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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
Armi1g00627 Sain12g00527 Ceso2g01443 Cati3g00664 Ccar2g01943 . . . . . . Pslu1g21489 . Lomi2g04412 Enbr6g01479 Ecan3g02085 Soca5g02791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00630 Sain12g00530 Ceso2g01446 Cati3g00667 . Cien5g03140 Cich4g04371 Lssa7g03330 Laca7g02719 . Tamo4g03010 Pslu1g21490 . Lomi2g04413 . . . . . . . . . . . . . . . Pdy4g00429 . Hean4g04337 . . Dapi16g01895 Dapi23g00255 Hetu11g00225 Hetu12g00223 Hetu10g00242 . . . Taer1g05576 Fro12g02432 Fso2g00141 Ftr4g03726 Fra11g02564 Fli1g00238 . . . . . . . . . . . . . . . . . . . . . .
. . . . Ccar2g01942 . . . . . . . Lomi1g00247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00640 . . Cati3g00669 Ccar2g01941 Cien5g03138 Cich4g04370 Lssa7g03329 Laca7g02718 Tako4g04099 Tamo4g03014 Pslu1g21491 Lomi1g00246 . . Ecan3g02080 . Glco3g00936 . . . . Chma7g08407 Chmo13g00675 . . . Chna2g00506 . . . Hean4g04338 . . Dapi16g01897 . Hetu11g00223 Hetu12g00222 Hetu10g00241 . . Smso26g01871 . . . . . . Stre6g00307 . . . . . . . . . . . . . . . . . . . . .
Armi1g00641 Sain12g00531 Ceso2g01447 Cati3g00671 Ccar2g01940 . . . . . . Pslu1g21494 Lomi1g00245 . Enbr6g01477 Ecan3g02079 Soca5g02799 . . . . . Chma7g08408 Chmo13g00672 Chmo14g00663 Chmo15g00533 . Chna2g00504 Cind3g03525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00642 Sain12g00532 Ceso2g01448 Cati3g00672 Ccar2g01939 . . . . . . Pslu1g21496 Lomi1g00243 Lomi2g04415 Enbr6g01475 Ecan3g02078 Soca5g02802 . . . . . Chma7g08411 Chmo13g00670 Chmo14g00661 Chmo15g00531 . Chna2g00502 Cind3g03527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00643 Sain12g00533 Ceso2g01449 Cati3g00673 Ccar2g01938 . Cich4g04368 Lssa7g03328 Laca7g02715 Tako4g04100 Tamo4g03015 Pslu1g21498 Lomi1g00242 Lomi2g04416 Enbr6g01474 Ecan3g02077 Soca5g02804 Glco3g00928 . . Aary13g03349 Aann4g01256 Chma7g08417 Chmo13g00669 Chmo14g00660 Chmo15g00530 . Chna2g00501 Cind3g03528 Pdy4g00426 . Hean4g04339 . . Dapi16g01900 Dapi23g00252 . . . . . Smso26g01873 Taer1g05579 . Fso2g00139 . Fra11g02567 Fli1g00235 . Mimi9g01464 Cobi4g03176 Hean11g00678 Bial4g03476 Bial16g02878 Dapi7g00232 Dapi23g00252 . . . . Smso7g00111 Smso29g00142 . . . . . Fli1g00236 . Mimi17g00324
Armi1g00644 Sain12g00534 . Cati3g00676 Ccar2g01937 . Cich4g04367 Lssa7g03326 Laca7g02713 Tako4g04102 . Pslu1g21499 Lomi1g00241 Lomi2g04417 Enbr6g01473 Ecan3g02076 Soca5g02805 Glco3g00926 . . Aary13g03354 Aann4g01258 . Chmo13g00667 Chmo14g00658 Chmo15g00529 . Chna2g00499 Cind3g03530 Pdy4g00425 . . . . . . . . . . . . . . . . . . . . . Hean11g00675 . . Dapi7g00231 Dapi23g00251 Hetu32g00532 Hetu31g00466 Hetu33g00622 . . . . . . . . . Stre6g00304 Mimi17g00322
