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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
Armi18g00040 Sain8g02041 . . Ccar5g01609 Cien7g02549 Cich8g01671 Lssa3g03608 Laca3g02838 Tako6g02994 Tamo6g02539 Pslu2g13918 . Lomi7g01718 Enbr1g09160 Ecan8g02665 Soca4g03383 Glco7g02102 . . . . Chma3g03610 Chmo25g01468 Chmo26g01595 Chmo27g01430 Chla9g03708 Chna8g01011 Cind9g04302 Pdy3g03090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00039 Sain8g02035 . . Ccar5g01608 Cien7g02550 Cich8g01673 Lssa3g03611 Laca3g02839 Tako6g03000 Tamo6g02543 . . . Enbr1g09159 Ecan8g02667 Soca4g03385 . . . . . Chma3g03628 Chmo25g01473 Chmo26g01598 Chmo27g01433 Chla9g03706 Chna8g01015 Cind9g03691 Pdy3g03091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00036 Sain8g02031 . . . . . . . . . Pslu2g13895 . Lomi7g01717 . Ecan8g02673 Soca4g03392 . . . . . Chma3g03667 . Chmo26g01608 Chmo27g01440 Chla9g03696 Chna8g01024 Cind9g02082 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00035 Sain8g02026 . . Ccar5g01604 . Cich8g01682 Lssa3g03615 . Tako6g03015 Tamo6g02559 Pslu2g13859 Lomi6g01945 Lomi7g01716 . Ecan8g02674 Soca4g03398 Glco7g02110 . . . . Chma3g03671 Chmo25g01483 Chmo26g01611 Chmo27g01444 . Chna8g01027 Cind9g03680 Pdy3g03097 Cobi3g02271 Hean15g01343 Bial14g01332 . Dapi30g00587 . Hetu43g01418 Hetu45g01446 Hetu44g01348 Amtr08g04009 . . Taer5g00706 Fro11g01652 Fso10g02382 Ftr12g02548 Fra7g01726 Fli2g01943 Stre11g01649 Mimi1g01851 . . . . . . . . . . . . . . . . . . . .
Armi18g00034 Sain8g02024 . . Ccar5g01602 Cien7g02558 Cich8g01685 Lssa3g03622 Laca3g02860 Tako6g03018 Tamo6g02565 Pslu2g13830 Lomi6g01944 . Enbr1g09154 Ecan8g02677 . Glco7g02112 . . . . Chma3g03673 Chmo25g01486 Chmo26g01613 Chmo27g01446 . Chna8g01030 Cind9g03676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00033 Sain8g02023 . . . Cien7g02563 Cich8g01686 Lssa3g03623 . Tako6g03019 Tamo6g02568 Pslu2g13829 . . Enbr1g09153 Ecan8g02679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00032 Sain8g02016 . . Ccar5g01601 Cien7g02564 Cich8g01687 Lssa3g03624 Laca3g02861 . Tamo6g02576 Pslu2g13818 Lomi6g01942 Lomi7g01715 Enbr1g09150 Ecan8g02680 Soca4g03403 Glco7g02114 . . . . Chma3g03675 Chmo25g01488 Chmo26g01615 Chmo27g01448 . Chna8g01031 Cind9g03674 Pdy3g03103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00031 Sain8g02015 . . . Cien7g02567 Cich8g01690 Lssa3g03625 Laca3g02864 Tako6g03028 Tamo6g02577 Pslu2g13793 Lomi6g01941 Lomi7g01714 Enbr9g00243 Ecan8g02682 Soca4g03406 Glco7g02116 . . . . Chma3g03676 Chmo25g01491 Chmo26g01617 Chmo27g01452 . Chna8g01032 Cind9g03673 Pdy3g03105 . Hean15g01347 Bial14g01330 . Dapi30g00585 Dapi14g00561 . . . Amtr08g04015 . . Taer5g00704 Fro11g01650 Fso10g02384 Ftr12g02550 Fra7g01728 Fli2g01940 Stre11g01652 Mimi1g01854 . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
