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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
Armi18g00100 Sain8g02150 . Cati1g00093 Ccar5g01550 . . . . . . Pslu2g02128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00099 Sain8g02148 Ceso1g00062 Cati1g00092 Ccar5g01551 Cien7g02456 . Lssa3g03385 . . Tamo6g02399 Pslu2g02119 . . Enbr1g08986 Ecan8g02608 Soca4g03330 Glco7g01986 Artr9g04486 . . Aann3g01550 . Chmo25g01377 Chmo26g01527 Chmo27g01266 Chla9g03801 Chna8g00973 Cind9g04201 Pdy3g03026 Cobi3g02242 Hean15g01291 . . . . . . . Amtr08g03938 . . Taer5g00728 Fro11g01673 Fso10g02358 . Fra7g01704 Fli2g01977 Stre11g01608 Mimi1g01826 . . . . . . . . . . . . . . . . . . . .
Armi18g00098 Sain8g02144 Ceso1g00061 Cati1g00091 Ccar5g01552 Cien7g02462 . Lssa3g03383 Laca3g02748 . Tamo6g02401 Pslu2g14298 Lomi6g00679 . Enbr1g08987 Ecan8g02611 Soca4g03331 Glco7g01988 . . . . . Chmo25g01378 Chmo26g01528 Chmo27g01265 Chla9g03797 Chna8g00974 Cind9g04203 Pdy3g03028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00097 Sain8g02143 . Cati1g00090 Ccar5g01553 Cien7g02464 Cich8g01590 Lssa3g03381 Laca3g02750 . Tamo6g02407 . . . Enbr1g08989 Ecan8g02613 Soca4g03333 Glco7g01995 . . . . . . . . Chla9g03795 Chna8g00976 Cind9g04206 Pdy3g03030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . Ceso1g00060 . Ccar5g01554 . . . . . . Pslu2g14298 . . . Ecan8g02614 Soca4g03334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00096 Sain8g02137 Ceso1g00059 Cati1g00088 Ccar5g01555 Cien7g02469 Cich8g01599 Lssa3g03374 Laca3g02753 Tako6g02848 . Pslu2g14292 Lomi6g01986 . Enbr1g08991 Ecan8g02615 Soca4g03335 Glco7g01997 Artr9g04523 Aary7g02303 Aary15g02200 Aann3g01564 . . . . . . . Pdy3g03031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00095 Sain8g02136 Ceso1g00058 Cati1g00087 Ccar5g01556 Cien7g02470 Cich8g01600 Lssa3g03373 . Tako6g02850 Tamo6g02414 Pslu2g14291 Lomi6g01985 . . Ecan8g02618 Soca4g03337 Glco7g01998 Artr9g04526 Aary7g02304 Aary15g02201 Aann3g01565 . . . . . . . Pdy3g03032 Cobi8g02633 Hean15g01292 . Bial5g03092 Dapi30g00610 Dapi14g00588 Hetu43g01377 Hetu45g01413 Hetu44g01306 Amtr08g03942 Smso2g00955 Smso23g00568 Taer5g00727 Fro11g01672 Fso10g02359 . Fra7g01705 Fli2g01976 Stre11g01624 Mimi1g01830 . . . . . . . . . . . . . . . . . . . .