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00645 Sain12g00538 . Cati3g00688 Ccar2g01936 . Cich4g04360 Lssa7g03324 Laca7g02711 Tako4g04107 . Pslu1g21500 Lomi1g00239 . Enbr6g01468 Ecan3g02073 Soca5g02807 . . . . . . . . . . . . Pdy4g00423 . Hean4g04343 . . Dapi16g01901 . Hetu11g00220 Hetu12g00217 Hetu10g00237 . . Smso26g01875 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 66907795 66913100 - chr4g0781231 Aann4g01256 1256
4 66987717 66989209 + chr4g0781281 Aann4g01258 1258
13 200877955 200882922 - Aargg13g33490.1 Aary13g03349 3349
13 201412068 201424949 + Aargg13g33540.1 Aary13g03354 3354
1 14701615 14706089 + AmiAMIRv0_Chr01g0006271 Armi1g00627 627
1 14789616 14789822 + AmiAMIRv0_Chr01g0006301 Armi1g00630 630
1 15048105 15052394 + AmiAMIRv0_Chr01g0006401 Armi1g00640 640
1 15086653 15089227 + AmiAMIRv0_Chr01g0006411 Armi1g00641 641
1 15090670 15095739 - AmiAMIRv0_Chr01g0006421 Armi1g00642 642
1 15100697 15106812 - AmiAMIRv0_Chr01g0006431 Armi1g00643 643
1 15125435 15129631 + AmiAMIRv0_Chr01g0006441 Armi1g00644 644
1 15157223 15158434 - AmiAMIRv0_Chr01g0006451 Armi1g00645 645
4 79093032 79098288 - g43315.t1 Bial4g03476 3476
16 73234627 73239886 - g127322.t1 Bial16g02878 2878
3 7319829 7329488 + CtAH03T0047700.2 Cati3g00664 664
3 7338701 7345491 + CtAH03T0047900.1 Cati3g00667 667
3 7338701 7342762 + CtAH03T0047900.3 Cati3g00669 669
3 7351275 7353656 + CtAH03T0048000.1 Cati3g00671 671
3 7354093 7360219 - CtAH03T0048100.1 Cati3g00672 672
3 7369413 7376366 - CtAH03T0048200.1 Cati3g00673 673
3 7390062 7394810 + CtAH03T0048400.1 Cati3g00676 676
3 7508242 7509444 - CtAH03T0049000.1 Cati3g00688 688
2 65920936 65922135 + gnl|WGS:LEKV|Ccrd_010982.mRNA.1_mrna Ccar2g01936 1936
2 65930682 65935691 - gnl|WGS:LEKV|Ccrd_010983.mRNA.1_mrna Ccar2g01937 1937
2 65939818 65946222 + gnl|WGS:LEKV|Ccrd_010984.mRNA.1_mrna Ccar2g01938 1938
2 65952749 65958855 + gnl|WGS:LEKV|Ccrd_010985.mRNA.1_mrna Ccar2g01939 1939
2 65959466 65962233 - gnl|WGS:LEKV|Ccrd_010986.mRNA.1_mrna Ccar2g01940 1940
2 65963831 65969383 - gnl|WGS:LEKV|Ccrd_010987.mRNA.1_mrna Ccar2g01941 1941
2 65972405 65990856 - gnl|WGS:LEKV|Ccrd_010988.mRNA.1_mrna Ccar2g01942 1942
2 66009958 66021485 - gnl|WGS:LEKV|Ccrd_010989.mRNA.1_mrna Ccar2g01943 1943
2 29963640 29968389 + >KAJ9560814.1 Ceso2g01443 1443
2 29981632 29985559 + >KAJ9560723.1 Ceso2g01446 1446
2 29994162 29996385 + >KAJ9560722.1 Ceso2g01447 1447
2 29997565 30002166 - >KAJ9560726.1 Ceso2g01448 1448
2 30007867 30013301 - >KAJ9560725.1 Ceso2g01449 1449
7 287361242 287373114 + CmaNakai_Chr07g0707091 Chma7g08407 8407
7 287417524 287418766 + CmaNakai_Chr07g0707101 Chma7g08408 8408
7 287471829 287475809 - CmaNakai_Chr07g0707131 Chma7g08411 8411
7 287541139 287544923 - CmaNakai_Chr07g0707191 Chma7g08417 8417
13 31298835 31305001 - evm.model.scaffold_530.187 Chmo13g00667 667
13 31505385 31510602 + evm.model.scaffold_530.200 Chmo13g00669 669
13 31530790 31535122 + evm.model.scaffold_530.201 Chmo13g00670 670
13 31546896 31548160 - evm.model.scaffold_530.203 Chmo13g00672 672
13 31632859 31637077 - evm.model.scaffold_530.213 Chmo13g00675 675
