Cobi4g03388 Hean16g01324 . . Dapi7g00039 Dapi23g00046 Hetu48g00937 . Hetu47g01111 Amtr01g04458 Smso7g00281 . . . . . . . Stre6g00083 .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g01094 Sain12g00864 . Cati3g01100 . Cien5g02980 Cich4g03973 Lssa7g02947 Laca7g02397 Tako4g04660 Tamo4g03388 Pslu1g21956 Lomi1g00053 Lomi2g04602 Enbr6g01895 Ecan3g01772 Soca5g03099 Glco3g00579 Artr3g13094 Aary5g03154 . Aann4g01731 Chma7g09367 Chmo13g00133 Chmo14g00189 Chmo15g00155 Chla6g06972 Chna2g00050 Cind3g03213 Pdy4g00076 . Hean4g04567 . . Dapi16g02102 Dapi23g00045 Hetu11g00038 Hetu12g00040 Hetu10g00065 Amtr06g04451 . Smso26g02104 Taer1g05767 . Fso2g00041 . Fra11g02711 Fli1g00059 Stre6g00081 . Cobi4g03389 Hean16g01323 . . Dapi7g00038 Dapi23g00045 Hetu48g01002 Hetu46g01150 Hetu47g01112 Amtr01g04461 Smso7g00282 Smso29g00321 Taer1g05767 . Fso2g00041 . Fra11g02711 Fli1g00059 Stre6g00081 Mimi17g00093
Armi1g01240 . . Cati3g01108 . . Cich4g03959 Lssa7g02941 . Tako4g04669 . Pslu1g21960 Lomi1g00052 . Enbr6g01896 Ecan3g01771 Soca5g03101 Glco3g00593 . . . . Chma7g09368 Chmo13g00132 Chmo14g00187 Chmo15g00151 Chla6g06974 Chna2g00049 Cind3g03212 . . . . . . . . . . . . . . . . . . . . . . Hean16g01313 . . . . . Hetu46g01162 . . . . . . . . . . Stre6g00072 .
Gene_GFF
Chromosome Start End Strand Old_gene Gene Num
4 78707077 78710720 + chr4g0792571 Aann4g01730 1730
4 78737045 78739771 + chr4g0792591 Aann4g01731 1731
5 192563370 192565970 + Aargg5g31530.1 Aary5g03153 3153
5 192616752 192618713 + Aargg5g31540.1 Aary5g03154 3154
13 219561430 219563959 - Aargg13g36470.1 Aary13g03647 3647
1 119784492 119786353 + AtrifAMIRv0_Chr01g0044581 Amtr01g04458 4458
1 119881858 119883910 + AtrifAMIRv0_Chr01g0044611 Amtr01g04461 4461
6 98442163 98444760 + AtrifAMIRv0_Chr06g0432761 Amtr06g04451 4451
1 29768325 29775006 + AmiAMIRv0_Chr01g0010781 Armi1g01078 1078
1 30173656 30175649 + AmiAMIRv0_Chr01g0010941 Armi1g01094 1094
1 35507141 35507647 + AmiAMIRv0_Chr01g0012401 Armi1g01240 1240
3 453339144 453341523 + AtridAMIRv0_Chr03g0438271 Artr3g13091 13091
3 453461868 453463819 + AtridAMIRv0_Chr03g0438301 Artr3g13094 13094
3 16032679 16038531 + CtAH03T0079400.1 Cati3g01099 1099
3 16145530 16147909 + CtAH03T0079500.1 Cati3g01100 1100
3 16409252 16420571 - CtAH03T0080000.1 Cati3g01108 1108
2 37024252 37028060 + >KAJ9561318.1 Ceso2g01696 1696
6 283498611 283508236 + ClaG1_Chr06g0442181 Chla6g06971 6971
6 283563016 283565130 + ClaG1_Chr06g0442191 Chla6g06972 6972
6 283629320 283630766 - ClaG1_Chr06g0442211 Chla6g06974 6974
7 311869114 311874273 + CmaNakai_Chr07g0716681 Chma7g09366 9366
7 311907607 311909574 + CmaNakai_Chr07g0716691 Chma7g09367 9367
