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Asteraceae Genomic Research Platform

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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
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00607 Sain12g00511 . Cati3g00648 Ccar2g01954 . . Lssa7g03370 Laca7g02737 Tako4g04043 Tamo4g02982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00609 Sain12g00512 . Cati3g00649 . . . Lssa7g03364 Laca7g02735 . Tamo4g02984 . . . . . . . . . . . Chma7g05115 . Chmo14g02494 Chmo15g02717 . Chna2g02645 Cind3g04339 Pdy4g01614 . . . . . . . . . . . . . . . . . . . . Cobi4g03158 Hean11g00694 Bial12g02400 Bial16g02849 . . . Hetu31g00496 . . Smso7g00092 Smso29g00125 . . . . . . Stre6g00340 Mimi17g00352
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00614 Sain12g00513 Ceso2g01438 Cati3g00650 Ccar2g01953 Cien5g03154 Cich4g04395 Lssa7g03360 Laca7g02731 . . Pslu1g21469 Lomi1g00260 Lomi2g04403 Enbr6g01490 Ecan3g02100 Soca5g02777 Glco3g00994 Artr3g11793 Aary5g02853 Aary13g03321 Aann4g01223 Chma7g08375 . Chmo14g00685 Chmo15g00564 . Chna2g00524 . Pdy4g00441 . . . . . . . . . . . . . . . . . . . . Cobi4g03163 Hean11g00691 Bial4g03460 Bial16g02865 Dapi7g00246 Dapi23g00266 Hetu32g00546 Hetu31g00481 Hetu33g00643 . . Smso29g00128 . . . . . . Stre6g00326 Mimi17g00335
Armi1g00615 Sain12g00515 . Cati3g00652 Ccar2g01951 . Cich4g04392 Lssa7g03357 Laca7g02730 . Tamo4g02998 . . . . . . Glco3g00987 Artr3g11813 Aary5g02851 Aary13g03324 Aann4g01229 Chma7g08385 Chmo13g00690 Chmo14g00681 Chmo15g00556 . Chna2g00519 Cind3g02782 Pdy4g00440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00616 Sain12g00517 . Cati3g00653 Ccar2g01950 . Cich4g04391 Lssa7g03356 Laca7g02729 . Tamo4g03001 Pslu1g21471 Lomi1g00259 Lomi2g04404 . Ecan3g02098 Soca5g02779 Glco3g00984 Artr3g11817 . Aary13g03325 Aann4g01232 Chma7g08386 Chmo13g00688 Chmo14g00680 Chmo15g00554 . Chna2g00518 Cind3g02780 Pdy4g00439 . Hean4g04335 . . Dapi16g01893 Dapi23g00263 Hetu11g00228 Hetu12g00226 Hetu10g00246 . . Smso26g01863 Taer1g05568 Fro12g02424 Fso2g00182 Ftr4g03716 Fra11g02556 Fli1g00246 Stre6g00314 . Cobi4g03165 Hean11g00688 Bial4g03465 Bial16g02868 Dapi7g00243 Dapi23g00263 Hetu32g00542 Hetu31g00479 Hetu33g00640 . Smso7g00097 Smso29g00131 Taer1g05568 Fro12g02424 Fso2g00182 Ftr4g03716 Fra11g02556 Fli1g00246 Stre6g00315 Mimi17g00333
Armi1g00617 Sain12g00518 . Cati3g00654 Ccar2g01949 . . . . . . Pslu1g21472 Lomi1g00258 Lomi2g04405 . Ecan3g02097 Soca5g02780 . . . . . Chma7g08387 Chmo13g00687 Chmo14g00679 Chmo15g00552 . Chna2g00517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 65548109 65552862 - chr4g0780131 Aann4g01223 1223
4 66302261 66315107 + chr4g0780551 Aann4g01229 1229
4 66395641 66400336 + chr4g0780671 Aann4g01232 1232
5 173209221 173218769 - Aargg5g28510.1 Aary5g02851 2851
5 173324370 173327160 + Aargg5g28530.1 Aary5g02853 2853
13 199670593 199673342 - Aargg13g33210.1 Aary13g03321 3321