14 29367291 29369001 - evm.model.scaffold_464.118 Chmo14g00658 658
14 29414953 29419166 + evm.model.scaffold_464.115 Chmo14g00660 660
14 29531050 29535711 + evm.model.scaffold_464.102 Chmo14g00661 661
14 29540650 29541892 - evm.model.scaffold_464.100 Chmo14g00663 663
15 27528660 27595531 - evm.model.scaffold_504.129 Chmo15g00529 529
15 27613448 27617666 + evm.model.scaffold_504.125 Chmo15g00530 530
15 27724784 27729449 + evm.model.scaffold_504.119 Chmo15g00531 531
15 27734419 27737586 - evm.model.scaffold_504.117 Chmo15g00533 533
2 34680494 34683335 - Cn0777930 Chna2g00499 499
2 34795247 34800776 + Cn0777970 Chna2g00501 501
2 34962787 34968167 + Cn0777990 Chna2g00502 502
2 34972934 34975230 - Cn0778010 Chna2g00504 504
2 35033041 35036539 - Cn0778040 Chna2g00506 506
4 127499292 127501248 + KAI3753495.1 Cich4g04360 4360
4 127607901 127611159 - KAI3753502.1 Cich4g04367 4367
4 127616332 127623142 + KAI3753503.1 Cich4g04368 4368
4 127644550 127647418 + KAI3753505.1 Cich4g04370 4370
4 127651986 127653742 + KAI3753506.1 Cich4g04371 4371
5 75389718 75391443 - KAI3509658.1 Cien5g03138 3138
5 75411002 75412958 - KAI3509660.1 Cien5g03140 3140
3 343149215 343150471 + D.indicum_Contig356_G00017.t1 Cind3g03525 3525
3 343155875 343159771 - D.indicum_Contig356_G00019.t1 Cind3g03527 3527
3 343182841 343186789 - D.indicum_Contig356_G00020.t1 Cind3g03528 3528
3 343394672 343399980 + D.indicum_Contig356_G00022.t1 Cind3g03530 3530
4 81295203 81299867 - h2tg000009l_1.g42103.t1 Cobi4g03176 3176
7 4674184 4677316 - h1tg000136l.g124433.t1 Dapi7g00231 231
7 4686961 4690862 + h1tg000136l.g124432.t1 Dapi7g00232 232
16 71525135 71528935 + h1tg000026l.g56848.t1 Dapi16g01895 1895
16 71600609 71603794 + h1tg000026l.g56850.t1 Dapi16g01897 1897
16 71779345 71783330 - h1tg000026l.g56853.t1 Dapi16g01900 1900
16 71832303 71833469 - h1tg000026l.g56854.t1 Dapi16g01901 1901
23 5212791 5215914 - h2tg000284l.g80794.t1 Dapi23g00251 251
23 5225384 5229767 + h2tg000284l.g80793.t1 Dapi23g00252 252
23 5269160 5271983 - h2tg000284l.g80790.t1 Dapi23g00255 255
3 31578791 31580593 + XM_043766873.1 Ecan3g02073 2073
3 31628852 31632390 - XM_043766439.1 Ecan3g02076 2076
3 31643348 31649798 + XM_043765484.1 Ecan3g02077 2077
3 31653078 31657246 + XM_043762714.1 Ecan3g02078 2078
3 31660731 31661822 - XM_043764142.1 Ecan3g02079 2079
3 31663100 31673558 - XM_043762715.1 Ecan3g02080 2080
3 31691753 31694361 - XM_043764145.1 Ecan3g02085 2085
6 50680934 50682647 + evm.model.ctg9497.3 Enbr6g01468 1468
6 50761660 50764685 - evm.model.ctg503.3 Enbr6g01473 1473
6 50777150 50781559 + evm.model.ctg503.4 Enbr6g01474 1474
6 50791939 50795578 + evm.model.ctg503.5 Enbr6g01475 1475
6 50799097 50800068 - evm.model.ctg503.7 Enbr6g01477 1477
6 50824354 50827954 - evm.model.ctg503.9 Enbr6g01479 1479
1 4762019 4764403 + FliAMIRv0_Chr01g0002301 Fli1g00235 235
1 4764439 4766059 + FliAMIRv0_Chr01g0002311 Fli1g00236 236
1 4778871 4782004 - FliAMIRv0_Chr01g0002331 Fli1g00238 238