Armi18g00092 Sain8g02132 Ceso1g00057 Cati1g00086 Ccar5g01557 Cien7g02472 . Lssa3g03371 . Tako6g02852 Tamo6g02419 Pslu2g14278 Lomi6g01984 . Enbr1g08992 Ecan8g02619 Soca4g03339 Glco7g02002 Artr9g04530 Aary7g02305 Aary15g02203 Aann3g01567 . . . . . . . Pdy3g03036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00091 Sain8g02131 Ceso1g00056 Cati1g00084 Ccar5g01558 Cien7g02473 Cich8g01601 Lssa3g03370 . Tako6g02853 Tamo6g02423 . . . . . . . . . . . . . . . . . . Pdy3g03037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00090 Sain8g02129 Ceso1g00055 . Ccar5g01559 Cien7g02474 Cich8g01602 Lssa3g03369 . Tako6g02856 Tamo6g02427 Pslu2g14267 . . Enbr1g08993 Ecan8g02621 Soca4g03343 Glco7g02003 Artr9g04532 Aary7g02307 Aary15g02205 Aann3g01571 . . . . . . . Pdy3g03038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
3 99883165 99887195 + chr3g0634331 Aann3g01550 1550
3 100447560 100454687 + chr3g0634841 Aann3g01564 1564
3 100454689 100459219 - chr3g0634851 Aann3g01565 1565
3 100474879 100477136 + chr3g0634881 Aann3g01567 1567
3 100481902 100488956 - chr3g0634921 Aann3g01571 1571
7 199537789 199542720 + Aargg7g23030.1 Aary7g02303 2303
7 199545040 199547160 - Aargg7g23040.1 Aary7g02304 2304
7 199636879 199639586 + Aargg7g23050.1 Aary7g02305 2305
7 199644851 199650750 - Aargg7g23070.1 Aary7g02307 2307
15 171546846 171551698 + Aargg15g22000.1 Aary15g02200 2200
15 171554590 171557088 - Aargg15g22010.1 Aary15g02201 2201
15 171621177 171624664 + Aargg15g22030.1 Aary15g02203 2203
15 171629438 171635630 - Aargg15g22050.1 Aary15g02205 2205
8 106316653 106318920 + AtrifAMIRv0_Chr08g0555201 Amtr08g03938 3938
8 106335803 106337890 - AtrifAMIRv0_Chr08g0555241 Amtr08g03942 3942
18 1680282 1686923 + AmiAMIRv0_Chr18g0470231 Armi18g00090 90
18 1689465 1690135 + AmiAMIRv0_Chr18g0470241 Armi18g00091 91
18 1691829 1696563 - AmiAMIRv0_Chr18g0470251 Armi18g00092 92
18 1733719 1736007 + AmiAMIRv0_Chr18g0470281 Armi18g00095 95
18 1739766 1744251 - AmiAMIRv0_Chr18g0470291 Armi18g00096 96
18 1769768 1774575 - AmiAMIRv0_Chr18g0470301 Armi18g00097 97
18 1786156 1790643 - AmiAMIRv0_Chr18g0470311 Armi18g00098 98
18 1793321 1795722 - AmiAMIRv0_Chr18g0470321 Armi18g00099 99
18 1809495 1810829 - AmiAMIRv0_Chr18g0470331 Armi18g00100 100
9 179666621 179682627 + AtridAMIRv0_Chr09g1090291 Artr9g04486 4486
9 181025778 181030170 + AtridAMIRv0_Chr09g1090661 Artr9g04523 4523
9 181034745 181036799 - AtridAMIRv0_Chr09g1090691 Artr9g04526 4526
9 181127436 181130025 + AtridAMIRv0_Chr09g1090731 Artr9g04530 4530
9 181135384 181138914 - AtridAMIRv0_Chr09g1090751 Artr9g04532 4532
5 77022145 77024198 + g94562.t1 Bial5g03092 3092
1 603737 605872 + CtAH01T0006300.1 Cati1g00084 84
1 607019 612652 - CtAH01T0006400.1 Cati1g00086 86
1 625043 635030 + CtAH01T0006500.1 Cati1g00087 87
1 629694 647131 - CtAH01T0006600.1 Cati1g00088 88
1 656846 662202 - CtAH01T0006700.2 Cati1g00090 90
1 671551 678193 - CtAH01T0006800.1 Cati1g00091 91
1 683941 688297 - CtAH01T0006900.1 Cati1g00092 92
1 699043 701216 - CtAH01T0007000.1 Cati1g00093 93
