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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
Armi18g00030 . . . . Cien7g02568 Cich8g01691 Lssa3g03631 Laca3g02865 Tako6g03030 Tamo6g02580 . Lomi6g01940 Lomi7g01713 . Ecan8g02683 Soca4g03407 Glco7g02122 . . . . Chma3g03693 . . Chmo27g01459 . Chna8g01039 Cind9g03667 Pdy3g03109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . Lssa3g03632 . . . . . . . . . . . . . . . . . . . . . Pdy3g03111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00029 Sain8g02014 . . Ccar5g01599 . . . . . . Pslu2g13791 Lomi6g01939 Lomi7g01712 Enbr1g09148 Ecan8g02684 Soca4g03408 . . . . . Chma3g03694 Chmo25g01496 Chmo26g01620 Chmo27g01461 . Chna8g01040 Cind9g03666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00027 Sain8g02011 Ceso1g00015 . Ccar5g01598 . . . . . . Pslu2g13790 Lomi6g01938 Lomi7g01711 . Ecan8g02685 Soca4g03409 . . . . . Chma3g03696 Chmo25g01498 Chmo26g01622 Chmo27g01462 . Chna8g01041 Cind9g03663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00026 . . . Ccar5g01597 Cien7g02587 Cich8g01704 Lssa3g03633 Laca3g02871 . . Pslu2g13786 Lomi6g01937 Lomi7g01710 . . . . . . . . . . . . . . . Pdy3g03114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00022 Sain8g02008 . . Ccar5g01596 Cien7g02588 Cich8g01705 Lssa3g03634 . Tako6g03035 . Pslu2g13765 Lomi6g01936 Lomi7g01708 . Ecan8g02687 Soca4g03410 Glco7g02123 . . . . Chma3g03699 Chmo25g01502 Chmo26g01624 Chmo27g01464 . Chna8g01043 Cind9g03661 Pdy3g03115 Cobi3g02272 Hean15g01348 Bial14g01329 . Dapi30g00584 Dapi14g00560 . . . . . . Taer5g00702 Fro11g01649 Fso10g02385 Ftr12g02551 Fra7g01730 Fli2g01938 Stre11g01656 Mimi1g01855 . . . . . . . . . . . . . . . . . . . .
Armi18g00021 Sain8g02004 . Cati1g00032 Ccar5g01595 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . Cati1g00031 . Cien7g02591 Cich8g01706 Lssa3g03635 Laca3g02875 . Tamo6g02589 . . . Enbr1g09146 Ecan8g02690 Soca4g03412 Glco7g02125 . . . . Chma3g03701 Chmo25g01503 Chmo26g01625 Chmo27g01465 . Chna8g01044 Cind9g03659 Pdy3g03117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi18g00020 Sain8g02003 . Cati1g00030 Ccar5g01594 Cien7g02593 Cich8g01709 Lssa3g03636 Laca3g02876 Tako6g03046 Tamo6g02590 Pslu2g13761 Lomi6g01935 Lomi7g01707 Enbr1g09367 Ecan8g02691 Soca4g03414 Glco7g02126 Artr9g01879 . . Aann3g00559 Chma3g03702 Chmo25g01504 Chmo26g01626 Chmo27g01466 . Chna8g01045 Cind9g03658 Pdy3g02207 Cobi3g02273 Hean15g01349 Bial14g01328 . Dapi30g00583 Dapi14g00558 Hetu43g01422 Hetu45g01455 . Amtr08g04016 . . Taer5g00700 Fro11g01648 Fso10g02386 Ftr12g02552 Fra7g01731 Fli2g01936 Stre11g01657 Mimi1g01857 . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
3 41838884 41844495 + chr3g0588301 Aann3g00559 559
8 107833771 107875171 + AtrifAMIRv0_Chr08g0555981 Amtr08g04016 4016
18 317641 322954 - AmiAMIRv0_Chr18g0469531 Armi18g00020 20
18 324484 327531 - AmiAMIRv0_Chr18g0469541 Armi18g00021 21
18 331977 333875 + AmiAMIRv0_Chr18g0469551 Armi18g00022 22
18 485198 490847 + AmiAMIRv0_Chr18g0469591 Armi18g00026 26
18 492571 492948 + AmiAMIRv0_Chr18g0469601 Armi18g00027 27