11 79285599 79288736 + FraAMIRv0_Chr11g0225861 Fra11g02564 2564
11 79301115 79305081 - FraAMIRv0_Chr11g0225891 Fra11g02567 2567
12 32140955 32143976 + FroAMIRv0_Chr12g0219801 Fro12g02432 2432
2 1956866 1959208 + FsoAMIRv0_Chr02g0029581 Fso2g00139 139
2 2000303 2003613 - FsoAMIRv0_Chr02g0029601 Fso2g00141 141
4 121087561 121090702 + FtrAMIRv0_Chr04g0131601 Ftr4g03726 3726
3 53176354 53180239 + GcoAMIRv0_Chr03g0165551 Glco3g00926 926
3 53279558 53283467 + GcoAMIRv0_Chr03g0165571 Glco3g00928 928
3 53811818 53817246 - GcoAMIRv0_Chr03g0165651 Glco3g00936 936
4 204053515 204058086 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189581 Hean4g04337 4337
4 204063374 204068281 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189591 Hean4g04338 4338
4 204070381 204077359 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189601 Hean4g04339 4339
4 204166599 204167159 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189641 Hean4g04343 4343
11 13727247 13729265 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0473771 Hean11g00675 675
11 13788558 13798388 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0473801 Hean11g00678 678
10 9809917 9811917 + >Htub.h1tg000798l.g453.t1 Hetu10g00237 237
10 9834444 9837324 - >Htub.h1tg000798l.g449.t1 Hetu10g00241 241
10 9840360 9843706 - >Htub.h1tg000798l.g448.t1 Hetu10g00242 242
11 7711861 7713773 + >Htub.h1tg000030l.g278.t1 Hetu11g00220 220
11 7767378 7771963 - >Htub.h1tg000030l.g281.t1 Hetu11g00223 223
11 7781395 7785003 - >Htub.h1tg000030l.g284.t1 Hetu11g00225 225
12 8119023 8121023 + >Htub.h1tg004588l.g151.t1 Hetu12g00217 217
12 8152486 8155366 - >Htub.h1tg000613l.g261.t1 Hetu12g00222 222
12 8158402 8161748 - >Htub.h1tg000613l.g260.t1 Hetu12g00223 223
31 15883344 15886571 - >Htub.h1tg001140l.g342.t1 Hetu31g00466 466
32 20812643 20813621 - >Htub.h1tg001632l.g239.t1 Hetu32g00532 532
33 20787678 20790862 - >Htub.h1tg000986l.g454.t1 Hetu33g00622 622
7 129626462 129627664 - CAI9294898.1 Laca7g02711 2711
7 129660725 129663555 - CAI9294900.1 Laca7g02713 2713
7 129737793 129743744 + CAI9294902.1 Laca7g02715 2715
7 129767199 129769543 + CAI9294905.1 Laca7g02718 2718
7 129815889 129818227 + CAI9294906.1 Laca7g02719 2719
1 2075149 2076518 + LmiAMIRv0_Chr01g0002391 Lomi1g00239 239
1 2078804 2080821 - LmiAMIRv0_Chr01g0002411 Lomi1g00241 241
1 2085943 2090204 + LmiAMIRv0_Chr01g0002421 Lomi1g00242 242
1 2091879 2095007 + LmiAMIRv0_Chr01g0002431 Lomi1g00243 243
1 2098414 2099420 - LmiAMIRv0_Chr01g0002451 Lomi1g00245 245
1 2103566 2106344 - LmiAMIRv0_Chr01g0002461 Lomi1g00246 246
1 2117589 2119128 - LmiAMIRv0_Chr01g0002471 Lomi1g00247 247
2 49395800 49398351 + LmiAMIRv0_Chr02g0089451 Lomi2g04412 4412
2 49404528 49406916 + LmiAMIRv0_Chr02g0089461 Lomi2g04413 4413
2 49418710 49422496 - LmiAMIRv0_Chr02g0089481 Lomi2g04415 4415
2 49424016 49428273 - LmiAMIRv0_Chr02g0089491 Lomi2g04416 4416
2 49438628 49441422 + LmiAMIRv0_Chr02g0089501 Lomi2g04417 4417
