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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
Armi1g00571 Sain12g00497 Ceso2g01416 Cati3g00629 . . Cich4g04415 Lssa7g03389 Laca7g02756 Tako4g04024 Tamo4g02962 . . Lomi2g04394 Enbr6g02956 Ecan3g02107 Soca5g02552 . Artr3g11774 . Aary13g03310 Aann4g01211 . . . . . . . Pdy4g00454 . Hean4g04323 . . Dapi16g01886 Dapi23g00281 Hetu11g00236 Hetu12g00233 . . . Smso26g01855 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00572 Sain12g00499 Ceso2g01417 Cati3g00631 Ccar2g01962 . Cich4g04413 Lssa7g03387 Laca7g02755 Tako4g04033 Tamo4g02963 Pslu1g21458 . . Enbr6g02957 Ecan3g02106 Soca5g02553 Glco3g01004 Artr3g11776 Aary5g02857 Aary13g03312 Aann4g01212 . . . . . . . Pdy4g00453 . Hean4g04325 . . Dapi16g01887 . Hetu11g00234 . Hetu10g00249 . . Smso26g01857 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00575 Sain12g00500 Ceso2g01418 Cati3g00632 . . Cich4g04411 Lssa7g03384 . Tako4g04035 Tamo4g02966 Pslu1g21459 Lomi1g00262 Lomi2g04395 Enbr6g02958 Ecan3g02105 Soca5g02554 Glco3g01000 Artr3g11783 . Aary13g03313 Aann4g01214 Chma7g08359 Chmo13g00704 Chmo14g00694 . . Chna2g00536 Cind3g02805 . . Hean4g04326 . . Dapi16g01889 . Hetu11g00232 Hetu12g00231 . . . Smso26g01858 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. Sain12g00504 Ceso2g01421 Cati3g00633 . . Cich4g04410 Lssa7g03383 Laca7g02753 Tako4g04037 Tamo4g02967 Pslu1g21462 Lomi1g00261 Lomi2g04396 . . . Glco3g00999 Artr3g11784 Aary5g02856 Aary13g03314 Aann4g01217 . Chmo13g00702 Chmo14g00693 . . Chna2g00535 Cind3g02804 Pdy4g00452 . Hean4g04327 . . Dapi16g01890 Dapi23g00280 Hetu11g00231 . Hetu10g00248 . . Smso26g01859 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00590 . Ceso2g01427 . Ccar2g01959 . . . . . . . . . . Ecan3g02104 Soca5g02773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00595 . Ceso2g01428 . Ccar2g01958 . . Lssa7g03379 Laca7g02744 . . Pslu1g21466 . Lomi2g04398 Enbr6g02959 Ecan3g02103 . . . . . . . . . . . . . Pdy4g01596 . . . . . . . . . . . . . . . . . . . . . Hean11g00858 . . . . . . . . Smso7g00091 . . . . . . . . .
Armi1g00596 Sain12g00509 Ceso2g01429 Cati3g00637 . . . Lssa7g03373 Laca7g02743 . Tamo4g02979 . . . . Ecan3g02102 Soca5g02776 . . . . . . . . . . . . Pdy4g01608 . . . . . . . . . . . . . . . . . . . . . Hean11g00859 . . . . . . . . . . . . . . . . . .