7 311955567 311956905 - CmaNakai_Chr07g0716701 Chma7g09368 9368
13 5448556 5449092 + evm.model.scaffold_113.145 Chmo13g00132 132
13 5536037 5538507 - evm.model.scaffold_113.141 Chmo13g00133 133
13 5581652 5584335 - evm.model.scaffold_113.139 Chmo13g00134 134
14 7862836 7869194 + evm.model.scaffold_1390.34 Chmo14g00187 187
14 8039120 8041507 - evm.model.scaffold_1390.39 Chmo14g00189 189
14 8082865 8086750 - evm.model.scaffold_1390.40 Chmo14g00190 190
15 9110159 9112144 + evm.model.scaffold_212.37 Chmo15g00151 151
15 9162946 9165331 - evm.model.scaffold_212.42 Chmo15g00155 155
15 9259474 9262432 - evm.model.scaffold_212.44.1 Chmo15g00156 156
2 1950818 1952493 + Cn0525660 Chna2g00049 49
2 2022629 2024858 - Cn0498910 Chna2g00050 50
2 2061236 2064493 - Cn0498920 Chna2g00051 51
4 117010792 117012319 + KAI3753094.1 Cich4g03959 3959
4 117304638 117306326 - KAI3753108.1 Cich4g03973 3973
4 117497243 117499170 - KAI3753112.1 Cich4g03977 3977
5 71189330 71191029 - KAI3509500.1 Cien5g02980 2980
3 373191196 373193065 - D.indicum_Contig308_G00023.t1 Cind3g03212 3212
3 373132258 373134189 + D.indicum_Contig308_G00024.t1 Cind3g03213 3213
3 373082065 373093244 + D.indicum_Contig308_G00025.t1 Cind3g03214 3214
4 84187105 84190259 + h2tg000064l_1.g27603.t1 Cobi4g03388 3388
4 84200024 84202597 + h2tg000064l_1.g27604.t1 Cobi4g03389 3389
7 841425 854828 - h1tg000136l.g124626.t1 Dapi7g00038 38
7 895493 897378 - h1tg000136l.g124625.t1 Dapi7g00039 39
16 83276736 83278850 + h1tg000026l.g57055.t1 Dapi16g02102 2102
23 1353135 1355376 - h2tg000064l.g12383.t1 Dapi23g00045 45
23 1392260 1394823 - h2tg000064l.g12384.t1 Dapi23g00046 46
3 28991149 28993254 + XM_043764087.1 Ecan3g01771 1771
3 29007971 29010456 - XM_043765550.1 Ecan3g01772 1772
3 29044985 29050022 - XM_043766287.1 Ecan3g01774 1774
6 66450272 66452112 + evm.model.ctg1815.3 Enbr6g01889 1889
6 66767359 66769580 + evm.model.ctg163.1 Enbr6g01895 1895
6 66802576 66803786 - evm.model.ctg163.2 Enbr6g01896 1896
1 952583 954354 - FliAMIRv0_Chr01g0000581 Fli1g00059 59
11 80653779 80655551 - FraAMIRv0_Chr11g0227331 Fra11g02711 2711
2 468350 470125 - FsoAMIRv0_Chr02g0028601 Fso2g00041 41
3 32107105 32110303 + GcoAMIRv0_Chr03g0162071 Glco3g00578 578
3 32213497 32215419 + GcoAMIRv0_Chr03g0162081 Glco3g00579 579
3 32962578 32964134 - GcoAMIRv0_Chr03g0162221 Glco3g00593 593
4 207325249 207327131 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0192181 Hean4g04567 4567
16 50108380 50110371 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr16g0738151 Hean16g01313 1313
16 50977601 50980060 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr16g0738251 Hean16g01323 1323