18 498192 498802 - AmiAMIRv0_Chr18g0469621 Armi18g00029 29
18 499623 501649 - AmiAMIRv0_Chr18g0469631 Armi18g00030 30
9 75334486 75335968 - AtridAMIRv0_Chr09g1064221 Artr9g01879 1879
14 24280243 24285232 - g101434.t1 Bial14g01328 1328
14 24287144 24292427 + g101435.t1 Bial14g01329 1329
1 238864 247685 + CtAH01T0002600.2 Cati1g00030 30
1 238864 247685 + CtAH01T0002600.3 Cati1g00031 31
1 238864 240191 + CtAH01T0002600.4 Cati1g00032 32
5 37007330 37012942 - gnl|WGS:LEKV|Ccrd_019289.mRNA.1_mrna Ccar5g01594 1594
5 37013434 37016650 - gnl|WGS:LEKV|Ccrd_019290.mRNA.1_mrna Ccar5g01595 1595
5 37018183 37020024 + gnl|WGS:LEKV|Ccrd_019291.mRNA.1_mrna Ccar5g01596 1596
5 37023373 37029698 + gnl|WGS:LEKV|Ccrd_019292.mRNA.1_mrna Ccar5g01597 1597
5 37031932 37032306 + gnl|WGS:LEKV|Ccrd_019293.mRNA.1_mrna Ccar5g01598 1598
5 37041032 37048554 - gnl|WGS:LEKV|Ccrd_019294.mRNA.1_mrna Ccar5g01599 1599
1 242131 242526 - >KAJ9564218.1 Ceso1g00015 15
3 153597659 153598993 + CmaNakai_Chr03g0266531 Chma3g03693 3693
3 153642576 153643667 + CmaNakai_Chr03g0266541 Chma3g03694 3694
3 153665424 153665798 - CmaNakai_Chr03g0266561 Chma3g03696 3696
3 153740236 153742233 - CmaNakai_Chr03g0266591 Chma3g03699 3699
3 153850931 153854531 + CmaNakai_Chr03g0266611 Chma3g03701 3701
3 153856355 153861529 + CmaNakai_Chr03g0266621 Chma3g03702 3702
25 125849098 125850739 + evm.model.scaffold_1102.4 Chmo25g01496 1496
25 125872019 125872690 - evm.model.scaffold_1102.6 Chmo25g01498 1498
25 125890551 125891990 - evm.model.scaffold_1102.10 Chmo25g01502 1502
25 125994175 125998480 + evm.model.scaffold_1102.13 Chmo25g01503 1503
25 125999829 126003079 + evm.model.scaffold_1102.14 Chmo25g01504 1504
26 135335434 135337067 + evm.model.scaffold_517.136 Chmo26g01620 1620
26 135346950 135347627 - evm.model.scaffold_517.133 Chmo26g01622 1622
26 135371555 135373773 - evm.model.scaffold_517.131 Chmo26g01624 1624
26 135401645 135405780 + evm.model.scaffold_517.130 Chmo26g01625 1625
26 135406982 135412809 + evm.model.scaffold_517.129 Chmo26g01626 1626
27 113397726 113403632 + evm.model.scaffold_5019.25 Chmo27g01459 1459
27 113414807 113415897 + evm.model.scaffold_5019.21 Chmo27g01461 1461
27 113451588 113452259 - evm.model.scaffold_5019.20 Chmo27g01462 1462
27 113503248 113505472 - evm.model.scaffold_5019.18 Chmo27g01464 1464
27 113640378 113645676 + evm.model.scaffold_5019.13_evm.model.scaffold_5019.14 Chmo27g01465 1465
27 113649461 113654607 + evm.model.scaffold_5019.12 Chmo27g01466 1466
8 101554388 101555891 - Cn0735070 Chna8g01039 1039
8 101581542 101582632 + Cn0735060 Chna8g01040 1040
8 101632608 101636753 - Cn0735040 Chna8g01041 1041
8 101668252 101670237 - Cn0735020 Chna8g01043 1043
8 101751555 101757030 + Cn0735000 Chna8g01044 1044
8 101757932 101763409 + Cn0734990 Chna8g01045 1045
8 56392397 56394184 + KAI3699937.1 Cich8g01691 1691
8 56903644 56909474 - KAI3699950.1 Cich8g01704 1704
8 56937469 56939433 - KAI3699951.1 Cich8g01705 1705
8 57028021 57031604 + KAI3699952.1 Cich8g01706 1706
8 57100012 57101063 + KAI3699955.1 Cich8g01709 1709