Armi1g00599 . Ceso2g01434 Cati3g00642 Ccar2g01957 . . Lssa7g03372 Laca7g02742 Tako4g04041 Tamo4g02981 Pslu1g21467 . Lomi2g04399 . . . . . . . . . . . . . . . Pdy4g01611 . . . . . . . . . . . . . . . . . . . . . Hean11g00860 . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 65282815 65284601 - chr4g0779781 Aann4g01211 1211
4 65375240 65376039 - chr4g0779901 Aann4g01212 1212
4 65385161 65386046 - chr4g0779921 Aann4g01214 1214
4 65439770 65441036 - chr4g0779991 Aann4g01217 1217
5 173659551 173660564 + Aargg5g28560.1 Aary5g02856 2856
5 173804051 173804949 + Aargg5g28570.1 Aary5g02857 2857
13 198565508 198566444 - Aargg13g33100.1 Aary13g03310 3310
13 198960265 198961501 + Aargg13g33120.1 Aary13g03312 3312
13 198982437 198983225 + Aargg13g33130.1 Aary13g03313 3313
13 199036389 199037162 + Aargg13g33140.1 Aary13g03314 3314
1 12712537 12713160 - AmiAMIRv0_Chr01g0005711 Armi1g00571 571
1 12737536 12738089 - AmiAMIRv0_Chr01g0005721 Armi1g00572 572
1 12778956 12832029 - AmiAMIRv0_Chr01g0005751 Armi1g00575 575
1 13483919 13486897 - AmiAMIRv0_Chr01g0005901 Armi1g00590 590
1 13706020 13709001 - AmiAMIRv0_Chr01g0005951 Armi1g00595 595
1 13729157 13732147 - AmiAMIRv0_Chr01g0005961 Armi1g00596 596
1 13753899 13756880 - AmiAMIRv0_Chr01g0005991 Armi1g00599 599
3 402710801 402712385 - AtridAMIRv0_Chr03g0425101 Artr3g11774 11774
3 402777749 402778225 + AtridAMIRv0_Chr03g0425121 Artr3g11776 11776
3 403135520 403141933 - AtridAMIRv0_Chr03g0425191 Artr3g11783 11783
3 403141181 403168556 - AtridAMIRv0_Chr03g0425201 Artr3g11784 11784
3 6687500 6688355 + CtAH03T0044900.2 Cati3g00629 629
3 6696780 6701042 - CtAH03T0045100.1 Cati3g00631 631
3 6760825 6761497 - CtAH03T0045200.1 Cati3g00632 632
3 6773612 6774965 - CtAH03T0045300.1 Cati3g00633 633
3 6879633 6880937 - CtAH03T0045700.1 Cati3g00637 637
3 6917963 6920899 - CtAH03T0045900.1 Cati3g00642 642
2 66213379 66214293 + gnl|WGS:LEKV|Ccrd_011004.mRNA.1_mrna Ccar2g01957 1957
2 66216107 66217993 + gnl|WGS:LEKV|Ccrd_011005.mRNA.1_mrna Ccar2g01958 1958
2 66219702 66220835 + gnl|WGS:LEKV|Ccrd_011006.mRNA.1_mrna Ccar2g01959 1959
2 66264613 66356771 + gnl|WGS:LEKV|Ccrd_011009.mRNA.1_mrna Ccar2g01962 1962
2 28987939 28988621 - >KAJ9560836.1 Ceso2g01416 1416
2 29000049 29000956 - >KAJ9560853.1 Ceso2g01417 1417
2 29009553 29010074 - >KAJ9560854.1 Ceso2g01418 1418
2 29040602 29041336 - >KAJ9560851.1 Ceso2g01421 1421
2 29253834 29258624 - >KAJ9560948.1 Ceso2g01427 1427
2 29258915 29259981 - >KAJ9560950.1 Ceso2g01428 1428
2 29262177 29264861 - >KAJ9560949.1 Ceso2g01429 1429
2 29532050 29535112 - >KAJ9560919.1 Ceso2g01434 1434
7 285241651 285242195 - CmaNakai_Chr07g0706611 Chma7g08359 8359
13 33426958 33431082 + evm.model.scaffold_597.20 Chmo13g00702 702
13 33511953 33512490 + evm.model.scaffold_597.23 Chmo13g00704 704
14 31721405 31722332 + evm.model.scaffold_5143.72 Chmo14g00693 693
14 31752296 31752837 + evm.model.scaffold_5143.71 Chmo14g00694 694
2 37259028 37259727 + Cn0778510 Chna2g00535 535
2 37401661 37402379 + Cn0778520 Chna2g00536 536