8 107711733 107712140 - AtrifAMIRv0_Chr08g0555911 Amtr08g04009 4009
8 107827375 107830024 + AtrifAMIRv0_Chr08g0555971 Amtr08g04015 4015
18 502629 505009 - AmiAMIRv0_Chr18g0469641 Armi18g00031 31
18 505715 509161 - AmiAMIRv0_Chr18g0469651 Armi18g00032 32
18 516070 517921 + AmiAMIRv0_Chr18g0469661 Armi18g00033 33
18 520142 526485 - AmiAMIRv0_Chr18g0469671 Armi18g00034 34
18 536075 536458 + AmiAMIRv0_Chr18g0469681 Armi18g00035 35
18 547343 548925 + AmiAMIRv0_Chr18g0469691 Armi18g00036 36
18 564392 567200 - AmiAMIRv0_Chr18g0469721 Armi18g00039 39
18 590859 594344 + AmiAMIRv0_Chr18g0469731 Armi18g00040 40
14 24375244 24378452 - g101436.t1 Bial14g01330 1330
14 24553529 24553879 + g101438.t1 Bial14g01332 1332
5 37049109 37053161 - gnl|WGS:LEKV|Ccrd_019296.mRNA.1_mrna Ccar5g01601 1601
5 37058784 37063268 - gnl|WGS:LEKV|Ccrd_019297.mRNA.1_mrna Ccar5g01602 1602
5 37070925 37071248 + gnl|WGS:LEKV|Ccrd_019299.mRNA.1_mrna Ccar5g01604 1604
5 37080031 37084113 - gnl|WGS:LEKV|Ccrd_019303.mRNA.1_mrna Ccar5g01608 1608
5 37089758 37094621 + gnl|WGS:LEKV|Ccrd_019304.mRNA.1_mrna Ccar5g01609 1609
9 131814260 131857103 + ClaG1_Chr09g0616571 Chla9g03696 3696
9 132392235 132398285 - ClaG1_Chr09g0616671 Chla9g03706 3706
9 132886799 132890601 + ClaG1_Chr09g0616691 Chla9g03708 3708
3 149585981 149590022 - CmaNakai_Chr03g0265701 Chma3g03610 3610
3 150390015 150390311 + CmaNakai_Chr03g0265881 Chma3g03628 3628
3 152277001 152279724 + CmaNakai_Chr03g0266271 Chma3g03667 3667
3 152698176 152698592 - CmaNakai_Chr03g0266311 Chma3g03671 3671
3 152771020 152775726 + CmaNakai_Chr03g0266331 Chma3g03673 3673
3 152788103 152797097 + CmaNakai_Chr03g0266351 Chma3g03675 3675
3 152815644 152818699 + CmaNakai_Chr03g0266361 Chma3g03676 3676
25 122273690 122277471 - evm.model.scaffold_6450.48 Chmo25g01468 1468
25 122948259 122953167 + evm.model.scaffold_6450.17 Chmo25g01473 1473
25 125600930 125601597 - evm.model.scaffold_517.163 Chmo25g01483 1483
25 125661037 125671371 + evm.model.scaffold_517.158.1 Chmo25g01486 1486
25 125683958 125691897 + evm.model.scaffold_517.156 Chmo25g01488 1488
25 125746083 125747173 + evm.model.scaffold_517.151 Chmo25g01491 1491
26 133262306 133266083 - evm.model.scaffold_11656.62 Chmo26g01595 1595
26 133769859 133782092 + evm.model.scaffold_11656.91 Chmo26g01598 1598
26 134671932 134696272 + evm.model.scaffold_8406.35 Chmo26g01608 1608
26 134940364 134941032 - evm.model.scaffold_8406.17 Chmo26g01611 1611
26 134979674 134981811 + evm.model.scaffold_8406.14 Chmo26g01613 1613
26 134995967 135002705 + evm.model.scaffold_8406.11 Chmo26g01615 1615
26 135196994 135199412 + evm.model.scaffold_8406.3 Chmo26g01617 1617
27 111005971 111010077 - evm.model.scaffold_1622.362 Chmo27g01430 1430