5 36621558 36624562 + gnl|WGS:LEKV|Ccrd_019245.mRNA.1_mrna Ccar5g01550 1550
5 36642351 36645654 + gnl|WGS:LEKV|Ccrd_019246.mRNA.1_mrna Ccar5g01551 1551
5 36649041 36653775 + gnl|WGS:LEKV|Ccrd_019247.mRNA.1_mrna Ccar5g01552 1552
5 36664981 36670251 + gnl|WGS:LEKV|Ccrd_019248.mRNA.1_mrna Ccar5g01553 1553
5 36677878 36685029 + gnl|WGS:LEKV|Ccrd_019249.mRNA.1_mrna Ccar5g01554 1554
5 36689183 36693300 + gnl|WGS:LEKV|Ccrd_019250.mRNA.1_mrna Ccar5g01555 1555
5 36697054 36699732 - gnl|WGS:LEKV|Ccrd_019251.mRNA.1_mrna Ccar5g01556 1556
5 36707095 36712192 + gnl|WGS:LEKV|Ccrd_019252.mRNA.1_mrna Ccar5g01557 1557
5 36714604 36715528 - gnl|WGS:LEKV|Ccrd_019253.mRNA.1_mrna Ccar5g01558 1558
5 36716657 36725698 - gnl|WGS:LEKV|Ccrd_019254.mRNA.1_mrna Ccar5g01559 1559
1 609813 621400 + >KAJ9564204.1 Ceso1g00055 55
1 623330 624308 + >KAJ9564202.1 Ceso1g00056 56
1 626002 631481 - >KAJ9564208.1 Ceso1g00057 57
1 638188 640609 + >KAJ9564203.1 Ceso1g00058 58
1 644595 649671 - >KAJ9564206.1 Ceso1g00059 59
1 653109 658534 - >KAJ9564211.1 Ceso1g00060 60
1 679523 685003 - >KAJ9564209.1 Ceso1g00061 61
1 690003 693225 - >KAJ9564169.1 Ceso1g00062 62
9 136989610 136993306 - ClaG1_Chr09g0617561 Chla9g03795 3795
9 137053811 137057910 - ClaG1_Chr09g0617581 Chla9g03797 3797
9 137177173 137180058 - ClaG1_Chr09g0617621 Chla9g03801 3801
25 117187983 117191818 + evm.model.scaffold_10194.13 Chmo25g01377 1377
25 117204171 117208443 + evm.model.scaffold_10194.9 Chmo25g01378 1378
26 129974726 129980273 + evm.model.scaffold_7588.24 Chmo26g01527 1527
26 129985739 129990323 + evm.model.scaffold_7588.21 Chmo26g01528 1528
27 102466462 102471047 - evm.model.scaffold_5310.64 Chmo27g01265 1265
27 102477391 102481229 - evm.model.scaffold_5310.61 Chmo27g01266 1266
8 95895771 95899655 + Cn0281630 Chna8g00973 973
8 95937755 95943451 + Cn0281640 Chna8g00974 974
8 95973149 95976929 + Cn0281670 Chna8g00976 976
8 52347881 52350753 + KAI3699836.1 Cich8g01590 1590
8 52814542 52816834 + KAI3699845.1 Cich8g01599 1599
8 52826253 52827486 - KAI3699846.1 Cich8g01600 1600
8 52866394 52867089 - KAI3699847.1 Cich8g01601 1601
8 52867754 52871069 - KAI3699848.1 Cich8g01602 1602
7 37002087 37005158 + KAI3503481.1 Cien7g02456 2456
7 37115124 37118475 + KAI3503487.1 Cien7g02462 2462
7 37176375 37179658 + KAI3503489.1 Cien7g02464 2464
7 37293723 37296032 + KAI3503494.1 Cien7g02469 2469
7 37304051 37305273 - KAI3503495.1 Cien7g02470 2470
7 37327215 37329198 + KAI3503497.1 Cien7g02472 2472
7 37330761 37332074 - KAI3503498.1 Cien7g02473 2473
7 37332154 37335439 - KAI3503499.1 Cien7g02474 2474
9 145119699 145121852 + D.indicum_Contig82_G00034.t1 Cind9g04201 4201
9 145158228 145159104 + D.indicum_Contig82_G00036.t1 Cind9g04203 4203
9 145239382 145241950 + D.indicum_Contig82_G00039.t1 Cind9g04206 4206
3 70020044 70022468 + h2tg000002l_1.g22329.t1 Cobi3g02242 2242
8 75748026 75750121 - h2tg000049l_1.g25238.t1 Cobi8g02633 2633
14 10607165 10609259 + h2tg000265l.g78806.t1 Dapi14g00588 588
30 10322357 10323906 + h1tg000008l.g131320.t1 Dapi30g00610 610
8 37138142 37142445 + XM_043750176.1 Ecan8g02608 2608