13 199917734 199929447 + Aargg13g33240.1 Aary13g03324 3324
13 199961444 199964373 + Aargg13g33250.1 Aary13g03325 3325
1 14175719 14177122 - AmiAMIRv0_Chr01g0006071 Armi1g00607 607
1 14241655 14244639 - AmiAMIRv0_Chr01g0006091 Armi1g00609 609
1 14421789 14424970 - AmiAMIRv0_Chr01g0006141 Armi1g00614 614
1 14474489 14479265 + AmiAMIRv0_Chr01g0006151 Armi1g00615 615
1 14493079 14495702 + AmiAMIRv0_Chr01g0006161 Armi1g00616 616
1 14521094 14521537 + AmiAMIRv0_Chr01g0006171 Armi1g00617 617
3 403773673 403776483 - AtridAMIRv0_Chr03g0425291 Artr3g11793 11793
3 404591347 404601337 + AtridAMIRv0_Chr03g0425491 Artr3g11813 11813
3 404825652 404828564 + AtridAMIRv0_Chr03g0425531 Artr3g11817 11817
4 78928459 78934204 - g43299.t1 Bial4g03460 3460
4 78983178 78992819 + g43304.t1 Bial4g03465 3465
12 54319306 54322187 - g35599.t1 Bial12g02400 2400
16 72819871 72822317 + g127351.t1 Bial16g02849 2849
16 73106767 73111347 - g127335.t1 Bial16g02865 2865
16 73144052 73147213 + g127332.t1 Bial16g02868 2868
3 7080353 7083304 - CtAH03T0046500.1 Cati3g00648 648
3 7129518 7138887 - CtAH03T0046600.1 Cati3g00649 649
3 7152841 7157178 - CtAH03T0046700.1 Cati3g00650 650
3 7170095 7196013 + CtAH03T0046800.2 Cati3g00652 652
3 7200395 7203183 + CtAH03T0046900.1 Cati3g00653 653
3 7216825 7218447 + CtAH03T0047000.1 Cati3g00654 654
2 66082032 66083676 - gnl|WGS:LEKV|Ccrd_010996.mRNA.1_mrna Ccar2g01949 1949
2 66091843 66094653 - gnl|WGS:LEKV|Ccrd_010997.mRNA.1_mrna Ccar2g01950 1950
2 66108726 66120457 - gnl|WGS:LEKV|Ccrd_010998.mRNA.1_mrna Ccar2g01951 1951
2 66129281 66145471 + gnl|WGS:LEKV|Ccrd_011000.mRNA.1_mrna Ccar2g01953 1953
2 66145132 66157903 - gnl|WGS:LEKV|Ccrd_011001.mRNA.1_mrna Ccar2g01954 1954
2 29790855 29794491 - >KAJ9560693.1 Ceso2g01438 1438
7 144113018 144113667 + CmaNakai_Chr07g0674171 Chma7g05115 5115
7 285698575 285700549 - CmaNakai_Chr07g0706771 Chma7g08375 8375
7 286294270 286305515 + CmaNakai_Chr07g0706871 Chma7g08385 8385
7 286373958 286377078 + CmaNakai_Chr07g0706881 Chma7g08386 8386
7 286530408 286532157 + CmaNakai_Chr07g0706891 Chma7g08387 8387
13 32270552 32272543 - evm.model.scaffold_530.245 Chmo13g00687 687
13 32299464 32302666 - evm.model.scaffold_530.247 Chmo13g00688 688
13 32341236 32357790 - evm.model.scaffold_530.250 Chmo13g00690 690
14 30448155 30450123 - evm.model.scaffold_464.58 Chmo14g00679 679
14 30475862 30479996 - evm.model.scaffold_464.56 Chmo14g00680 680
14 30494754 30510588 - evm.model.scaffold_464.55 Chmo14g00681 681
14 31253219 31258197 + evm.model.scaffold_464.19 Chmo14g00685 685
14 181813839 181814435 - evm.model.scaffold_297.192 Chmo14g02494 2494
15 28715932 28717886 - evm.model.scaffold_504.76 Chmo15g00552 552
15 29047465 29050582 - evm.model.scaffold_504.64 Chmo15g00554 554
15 29072192 29100406 - evm.model.scaffold_504.61 Chmo15g00556 556
15 30097667 30100641 + evm.model.scaffold_504.12 Chmo15g00564 564
15 186387950 186389080 - evm.model.scaffold_190.30 Chmo15g02717 2717