4 128894817 128895508 + KAI3753545.1 Cich4g04410 4410
4 128926343 128927035 + KAI3753546.1 Cich4g04411 4411
4 128963654 128964387 + KAI3753548.1 Cich4g04413 4413
4 129031834 129032521 + KAI3753550.1 Cich4g04415 4415
3 340079297 340079705 - D.indicum_Contig290_G00028.t1 Cind3g02804 2804
3 340055292 340055834 - D.indicum_Contig290_G00029.t1 Cind3g02805 2805
16 70986970 70987598 - h1tg000026l.g56839.t1 Dapi16g01886 1886
16 71066441 71067069 - h1tg000026l.g56840.t1 Dapi16g01887 1887
16 71115839 71116731 - h1tg000026l.g56842.t1 Dapi16g01889 1889
16 71196624 71197458 - h1tg000026l.g56843.t1 Dapi16g01890 1890
23 5726605 5727136 + h2tg000284l.g80765.t1 Dapi23g00280 280
23 5749430 5749924 + h2tg000284l.g80764.t1 Dapi23g00281 281
3 31808387 31810595 + XM_043763215.1 Ecan3g02102 2102
3 31814825 31815982 + XM_043764150.1 Ecan3g02103 2103
3 31819501 31824897 + XM_043764151.1 Ecan3g02104 2104
3 31826900 31828072 + XM_043766385.1 Ecan3g02105 2105
3 31840046 31840801 + XM_043766334.1 Ecan3g02106 2106
3 31849232 31850108 + XM_043766374.1 Ecan3g02107 2107
6 108392625 108393198 - evm.model.ctg812.8 Enbr6g02956 2956
6 108413062 108413492 - evm.model.ctg812.9 Enbr6g02957 2957
6 108492695 108493512 - evm.model.ctg812.10 Enbr6g02958 2958
6 108496337 108498175 - evm.model.ctg812.11 Enbr6g02959 2959
3 56180079 56180505 - GcoAMIRv0_Chr03g0166281 Glco3g00999 999
3 56511305 56512596 + GcoAMIRv0_Chr03g0166291 Glco3g01000 1000
3 56773158 56773881 + GcoAMIRv0_Chr03g0166331 Glco3g01004 1004
4 203812253 203812747 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189441 Hean4g04323 4323
4 203824422 203824818 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189461 Hean4g04325 4325
4 203833111 203833432 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189471 Hean4g04326 4326
4 203842534 203843068 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189481 Hean4g04327 4327
11 20241710 20242504 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0475951 Hean11g00858 858
11 20242738 20244193 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0475961 Hean11g00859 859
11 20256515 20257309 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0475971 Hean11g00860 860
10 10124959 10126114 + >Htub.h1tg000798l.g442.t1 Hetu10g00248 248
10 10158022 10159277 + >Htub.h1tg000798l.g441.t1 Hetu10g00249 249
11 8186146 8189938 + >Htub.h1tg000030l.g290.t1 Hetu11g00231 231
11 8201669 8201998 + >Htub.h1tg000030l.g291.t1 Hetu11g00232 232
11 8226703 8227344 + >Htub.h1tg000030l.g293.t1 Hetu11g00234 234
11 8303394 8303723 + >Htub.h1tg000030l.g295.t1 Hetu11g00236 236
12 8553835 8554347 + >Htub.h1tg000613l.g252.t1 Hetu12g00231 231
12 8704612 8704941 + >Htub.h1tg000613l.g250.t1 Hetu12g00233 233
7 130183587 130186460 + CAI9294930.1 Laca7g02742 2742
7 130205786 130210689 + CAI9294931.1 Laca7g02743 2743
7 130257610 130260920 + CAI9294932.1 Laca7g02744 2744
7 130959020 130959880 + CAI9294941.1 Laca7g02753 2753
7 130981978 130982984 + CAI9294943.1 Laca7g02755 2755
7 130983712 130987651 + CAI9294944.1 Laca7g02756 2756