8 37151341 37155422 + XM_043751819.1 Ecan8g02611 2611
8 37170731 37174196 + XM_043751765.1 Ecan8g02613 2613
8 37181553 37185208 + XM_043752749.1 Ecan8g02614 2614
8 37202915 37207723 + XM_043751640.1 Ecan8g02615 2615
8 37221970 37224068 - XM_043751564.1 Ecan8g02618 2618
8 37233883 37236799 + XM_043750258.1 Ecan8g02619 2619
8 37247483 37252322 - XM_043784044.1 Ecan8g02621 2621
1 278748899 278751475 + evm.model.ctg3306.2 Enbr1g08986 8986
1 278756039 278760156 + evm.model.ctg3306.3 Enbr1g08987 8987
1 278772984 278775855 + evm.model.ctg3306.5 Enbr1g08989 8989
1 278865620 278898120 + evm.model.ctg5385.1 Enbr1g08991 8991
1 278929236 278931005 + evm.model.ctg5385.3 Enbr1g08992 8992
1 278932599 278935962 - evm.model.ctg5385.4 Enbr1g08993 8993
2 35979456 35981155 + FliAMIRv0_Chr02g0054001 Fli2g01976 1976
2 35985218 35987679 - FliAMIRv0_Chr02g0054011 Fli2g01977 1977
7 74404687 74407097 + FraAMIRv0_Chr07g0115681 Fra7g01704 1704
7 74409704 74411251 - FraAMIRv0_Chr07g0115691 Fra7g01705 1705
11 15125493 15127124 + FroAMIRv0_Chr11g0177161 Fro11g01672 1672
11 15130490 15133132 - FroAMIRv0_Chr11g0177171 Fro11g01673 1673
10 65612845 65615304 + FsoAMIRv0_Chr10g0240741 Fso10g02358 2358
10 65618688 65620314 - FsoAMIRv0_Chr10g0240751 Fso10g02359 2359
7 336222983 336225638 + GcoAMIRv0_Chr07g0467711 Glco7g01986 1986
7 336384332 336390722 + GcoAMIRv0_Chr07g0467731 Glco7g01988 1988
7 336522834 336526079 + GcoAMIRv0_Chr07g0467801 Glco7g01995 1995
7 337504957 337509510 + GcoAMIRv0_Chr07g0467821 Glco7g01997 1997
7 337513616 337515639 - GcoAMIRv0_Chr07g0467831 Glco7g01998 1998
7 337699323 337701032 + GcoAMIRv0_Chr07g0467871 Glco7g02002 2002
7 337702709 337707866 - GcoAMIRv0_Chr07g0467881 Glco7g02003 2003
15 30755241 30758492 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0685661 Hean15g01291 1291
15 30763272 30765972 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0685681 Hean15g01292 1292
43 96359019 96361006 - >Htub.h1tg000809l.g466.t1 Hetu43g01377 1377
44 83021507 83023468 - >Htub.h1tg001734l.g492.t1 Hetu44g01306 1306
45 93375732 93377692 - >Htub.h1tg001533l.g416.t1 Hetu45g01413 1413
3 112786182 112789392 + CAI9277107.1 Laca3g02748 2748
3 112968926 112972813 + CAI9277109.1 Laca3g02750 2750
3 113221997 113224193 + CAI9277112.1 Laca3g02753 2753
6 7804841 7808116 - LmiAMIRv0_Chr06g0193171 Lomi6g00679 679
6 27900687 27903017 - LmiAMIRv0_Chr06g0206221 Lomi6g01984 1984
6 27910658 27912407 + LmiAMIRv0_Chr06g0206231 Lomi6g01985 1985
6 27915015 27917304 - LmiAMIRv0_Chr06g0206241 Lomi6g01986 1986
3 179264780 179268746 + >KAJ0217126.1 Lssa3g03369 3369
3 179300494 179301502 + >KAJ0217837.1 Lssa3g03370 3370
3 179302414 179305782 - >KAJ0218373.1 Lssa3g03371 3371
3 179701022 179702797 + >KAJ0217163.1 Lssa3g03373 3373
3 179857897 179860288 - >KAJ0215387.1 Lssa3g03374 3374
3 180940288 180943761 - >KAJ0215258.1 Lssa3g03381 3381
3 181152748 181155891 - >KAJ0216517.1 Lssa3g03383 3383
3 181275755 181279209 - >KAJ0217581.1 Lssa3g03385 3385
1 89202909 89205365 + KAD7478690.1 Mimi1g01826 1826