2 35813258 35819887 - Cn0778250 Chna2g00517 517
2 35825785 35829032 - Cn0778260 Chna2g00518 518
2 35867608 35879360 - Cn0778270 Chna2g00519 519
2 36604243 36606452 + Cn0778380 Chna2g00524 524
2 298772694 298773845 - Cn0699870 Chna2g02645 2645
4 127927647 127929672 - KAI3753526.1 Cich4g04391 4391
4 127929716 127940322 - KAI3753527.1 Cich4g04392 4392
4 127995992 127998673 + KAI3753530.1 Cich4g04395 4395
5 75771375 75774147 + KAI3509674.1 Cien5g03154 3154
3 341348108 341350904 + D.indicum_Contig290_G00004.t1 Cind3g02780 2780
3 341277132 341289635 + D.indicum_Contig290_G00006.t1 Cind3g02782 2782
3 369150798 369156547 - D.indicum_Contig50_G00155.t1 Cind3g04339 4339
4 81130684 81133095 + h2tg000009l_1.g42121.t1 Cobi4g03158 3158
4 81185069 81188236 - h2tg000009l_1.g42116.t1 Cobi4g03163 3163
4 81205300 81207883 + h2tg000009l_1.g42114.t1 Cobi4g03165 3165
7 4785156 4787820 - h1tg000136l.g124421.t1 Dapi7g00243 243
7 4861652 4864400 + h1tg000136l.g124418.t1 Dapi7g00246 246
16 71450559 71453353 + h1tg000026l.g56846.t1 Dapi16g01893 1893
23 5343437 5346529 - h2tg000284l.g80782.t1 Dapi23g00263 263
23 5381862 5384946 + h2tg000284l.g80779.t1 Dapi23g00266 266
3 31764758 31766662 - XM_043765376.1 Ecan3g02097 2097
3 31770711 31775279 - XM_043765513.1 Ecan3g02098 2098
3 31786861 31789703 - XM_043766038.1 Ecan3g02100 2100
6 51025466 51027664 + evm.model.ctg9218.1 Enbr6g01490 1490
1 4865228 4868722 - FliAMIRv0_Chr01g0002411 Fli1g00246 246
11 79242748 79245567 + FraAMIRv0_Chr11g0225781 Fra11g02556 2556
12 32088355 32091183 + FroAMIRv0_Chr12g0219721 Fro12g02424 2424
2 2576781 2576993 + FsoAMIRv0_Chr02g0030011 Fso2g00182 182
4 121040317 121042641 + FtrAMIRv0_Chr04g0131501 Ftr4g03716 3716
3 55727531 55730160 - GcoAMIRv0_Chr03g0166131 Glco3g00984 984
3 55770104 55783971 - GcoAMIRv0_Chr03g0166161 Glco3g00987 987
3 56050869 56053686 + GcoAMIRv0_Chr03g0166231 Glco3g00994 994
4 204029250 204034103 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189561 Hean4g04335 4335
11 14057079 14062419 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0473931 Hean11g00688 688
11 14105222 14108866 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0473961 Hean11g00691 691
11 14156533 14159514 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0473991 Hean11g00694 694
10 9974483 9975957 - >Htub.h1tg000798l.g444.t1 Hetu10g00246 246
11 7894835 7896342 - >Htub.h1tg000030l.g287.t1 Hetu11g00228 228
12 8255281 8256390 - >Htub.h1tg000613l.g257.t1 Hetu12g00226 226
31 16203778 16206572 - >Htub.h1tg001140l.g328.t1 Hetu31g00479 479
31 16282036 16286567 + >Htub.h1tg001140l.g326.t1 Hetu31g00481 481
31 17698083 17698808 + >Htub.h1tg001140l.g311.t1 Hetu31g00496 496
32 21137291 21141444 - >Htub.h1tg001952l.g223.t1 Hetu32g00542 542
32 21186935 21190310 + >Htub.h1tg001952l.g219.t1 Hetu32g00546 546
33 21317759 21321982 - >Htub.h1tg000986l.g435.t1 Hetu33g00640 640
33 21350674 21354159 + >Htub.h1tg000986l.g432.t1 Hetu33g00643 643