27 111573529 111578555 + evm.model.scaffold_5019.119 Chmo27g01433 1433
27 112133888 112146568 - evm.model.scaffold_5019.82 Chmo27g01440 1440
27 112643239 112643941 - evm.model.scaffold_5019.67 Chmo27g01444 1444
27 112658200 112677114 + evm.model.scaffold_5019.65 Chmo27g01446 1446
27 112682180 112689224 + evm.model.scaffold_5019.63 Chmo27g01448 1448
27 113003478 113005639 + evm.model.scaffold_5019.54 Chmo27g01452 1452
8 98966234 98970318 - Cn0735860 Chna8g01011 1011
8 99457374 99463860 + Cn0735770 Chna8g01015 1015
8 99967329 99970336 + Cn0735650 Chna8g01024 1024
8 100218407 100218823 - Cn0735600 Chna8g01027 1027
8 100461699 100470302 + Cn0735550 Chna8g01030 1030
8 100570074 100576846 + Cn0735430 Chna8g01031 1031
8 100785712 100789302 + Cn0735410 Chna8g01032 1032
8 55462112 55465716 - KAI3699917.1 Cich8g01671 1671
8 55521747 55523874 + KAI3699919.1 Cich8g01673 1673
8 55742187 55742552 - KAI3699928.1 Cich8g01682 1682
8 55908313 55910113 - KAI3699931.1 Cich8g01685 1685
8 55946851 55948980 - KAI3699932.1 Cich8g01686 1686
8 56128940 56133080 + KAI3699933.1 Cich8g01687 1687
8 56349226 56353099 + KAI3699936.1 Cich8g01690 1690
7 38946083 38949428 - KAI3503574.1 Cien7g02549 2549
7 38980172 38983625 + KAI3503575.1 Cien7g02550 2550
7 39146707 39148506 + KAI3503583.1 Cien7g02558 2558
7 39356107 39358257 - KAI3503588.1 Cien7g02563 2563
7 39436672 39440379 + KAI3503589.1 Cien7g02564 2564
7 39541829 39546149 + KAI3503592.1 Cien7g02567 2567
9 242162134 242164838 - D.indicum_Contig31_G00002.t1 Cind9g02082 2082
9 152937222 152940347 + D.indicum_Contig59_G00100.t1 Cind9g03673 3673
9 152754406 152780234 + D.indicum_Contig59_G00101.t1 Cind9g03674 3674
9 152718136 152721406 + D.indicum_Contig59_G00103.t1 Cind9g03676 3676
9 152668654 152669070 - D.indicum_Contig59_G00107.t1 Cind9g03680 3680
9 151005305 151012654 + D.indicum_Contig59_G00118.t1 Cind9g03691 3691
9 150584399 150588201 - D.indicum_Contig82_G00135.t1 Cind9g04302 4302
3 70593301 70593651 - h2tg000002l_1.g22300.t1 Cobi3g02271 2271
14 10056248 10058974 - h2tg000265l.g78833.t1 Dapi14g00561 561
30 9931670 9934561 - h1tg000008l.g131295.t1 Dapi30g00585 585
30 10002551 10002934 + h1tg000008l.g131297.t1 Dapi30g00587 587
8 37574293 37578392 - XM_043784141.1 Ecan8g02665 2665
8 37589579 37593702 + XM_043751273.1 Ecan8g02667 2667
8 37647286 37662991 - XM_043752111.1 Ecan8g02673 2673
8 37674658 37675226 - XM_043752282.1 Ecan8g02674 2674
8 37720614 37730413 + XM_043750202.1 Ecan8g02677 2677
8 37726643 37728448 - XM_043750201.1 Ecan8g02679 2679
8 37750070 37758531 + XM_043749931.1 Ecan8g02680 2680
8 37763915 37766923 + XM_043784330.1 Ecan8g02682 2682
1 283804744 283810286 - evm.model.ctg1541.2 Enbr1g09150 9150
1 283934249 283938192 + evm.model.ctg678.6 Enbr1g09153 9153