7 39561970 39563709 + KAI3503593.1 Cien7g02568 2568
7 40086339 40091936 - KAI3503612.1 Cien7g02587 2587
7 40101963 40103918 - KAI3503613.1 Cien7g02588 2588
7 40150996 40153463 + KAI3503616.1 Cien7g02591 2591
7 40157092 40161303 + KAI3503618.1 Cien7g02593 2593
9 153679566 153684752 + D.indicum_Contig59_G00085.t1 Cind9g03658 3658
9 153673113 153677411 + D.indicum_Contig59_G00086.t1 Cind9g03659 3659
9 153560228 153562219 - D.indicum_Contig59_G00088.t1 Cind9g03661 3661
9 153483998 153484372 - D.indicum_Contig59_G00090.t1 Cind9g03663 3663
9 153457803 153458150 + D.indicum_Contig59_G00093.t1 Cind9g03666 3666
9 153451741 153453482 + D.indicum_Contig59_G00094.t1 Cind9g03667 3667
3 70672615 70676109 - h2tg000002l_1.g22299.t1 Cobi3g02272 2272
3 70687460 70690853 + h2tg000002l_1.g22298.t1 Cobi3g02273 2273
14 10025943 10030749 - h2tg000265l.g78836.t1 Dapi14g00558 558
14 10052377 10055567 + h2tg000265l.g78834.t1 Dapi14g00560 560
30 9915867 9920508 - h1tg000008l.g131293.t1 Dapi30g00583 583
30 9927602 9930715 + h1tg000008l.g131294.t1 Dapi30g00584 584
8 37770090 37774172 + XM_043783727.1 Ecan8g02683 2683
8 37775683 37776771 + XM_043751262.1 Ecan8g02684 2684
8 37784151 37785022 - XM_043751378.1 Ecan8g02685 2685
8 37803915 37805903 - XM_043752742.1 Ecan8g02687 2687
8 37812360 37816589 + XM_043750049.1 Ecan8g02690 2690
8 37823607 37828969 + XM_043749905.1 Ecan8g02691 2691
1 283670204 283674313 - evm.model.ctg1541.8 Enbr1g09146 9146
1 283734081 283739382 - evm.model.ctg1541.4 Enbr1g09148 9148
1 291931937 291934496 + evm.model.ctg4916.1 Enbr1g09367 9367
2 35407271 35411660 - FliAMIRv0_Chr02g0053601 Fli2g01936 1936
2 35450021 35451982 + FliAMIRv0_Chr02g0053621 Fli2g01938 1938
7 74645303 74647246 - FraAMIRv0_Chr07g0115941 Fra7g01730 1730
7 74665099 74669347 + FraAMIRv0_Chr07g0115951 Fra7g01731 1731
11 14930997 14935206 - FroAMIRv0_Chr11g0176921 Fro11g01648 1648
11 14942675 14944639 + FroAMIRv0_Chr11g0176931 Fro11g01649 1649
10 65865832 65867796 - FsoAMIRv0_Chr10g0241011 Fso10g02385 2385
10 65879815 65884101 + FsoAMIRv0_Chr10g0241021 Fso10g02386 2386
12 88985836 88987779 - FtrAMIRv0_Chr12g0356611 Ftr12g02551 2551
12 89014249 89018511 + FtrAMIRv0_Chr12g0356621 Ftr12g02552 2552
7 347041490 347043900 - GcoAMIRv0_Chr07g0469071 Glco7g02122 2122
7 347049299 347051308 + GcoAMIRv0_Chr07g0469081 Glco7g02123 2123
7 347172075 347176931 + GcoAMIRv0_Chr07g0469101 Glco7g02125 2125
7 347214042 347219669 + GcoAMIRv0_Chr07g0469111 Glco7g02126 2126
15 33027350 33029383 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0686341 Hean15g01348 1348
15 33045880 33050835 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0686351 Hean15g01349 1349
43 98680259 98685241 + >Htub.h1tg003716l.g215.t1 Hetu43g01422 1422
45 94946431 94950775 + >Htub.h1tg003389l.g225.t1 Hetu45g01455 1455
3 121064298 121067171 + CAI9277227.1 Laca3g02865 2865
3 121449292 121457856 - CAI9277233.1 Laca3g02871 2871
3 121851959 121855157 + CAI9277239.1 Laca3g02875 2875
3 121974564 121979650 + CAI9277241.1 Laca3g02876 2876
6 27270990 27275324 - LmiAMIRv0_Chr06g0205731 Lomi6g01935 1935