7 129973389 129975651 - CAI9294916.1 Laca7g02729 2729
7 129975703 129989068 - CAI9294918.1 Laca7g02730 2730
7 130013980 130016652 + CAI9294919.1 Laca7g02731 2731
7 130077346 130080374 + CAI9294923.1 Laca7g02735 2735
7 130123197 130126178 + CAI9294925.1 Laca7g02737 2737
1 2170092 2170535 - LmiAMIRv0_Chr01g0002581 Lomi1g00258 258
1 2174805 2178039 - LmiAMIRv0_Chr01g0002591 Lomi1g00259 259
1 2181586 2183478 - LmiAMIRv0_Chr01g0002601 Lomi1g00260 260
2 49330201 49332091 + LmiAMIRv0_Chr02g0089361 Lomi2g04403 4403
2 49344459 49347011 + LmiAMIRv0_Chr02g0089371 Lomi2g04404 4404
2 49352931 49353374 + LmiAMIRv0_Chr02g0089381 Lomi2g04405 4405
7 177738669 177742420 - >KAJ0197030.1 Lssa7g03356 3356
7 177753396 177759319 - >KAJ0194778.1 Lssa7g03357 3357
7 177810082 177812149 + >KAJ0196764.1 Lssa7g03360 3360
7 177916115 177920573 + >KAJ0195125.1 Lssa7g03364 3364
7 177992412 177993317 + >KAJ0197975.1 Lssa7g03370 3370
17 9827618 9836456 - KAD3066655.1 Mimi17g00333 333
17 9906899 9912484 + KAD3066657.1 Mimi17g00335 335
17 10716925 10719597 + KAD3066674.1 Mimi17g00352 352
4 8189089 8191428 - PdyAMIRv0_Chr04g0152471 Pdy4g00439 439
4 8208169 8220382 - PdyAMIRv0_Chr04g0152481 Pdy4g00440 440
4 8225879 8229283 + PdyAMIRv0_Chr04g0152491 Pdy4g00441 441
4 42412618 42415638 + PdyAMIRv0_Chr04g0164211 Pdy4g01614 1614
1 154157470 154159387 + PluAMIRv0_Chr01g0213741 Pslu1g21469 21469
1 154178381 154180961 + PluAMIRv0_Chr01g0213761 Pslu1g21471 21471
1 154184748 154185191 + PluAMIRv0_Chr01g0213771 Pslu1g21472 21472
12 11599840 11602821 - SinAMIRv0_Chr12g0360751 Sain12g00511 511
12 11605621 11606439 - SinAMIRv0_Chr12g0360761 Sain12g00512 512
12 11658629 11661737 - SinAMIRv0_Chr12g0360771 Sain12g00513 513
12 11676913 11685730 + SinAMIRv0_Chr12g0360791 Sain12g00515 515
12 11709940 11712744 + SinAMIRv0_Chr12g0360811 Sain12g00517 517
12 11740191 11740634 + SinAMIRv0_Chr12g0360821 Sain12g00518 518
7 1813240 1814496 - KAI3809672.1 Smso7g00092 92
7 1841477 1844618 + KAI3809677.1 Smso7g00097 97
26 35925772 35929176 + KAI3695348.1 Smso26g01863 1863
29 2144929 2145921 - KAI3675119.1 Smso29g00125 125
29 2177739 2180904 - KAI3675122.1 Smso29g00128 128
29 2213539 2216859 + KAI3675125.1 Smso29g00131 131
5 30810438 30813216 + transfrag32033.t01 Soca5g02777 2777
5 30838376 30842303 + transfrag32031.t01 Soca5g02779 2779
5 30850167 30852187 + transfrag32030.t01 Soca5g02780 2780
6 8327567 8331074 - Streb.6G003140.1 Stre6g00314 314
6 8349252 8350975 - Streb.6G003150.1 Stre6g00315 315
6 8906365 8909050 + Streb.6G003260.1 Stre6g00326 326
6 9173583 9176582 + Streb.6G003400.1 Stre6g00340 340
1 50799032 50801159 + >KAK1439748.1 Taer1g05568 5568
4 91204100 91210396 - TkA04G362320.3 Tako4g04043 4043
4 56953476 56961292 - TbA04G025840.1 Tamo4g02982 2982
4 56971075 56972992 - TbA04G025820.1 Tamo4g02984 2984
4 57370135 57376827 + TbA04G025260.1 Tamo4g02998 2998
4 57418166 57422396 + TbA04G025190.1 Tamo4g03001 3001
       
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