1 2199657 2200214 + LmiAMIRv0_Chr01g0002611 Lomi1g00261 261
1 2220912 2221494 + LmiAMIRv0_Chr01g0002621 Lomi1g00262 262
2 49271373 49271914 - LmiAMIRv0_Chr02g0089271 Lomi2g04394 4394
2 49275469 49276009 - LmiAMIRv0_Chr02g0089281 Lomi2g04395 4395
2 49278492 49279104 - LmiAMIRv0_Chr02g0089291 Lomi2g04396 4396
2 49297728 49298009 - LmiAMIRv0_Chr02g0089311 Lomi2g04398 4398
2 49309121 49312090 - LmiAMIRv0_Chr02g0089321 Lomi2g04399 4399
7 178045722 178050134 + >KAJ0195001.1 Lssa7g03372 3372
7 178091479 178095754 + >KAJ0198566.1 Lssa7g03373 3373
7 178329590 178333430 + >KAJ0198494.1 Lssa7g03379 3379
7 178601970 178620707 + >KAJ0198192.1 Lssa7g03383 3383
7 178680476 178681427 + >KAJ0195684.1 Lssa7g03384 3384
7 178717253 178718181 + >KAJ0196371.1 Lssa7g03387 3387
7 178729440 178730309 + >KAJ0197266.1 Lssa7g03389 3389
4 8465396 8466165 + PdyAMIRv0_Chr04g0152601 Pdy4g00452 452
4 8496955 8497710 + PdyAMIRv0_Chr04g0152611 Pdy4g00453 453
4 8500742 8527380 + PdyAMIRv0_Chr04g0152621 Pdy4g00454 454
4 41903204 41906236 + PdyAMIRv0_Chr04g0164031 Pdy4g01596 1596
4 42291732 42293486 + PdyAMIRv0_Chr04g0164151 Pdy4g01608 1608
4 42357157 42360099 + PdyAMIRv0_Chr04g0164181 Pdy4g01611 1611
1 154098418 154098956 - PluAMIRv0_Chr01g0213631 Pslu1g21458 21458
1 154101620 154102169 - PluAMIRv0_Chr01g0213641 Pslu1g21459 21459
1 154112169 154112765 - PluAMIRv0_Chr01g0213671 Pslu1g21462 21462
1 154130275 154133235 - PluAMIRv0_Chr01g0213711 Pslu1g21466 21466
1 154140710 154143667 - PluAMIRv0_Chr01g0213721 Pslu1g21467 21467
12 10992620 10993145 - SinAMIRv0_Chr12g0360611 Sain12g00497 497
12 11057193 11058518 - SinAMIRv0_Chr12g0360631 Sain12g00499 499
12 11083630 11084902 - SinAMIRv0_Chr12g0360641 Sain12g00500 500
12 11314553 11315424 - SinAMIRv0_Chr12g0360681 Sain12g00504 504
12 11493205 11495814 - SinAMIRv0_Chr12g0360731 Sain12g00509 509
7 1798437 1801003 - KAI3809671.1 Smso7g00091 91
26 35343305 35345569 - KAI3695340.1 Smso26g01855 1855
26 35509053 35509560 - KAI3695342.1 Smso26g01857 1857
26 35733049 35733551 - KAI3695343.1 Smso26g01858 1858
26 35740898 35741412 - KAI3695344.1 Smso26g01859 1859
5 27920637 27921916 - transfrag11178.t01 Soca5g02552 2552
5 27939230 27939951 - transfrag11180.t01 Soca5g02553 2553
5 27942611 27946618 - augustus16822.t01 Soca5g02554 2554
5 30779292 30782276 - augustus47863.t01 Soca5g02773 2773
5 30801591 30805113 - transfrag32034.t01 Soca5g02776 2776
4 90698110 90699732 + TkA04G360070.1 Tako4g04024 4024
4 91009789 91010744 + TkA04G361520.1 Tako4g04033 4033
4 91033684 91034614 + TkA04G361590.1 Tako4g04035 4035
4 91065509 91066086 + TkA04G361630.1 Tako4g04037 4037
4 91202736 91210396 - TkA04G362320.1 Tako4g04041 4041
4 56548468 56549345 - TbA04G026320.1 Tamo4g02962 2962
4 56582440 56583361 - TbA04G026290.1 Tamo4g02963 2963
4 56616338 56617286 - TbA04G026240.1 Tamo4g02966 2966
4 56618487 56619075 - TbA04G026230.1 Tamo4g02967 2967
4 56867434 56877540 - TbA04G025940.1 Tamo4g02979 2979
4 56949159 56950340 - TbA04G025850.1 Tamo4g02981 2981
       
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