6 27285790 27287727 - LmiAMIRv0_Chr06g0205741 Lomi6g01936 1936
6 27301539 27310462 + LmiAMIRv0_Chr06g0205751 Lomi6g01937 1937
6 27322816 27323196 + LmiAMIRv0_Chr06g0205761 Lomi6g01938 1938
6 27337964 27338880 - LmiAMIRv0_Chr06g0205771 Lomi6g01939 1939
6 27339901 27342441 - LmiAMIRv0_Chr06g0205781 Lomi6g01940 1940
7 27470554 27475418 - LmiAMIRv0_Chr07g0231771 Lomi7g01707 1707
7 27482092 27484029 - LmiAMIRv0_Chr07g0231781 Lomi7g01708 1708
7 27495613 27500960 + LmiAMIRv0_Chr07g0231801 Lomi7g01710 1710
7 27518987 27519370 + LmiAMIRv0_Chr07g0231811 Lomi7g01711 1711
7 27539372 27540348 - LmiAMIRv0_Chr07g0231821 Lomi7g01712 1712
7 27541822 27544337 - LmiAMIRv0_Chr07g0231831 Lomi7g01713 1713
3 211949235 211952999 + >KAJ0219429.1 Lssa3g03631 3631
3 211968079 211970555 - >KAJ0218885.1 Lssa3g03632 3632
3 212547835 212550055 - >KAJ0215842.1 Lssa3g03633 3633
3 212610674 212612638 - >KAJ0215279.1 Lssa3g03634 3634
3 213070285 213073679 + >KAJ0217067.1 Lssa3g03635 3635
3 213169019 213172447 + >KAJ0218859.1 Lssa3g03636 3636
1 89782386 89785192 - KAD7478719.1 Mimi1g01855 1855
1 89867249 89871007 + KAD7478721.1 Mimi1g01857 1857
3 70966902 70967792 + PdyAMIRv0_Chr03g0120461 Pdy3g02207 2207
3 88906532 88908633 + PdyAMIRv0_Chr03g0129481 Pdy3g03109 3109
3 88912777 88917093 - PdyAMIRv0_Chr03g0129501 Pdy3g03111 3111
3 88960241 88968446 - PdyAMIRv0_Chr03g0129531 Pdy3g03114 3114
3 88985586 88987553 - PdyAMIRv0_Chr03g0129541 Pdy3g03115 3115
3 89008027 89012635 + PdyAMIRv0_Chr03g0129561 Pdy3g03117 3117
2 102607749 102612984 - PluAMIRv0_Chr02g0358061 Pslu2g13761 13761
2 102623489 102625429 - PluAMIRv0_Chr02g0358101 Pslu2g13765 13765
2 102742237 102747462 + PluAMIRv0_Chr02g0358311 Pslu2g13786 13786
2 102770009 102770389 + PluAMIRv0_Chr02g0358351 Pslu2g13790 13790
2 102779142 102784106 - PluAMIRv0_Chr02g0358361 Pslu2g13791 13791
8 133956812 133971438 - SinAMIRv0_Chr08g0197361 Sain8g02003 2003
8 134062318 134065407 - SinAMIRv0_Chr08g0197371 Sain8g02004 2004
8 134340648 134342567 + SinAMIRv0_Chr08g0197411 Sain8g02008 2008
8 134508989 134509339 + SinAMIRv0_Chr08g0197441 Sain8g02011 2011
8 134950001 134950629 - SinAMIRv0_Chr08g0197471 Sain8g02014 2014
4 64552898 64555588 + augustus55898.t01 Soca4g03407 3407
4 64556795 64557812 + augustus55897.t01 Soca4g03408 3408
4 64563925 64564665 - augustus55896.t01 Soca4g03409 3409
4 64598633 64600721 - transfrag37597.t01 Soca4g03410 3410
4 64603749 64611803 + augustus55893.t03 Soca4g03412 3412
4 64614028 64619857 + asmbl_6618.p1 Soca4g03414 3414
11 90676782 90679640 - Streb.11G016560.1 Stre11g01656 1656
11 90697592 90702652 + Streb.11G016570.1 Stre11g01657 1657
5 6032568 6037241 - >KAK1423229.1 Taer5g00700 700
5 6042012 6045282 + >KAK1423231.1 Taer5g00702 702
6 57054241 57060427 + TkA06G221140.2 Tako6g03030 3030
6 57441418 57443343 - TkA06G222780.1 Tako6g03035 3035
6 57958320 57966686 + TkA06G224910.1 Tako6g03046 3046
6 42700128 42702167 + TbA06G057550.1 Tamo6g02580 2580
6 43103915 43106516 + TbA06G056950.1 Tamo6g02589 2589
6 43186740 43190745 + TbA06G056780.1 Tamo6g02590 2590
       
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