1 283939820 283943581 - evm.model.ctg678.5 Enbr1g09154 9154
1 284736211 284738423 - evm.model.ctg160.3 Enbr1g09159 9159
1 284783951 284788436 + evm.model.ctg4797.9 Enbr1g09160 9160
9 10048024 10051273 + evm.model.ctg2024.4 Enbr9g00243 243
2 35467148 35470161 - FliAMIRv0_Chr02g0053641 Fli2g01940 1940
2 35501316 35501720 + FliAMIRv0_Chr02g0053671 Fli2g01943 1943
7 74616713 74617117 - FraAMIRv0_Chr07g0115901 Fra7g01726 1726
7 74634301 74637321 + FraAMIRv0_Chr07g0115921 Fra7g01728 1728
11 14946911 14949902 - FroAMIRv0_Chr11g0176941 Fro11g01650 1650
11 14969092 14969496 + FroAMIRv0_Chr11g0176961 Fro11g01652 1652
10 65822992 65823396 - FsoAMIRv0_Chr10g0240981 Fso10g02382 2382
10 65854504 65857529 + FsoAMIRv0_Chr10g0241001 Fso10g02384 2384
12 88926393 88926857 - FtrAMIRv0_Chr12g0356581 Ftr12g02548 2548
12 88976482 88978827 + FtrAMIRv0_Chr12g0356601 Ftr12g02550 2550
7 344505211 344508716 - GcoAMIRv0_Chr07g0468871 Glco7g02102 2102
7 345378720 345379133 - GcoAMIRv0_Chr07g0468951 Glco7g02110 2110
7 345736698 345740414 + GcoAMIRv0_Chr07g0468971 Glco7g02112 2112
7 345918278 345925710 + GcoAMIRv0_Chr07g0468991 Glco7g02114 2114
7 346022919 346026623 + GcoAMIRv0_Chr07g0469011 Glco7g02116 2116
15 32878553 32879171 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0686281 Hean15g01343 1343
15 33022801 33026118 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0686331 Hean15g01347 1347
43 98446790 98447167 - >Htub.h1tg003716l.g219.t1 Hetu43g01418 1418
44 85363761 85364204 - >Htub.h1tg001734l.g448.t1 Hetu44g01348 1348
45 94774726 94775103 - >Htub.h1tg003389l.g216.t1 Hetu45g01446 1446
3 119148759 119152239 - CAI9277200.1 Laca3g02838 2838
3 119486022 119487753 + CAI9277201.1 Laca3g02839 2839
3 120688539 120692666 - CAI9277222.1 Laca3g02860 2860
3 120728553 120733417 + CAI9277223.1 Laca3g02861 2861
3 120969955 120973663 + CAI9277226.1 Laca3g02864 2864
6 27345632 27348418 - LmiAMIRv0_Chr06g0205791 Lomi6g01941 1941
6 27371846 27375948 - LmiAMIRv0_Chr06g0205801 Lomi6g01942 1942
6 27385040 27390280 - LmiAMIRv0_Chr06g0205821 Lomi6g01944 1944
6 27428359 27428763 + LmiAMIRv0_Chr06g0205831 Lomi6g01945 1945
7 27553920 27556607 - LmiAMIRv0_Chr07g0231841 Lomi7g01714 1714
7 27562780 27567639 - LmiAMIRv0_Chr07g0231851 Lomi7g01715 1715
7 27614388 27614798 + LmiAMIRv0_Chr07g0231861 Lomi7g01716 1716
7 27625737 27641480 + LmiAMIRv0_Chr07g0231871 Lomi7g01717 1717
7 27705657 27709134 + LmiAMIRv0_Chr07g0231881 Lomi7g01718 1718
3 209201483 209204943 - >KAJ0218095.1 Lssa3g03608 3608
3 209812637 209814216 + >KAJ0215999.1 Lssa3g03611 3611
3 210227055 210227435 - >KAJ0218865.1 Lssa3g03615 3615
3 210781094 210784351 - >KAJ0218985.1 Lssa3g03622 3622
3 210838071 210839555 - >KAJ0217729.1 Lssa3g03623 3623
3 211119428 211124673 + >KAJ0215949.1 Lssa3g03624 3624