16 51045126 51048126 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr16g0738261 Hean16g01324 1324
10 2758029 2760050 - >Htub.h1tg003335l.g258.t1 Hetu10g00065 65
11 1938379 1940203 - >Htub.h1tg000030l.g89.t1 Hetu11g00038 38
12 2387945 2389946 - >Htub.h1tg000754l.g243.t1 Hetu12g00040 40
46 58599520 58601428 + >Htub.h1tg000999l.g219.t1 Hetu46g01150 1150
46 59548264 59549258 - >Htub.h1tg000999l.g232.t1 Hetu46g01162 1162
47 62933090 62936606 + >Htub.h1tg000672l.g90.t1 Hetu47g01111 1111
47 63067576 63069385 + >Htub.h1tg000672l.g91.t1 Hetu47g01112 1112
48 51045054 51048845 - >Htub.h1tg001458l.g79.t1 Hetu48g00937 937
48 55991451 55993265 + >Htub.h1tg001111l.g51.t1 Hetu48g01002 1002
7 114244237 114246284 - CAI9294567.1 Laca7g02397 2397
7 114499109 114500843 - CAI9294569.1 Laca7g02399 2399
1 558259 559748 + LmiAMIRv0_Chr01g0000521 Lomi1g00052 52
1 566070 567916 - LmiAMIRv0_Chr01g0000531 Lomi1g00053 53
1 572498 575798 - LmiAMIRv0_Chr01g0000541 Lomi1g00054 54
2 50972100 50975661 + LmiAMIRv0_Chr02g0091341 Lomi2g04601 4601
2 50980248 50982088 + LmiAMIRv0_Chr02g0091351 Lomi2g04602 4602
7 155973206 155975502 + >KAJ0198383.1 Lssa7g02941 2941
7 156462745 156464993 - >KAJ0194954.1 Lssa7g02947 2947
7 156764733 156766683 - >KAJ0196945.1 Lssa7g02949 2949
17 2880156 2881824 - KAD3066415.1 Mimi17g00093 93
4 1458803 1461129 - PdyAMIRv0_Chr04g0148841 Pdy4g00076 76
4 1484931 1490082 - PdyAMIRv0_Chr04g0148851 Pdy4g00077 77
1 157469689 157472173 + PluAMIRv0_Chr01g0218521 Pslu1g21948 21948
1 157520011 157521839 + PluAMIRv0_Chr01g0218601 Pslu1g21956 21956
1 157554363 157555904 - PluAMIRv0_Chr01g0218641 Pslu1g21960 21960
12 22923472 22937012 + SinAMIRv0_Chr12g0364271 Sain12g00863 863
12 22986594 22988512 + SinAMIRv0_Chr12g0364281 Sain12g00864 864
7 4884612 4886927 + KAI3809861.1 Smso7g00281 281
7 4903486 4905140 + KAI3809862.1 Smso7g00282 282
26 48453700 48455820 + KAI3695589.1 Smso26g02104 2104
29 5136223 5137928 + KAI3675315.1 Smso29g00321 321
5 34642696 34645683 + transfrag28585.t01 Soca5g03099 3099
5 34694311 34695522 - augustus42812.t02 Soca5g03101 3101
6 1660729 1662628 + Streb.6G000720.1 Stre6g00072 72
6 2077737 2078491 - Streb.6G000810.1 Stre6g00081 81
6 2124622 2138097 - Streb.6G000830.1 Stre6g00083 83
1 52357848 52359761 + >KAK1439942.1 Taer1g05767 5767
4 107807076 107809320 + TkA04G427140.1 Tako4g04659 4659
4 107853141 107855460 + TkA04G427370.1 Tako4g04660 4660
4 108221949 108223558 - TkA04G428810.1 Tako4g04669 4669
4 65505224 65507347 + TbA04G015220.1 Tamo4g03387 3387
4 65529297 65533283 + TbA04G015210.1 Tamo4g03388 3388
       
DecoBrowse