1 89242953 89244857 - KAD7478694.1 Mimi1g01830 1830
3 87727357 87729581 + PdyAMIRv0_Chr03g0128651 Pdy3g03026 3026
3 87760579 87764457 + PdyAMIRv0_Chr03g0128671 Pdy3g03028 3028
3 87781788 87785348 + PdyAMIRv0_Chr03g0128691 Pdy3g03030 3030
3 87810448 87813467 + PdyAMIRv0_Chr03g0128701 Pdy3g03031 3031
3 87817891 87820165 - PdyAMIRv0_Chr03g0128711 Pdy3g03032 3032
3 87876518 87878900 + PdyAMIRv0_Chr03g0128751 Pdy3g03036 3036
3 87880560 87881399 - PdyAMIRv0_Chr03g0128761 Pdy3g03037 3037
3 87885337 87889034 - PdyAMIRv0_Chr03g0128771 Pdy3g03038 3038
2 13985198 13987753 - PluAMIRv0_Chr02g0242211 Pslu2g02119 2119
2 14059199 14061677 - PluAMIRv0_Chr02g0242301 Pslu2g02128 2128
2 106232998 106235920 + PluAMIRv0_Chr02g0363111 Pslu2g14267 14267
2 106284873 106287425 - PluAMIRv0_Chr02g0363221 Pslu2g14278 14278
2 106401043 106402720 + PluAMIRv0_Chr02g0363351 Pslu2g14291 14291
2 106405892 106408136 - PluAMIRv0_Chr02g0363361 Pslu2g14292 14292
2 106431336 106435306 - PluAMIRv0_Chr02g0363421 Pslu2g14298 14298
8 140186508 140193164 + SinAMIRv0_Chr08g0198621 Sain8g02129 2129
8 140283957 140284639 + SinAMIRv0_Chr08g0198641 Sain8g02131 2131
8 140286432 140292329 - SinAMIRv0_Chr08g0198651 Sain8g02132 2132
8 140514636 140516832 + SinAMIRv0_Chr08g0198691 Sain8g02136 2136
8 140524719 140528035 - SinAMIRv0_Chr08g0198701 Sain8g02137 2137
8 140894890 140899232 - SinAMIRv0_Chr08g0198761 Sain8g02143 2143
8 140977642 140982545 - SinAMIRv0_Chr08g0198771 Sain8g02144 2144
8 141052166 141056173 - SinAMIRv0_Chr08g0198811 Sain8g02148 2148
8 141318876 141320519 - SinAMIRv0_Chr08g0198831 Sain8g02150 2150
2 14835472 14837438 + KAI3823988.1 Smso2g00955 955
23 11747748 11748632 + KAI3716968.1 Smso23g00568 568
4 63616019 63620428 + asmbl_6623.p1 Soca4g03330 3330
4 63623785 63628383 + augustus55968.t01 Soca4g03331 3331
4 63652079 63655822 + augustus55966.t01 Soca4g03333 3333
4 63662928 63666379 + transfrag37660.t01 Soca4g03334 3334
4 63667826 63673126 + asmbl_6622.p1 Soca4g03335 3335
4 63681008 63683240 - transfrag37658.t01 Soca4g03337 3337
4 63713508 63716793 + asmbl_6639.p1 Soca4g03339 3339
4 63725531 63739798 - augustus55958.t02 Soca4g03343 3343
11 89710660 89713615 + Streb.11G016080.1 Stre11g01608 1608
11 90001066 90003294 - Streb.11G016240.1 Stre11g01624 1624
5 6233295 6235868 + >KAK1423256.1 Taer5g00727 727
5 6236941 6239574 - >KAK1423257.1 Taer5g00728 728
6 50926369 50936193 + TkA06G195520.1 Tako6g02848 2848
6 51064880 51066823 - TkA06G196120.2 Tako6g02850 2850
6 51204587 51206954 + TkA06G196710.2 Tako6g02852 2852
6 51206938 51208153 - TkA06G196720.1 Tako6g02853 2853
6 51219305 51223083 - TkA06G196780.2 Tako6g02856 2856
6 37637598 37640499 + TbA06G064340.1 Tamo6g02399 2399
6 37662495 37665294 + TbA06G064320.1 Tamo6g02401 2401
6 37771206 37772590 + TbA06G064120.1 Tamo6g02407 2407
6 37921560 37923616 - TbA06G063940.1 Tamo6g02414 2414
6 38074742 38085821 + TbA06G063700.1 Tamo6g02419 2419
6 38112798 38114033 - TbA06G063660.1 Tamo6g02423 2423
6 38167046 38170798 - TbA06G063560.1 Tamo6g02427 2427
       
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