3 211590873 211594470 + >KAJ0218711.1 Lssa3g03625 3625
1 89633554 89634704 - KAD7478715.1 Mimi1g01851 1851
1 89761848 89766252 + KAD7478718.1 Mimi1g01854 1854
3 88562897 88565496 - PdyAMIRv0_Chr03g0129291 Pdy3g03090 3090
3 88594015 88596659 + PdyAMIRv0_Chr03g0129301 Pdy3g03091 3091
3 88679720 88680103 - PdyAMIRv0_Chr03g0129361 Pdy3g03097 3097
3 88769773 88774960 + PdyAMIRv0_Chr03g0129421 Pdy3g03103 3103
3 88817138 88820443 + PdyAMIRv0_Chr03g0129441 Pdy3g03105 3105
2 102787995 102790836 - PluAMIRv0_Chr02g0358381 Pslu2g13793 13793
2 103045820 103047937 - PluAMIRv0_Chr02g0358631 Pslu2g13818 13818
2 103095330 103098710 + PluAMIRv0_Chr02g0358741 Pslu2g13829 13829
2 103098729 103103718 - PluAMIRv0_Chr02g0358751 Pslu2g13830 13830
2 103248993 103249409 + PluAMIRv0_Chr02g0359041 Pslu2g13859 13859
2 103507389 103507595 + PluAMIRv0_Chr02g0359401 Pslu2g13895 13895
2 103667604 103671014 + PluAMIRv0_Chr02g0359631 Pslu2g13918 13918
8 134954839 134957303 - SinAMIRv0_Chr08g0197481 Sain8g02015 2015
8 134958072 134962582 - SinAMIRv0_Chr08g0197491 Sain8g02016 2016
8 135257267 135258760 + SinAMIRv0_Chr08g0197561 Sain8g02023 2023
8 135259077 135261202 - SinAMIRv0_Chr08g0197571 Sain8g02024 2024
8 135354501 135354884 + SinAMIRv0_Chr08g0197591 Sain8g02026 2026
8 135836378 135839351 + SinAMIRv0_Chr08g0197641 Sain8g02031 2031
8 135865098 135867740 - SinAMIRv0_Chr08g0197681 Sain8g02035 2035
8 136023339 136026311 + SinAMIRv0_Chr08g0197741 Sain8g02041 2041
4 64228751 64233203 - asmbl_6656.p1 Soca4g03383 3383
4 64283618 64287615 + transfrag37611.t01 Soca4g03385 3385
4 64330014 64342390 - augustus55911.t06 Soca4g03392 3392
4 64402332 64402902 - transfrag37607.t01 Soca4g03398 3398
4 64531219 64539684 + asmbl_6619.p1 Soca4g03403 3403
4 64547641 64551466 + transfrag37602.t01 Soca4g03406 3406
11 90515053 90515785 - Streb.11G016490.1 Stre11g01649 1649
11 90598239 90602702 + Streb.11G016520.1 Stre11g01652 1652
5 6054381 6057609 - >KAK1423233.1 Taer5g00704 704
5 6076390 6076776 + >KAK1423235.1 Taer5g00706 706
6 55526103 55528969 - TkA06G214660.1 Tako6g02994 2994
6 55736586 55737928 + TkA06G215510.1 Tako6g03000 3000
6 56360736 56361104 - TkA06G218070.1 Tako6g03015 3015
6 56499121 56500735 - TkA06G218640.2 Tako6g03018 3018
6 56550301 56552311 - TkA06G218830.1 Tako6g03019 3019
6 57049376 57052359 + TkA06G221120.1 Tako6g03028 3028
6 41037930 41040949 - TbA06G059520.1 Tamo6g02539 2539
6 41212979 41214320 + TbA06G059310.1 Tamo6g02543 2543
6 41838667 41839035 - TbA06G058530.1 Tamo6g02559 2559
6 42100862 42104018 - TbA06G058160.1 Tamo6g02565 2565
6 42174083 42176176 - TbA06G058050.1 Tamo6g02568 2568
6 42599750 42603318 + TbA06G057660.1 Tamo6g02576 2576
6 42675670 42679169 + TbA06G057610.1 Tamo6g02577 2577
       
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