7 177032492 177033694 + >KAJ0195635.1 Lssa7g03324 3324
7 177078581 177080288 - >KAJ0197359.1 Lssa7g03326 3326
7 177118687 177124687 + >KAJ0196465.1 Lssa7g03328 3328
7 177158481 177160439 + >KAJ0195432.1 Lssa7g03329 3329
7 177187464 177189660 + >KAJ0195742.1 Lssa7g03330 3330
9 50664079 50670058 - KAD5318199.1 Mimi9g01464 1464
17 9458009 9460382 - KAD3066644.1 Mimi17g00322 322
17 9516808 9522828 + KAD3066646.1 Mimi17g00324 324
4 8031387 8032592 + PdyAMIRv0_Chr04g0152311 Pdy4g00423 423
4 8036865 8041853 - PdyAMIRv0_Chr04g0152331 Pdy4g00425 425
4 8053780 8057709 + PdyAMIRv0_Chr04g0152341 Pdy4g00426 426
4 8072367 8075908 - PdyAMIRv0_Chr04g0152371 Pdy4g00429 429
1 154300324 154303305 + PluAMIRv0_Chr01g0213941 Pslu1g21489 21489
1 154305120 154309902 + PluAMIRv0_Chr01g0213951 Pslu1g21490 21490
1 154311530 154316427 + PluAMIRv0_Chr01g0213961 Pslu1g21491 21491
1 154322390 154323408 + PluAMIRv0_Chr01g0213991 Pslu1g21494 21494
1 154326875 154329900 - PluAMIRv0_Chr01g0214011 Pslu1g21496 21496
1 154349324 154353596 - PluAMIRv0_Chr01g0214031 Pslu1g21498 21498
1 154361544 154364932 + PluAMIRv0_Chr01g0214041 Pslu1g21499 21499
1 154366970 154368605 - PluAMIRv0_Chr01g0214051 Pslu1g21500 21500
12 11838613 11848615 + SinAMIRv0_Chr12g0360911 Sain12g00527 527
12 11889174 11891744 + SinAMIRv0_Chr12g0360941 Sain12g00530 530
12 11894715 11896917 + SinAMIRv0_Chr12g0360951 Sain12g00531 531
12 11897607 11902939 - SinAMIRv0_Chr12g0360961 Sain12g00532 532
12 11906045 11911556 - SinAMIRv0_Chr12g0360971 Sain12g00533 533
12 11926240 11931617 + SinAMIRv0_Chr12g0360981 Sain12g00534 534
12 11962537 11963730 - SinAMIRv0_Chr12g0361021 Sain12g00538 538
7 1951305 1955276 - KAI3809691.1 Smso7g00111 111
26 36191665 36193830 + KAI3695356.1 Smso26g01871 1871
26 36221790 36225627 - KAI3695358.1 Smso26g01873 1873
26 36312934 36314705 - KAI3695360.1 Smso26g01875 1875
29 2302534 2306489 - KAI3675136.1 Smso29g00142 142
5 30952490 30955164 + augustus47842.t03 Soca5g02791 2791
5 30976445 30977620 + transfrag32017.t01 Soca5g02799 2799
5 30981562 30985927 - augustus47835.t03 Soca5g02802 2802
5 30988065 30993639 - transfrag32015.t01 Soca5g02804 2804
5 31006043 31008423 + transfrag32014.t01 Soca5g02805 2805
5 31021231 31022707 - augustus47829.t01 Soca5g02807 2807
6 8217252 8219821 - Streb.6G003040.1 Stre6g00304 304
6 8255998 8260375 - Streb.6G003070.1 Stre6g00307 307
1 50843660 50846534 + >KAK1439756.1 Taer1g05576 5576
1 50864273 50868047 - >KAK1439759.1 Taer1g05579 5579
4 92603581 92606137 - TkA04G368350.1 Tako4g04099 4099
4 92614639 92620704 - TkA04G368370.1 Tako4g04100 4100
4 92623393 92626476 + TkA04G368380.2 Tako4g04102 4102
4 92703786 92704982 - TkA04G368630.1 Tako4g04107 4107
4 57556464 57559006 - TbA04G025040.1 Tamo4g03010 3010
4 57648892 57651593 - TbA04G024960.1 Tamo4g03014 3014
4 57659238 57665353 - TbA04G024940.1 Tamo4g03015 3015
       
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