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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
Armi1g00545 Sain12g00487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. Sain12g00489 Ceso2g01395 Cati3g00605 Ccar2g01968 . . . . . . . . . . . . . . . . . . Chmo13g00716 Chmo14g00706 Chmo15g00580 . Chna2g00552 Cind3g02824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00559 Sain12g00490 Ceso2g01396 Cati3g00607 Ccar2g01967 Cien5g03165 Cich4g04426 Lssa7g03395 . . Tamo4g02949 Pslu1g21446 Lomi1g00264 Lomi2g04390 Enbr6g02949 Ecan3g02110 Soca5g02548 Glco3g01010 Artr3g11771 . Aary13g03306 Aann4g01194 . Chmo13g00714 . Chmo15g00577 . Chna2g00549 Cind3g02822 Pdy4g00460 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00562 Sain12g00493 . Cati3g00611 Ccar2g01965 . . . . . . . . Lomi2g04392 . . . . . . . . Chma7g08356 Chmo13g00708 Chmo14g00696 . . Chna2g00542 Cind3g02810 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00569 Sain12g00496 Ceso2g01415 Cati3g00628 . . Cich4g04416 Lssa7g03390 Laca7g02757 Tako4g04023 Tamo4g02957 Pslu1g21457 . Lomi2g04393 Enbr6g02952 Ecan3g02108 Soca5g02551 . . . Aary13g03309 Aann4g01206 . Chmo13g00707 Chmo14g00695 . . Chna2g00541 Cind3g02809 Pdy4g00455 . Hean4g04321 . . Dapi16g01885 . Hetu11g00239 Hetu12g00234 Hetu10g00251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 64739925 64744618 - chr4g0779301 Aann4g01194 1194
4 65183959 65186460 - chr4g0779671 Aann4g01206 1206
13 198204955 198209122 - Aargg13g33060.1 Aary13g03306 3306
13 198541117 198542272 - Aargg13g33090.1 Aary13g03309 3309
1 11891637 11891933 - AmiAMIRv0_Chr01g0005451 Armi1g00545 545
1 12136603 12141153 - AmiAMIRv0_Chr01g0005591 Armi1g00559 559
1 12228241 12229111 - AmiAMIRv0_Chr01g0005621 Armi1g00562 562
1 12697686 12698310 - AmiAMIRv0_Chr01g0005691 Armi1g00569 569
3 402446758 402451937 + AtridAMIRv0_Chr03g0425071 Artr3g11771 11771
3 6345373 6348492 + CtAH03T0043000.1 Cati3g00605 605
3 6349353 6354340 - CtAH03T0043100.1 Cati3g00607 607
3 6446590 6447560 - CtAH03T0043500.1 Cati3g00611 611
3 6687259 6688355 + CtAH03T0044900.1 Cati3g00628 628
2 66397875 66399178 + gnl|WGS:LEKV|Ccrd_011012.mRNA.1_mrna Ccar2g01965 1965
2 66415232 66419216 + gnl|WGS:LEKV|Ccrd_011014.mRNA.1_mrna Ccar2g01967 1967
2 66420873 66424564 - gnl|WGS:LEKV|Ccrd_011015.mRNA.1_mrna Ccar2g01968 1968
2 28630413 28631990 + >KAJ9560640.1 Ceso2g01395 1395
2 28635132 28640875 - >KAJ9560642.1 Ceso2g01396 1396
2 28970004 28970675 - >KAJ9560834.1 Ceso2g01415 1415
7 285208766 285209455 - CmaNakai_Chr07g0706581 Chma7g08356 8356
13 33604603 33605835 + evm.model.scaffold_597.27 Chmo13g00707 707
13 33703655 33704631 + evm.model.scaffold_597.32 Chmo13g00708 708
13 34254757 34262629 + evm.model.scaffold_597.53 Chmo13g00714 714
13 34357414 34362064 - evm.model.scaffold_597.57 Chmo13g00716 716
14 31866053 31867285 + evm.model.scaffold_5143.64 Chmo14g00695 695
14 31973341 31974321 + evm.model.scaffold_5143.62 Chmo14g00696 696
14 32522755 32527048 - evm.model.scaffold_5143.42 Chmo14g00706 706
15 31037307 31041203 + evm.model.scaffold_1740.30 Chmo15g00577 577
15 31245093 31249990 - evm.model.scaffold_1740.50 Chmo15g00580 580
2 37569657 37570876 + Cn0778610 Chna2g00541 541
2 37826067 37827073 + Cn0778620 Chna2g00542 542
2 38846205 38848923 + Cn0778770 Chna2g00549 549
2 39099191 39103372 - Cn0778830 Chna2g00552 552
4 129068929 129069644 + KAI3753551.1 Cich4g04416 4416
4 129529920 129532945 + KAI3753561.1 Cich4g04426 4426
5 76496959 76499985 + KAI3509685.1 Cien5g03165 3165
3 339997651 340000685 - D.indicum_Contig290_G00033.t1 Cind3g02809 2809
3 339808775 339809460 - D.indicum_Contig290_G00034.t1 Cind3g02810 2810
3 339089850 339095563 - D.indicum_Contig290_G00046.t1 Cind3g02822 2822
3 338908205 338910059 + D.indicum_Contig290_G00048.t1 Cind3g02824 2824
16 70966215 70966626 - h1tg000026l.g56838.t1 Dapi16g01885 1885
3 31853981 31854694 + XM_043762712.1 Ecan3g02108 2108
3 31873008 31876958 + XM_043763303.1 Ecan3g02110 2110
6 108302655 108306475 - evm.model.ctg812.1 Enbr6g02949 2949
6 108329035 108329649 - evm.model.ctg812.4 Enbr6g02952 2952
3 57424030 57425487 + GcoAMIRv0_Chr03g0166391 Glco3g01010 1010
4 203800424 203817149 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr04g0189421 Hean4g04321 4321
10 10221581 10222264 + >Htub.h1tg000798l.g439.t1 Hetu10g00251 251
11 8385520 8388080 + >Htub.h1tg000030l.g298.t1 Hetu11g00239 239
12 8740776 8743035 + >Htub.h1tg000613l.g249.t1 Hetu12g00234 234
7 131023649 131024761 + CAI9294945.1 Laca7g02757 2757
1 2233711 2238268 + LmiAMIRv0_Chr01g0002641 Lomi1g00264 264
2 49248676 49252188 - LmiAMIRv0_Chr02g0089231 Lomi2g04390 4390
2 49263579 49264161 - LmiAMIRv0_Chr02g0089251 Lomi2g04392 4392
2 49268424 49268963 - LmiAMIRv0_Chr02g0089261 Lomi2g04393 4393
7 178760464 178761327 + >KAJ0195796.1 Lssa7g03390 3390
7 178974944 178979430 + >KAJ0197551.1 Lssa7g03395 3395
4 8535667 8536266 + PdyAMIRv0_Chr04g0152631 Pdy4g00455 455
4 8609619 8613530 + PdyAMIRv0_Chr04g0152681 Pdy4g00460 460
1 154048213 154051852 - PluAMIRv0_Chr01g0213511 Pslu1g21446 21446
1 154093466 154094029 - PluAMIRv0_Chr01g0213621 Pslu1g21457 21457
12 10746367 10746654 - SinAMIRv0_Chr12g0360511 Sain12g00487 487
12 10773350 10774892 + SinAMIRv0_Chr12g0360531 Sain12g00489 489
12 10775932 10784421 - SinAMIRv0_Chr12g0360541 Sain12g00490 490
12 10861129 10862937 - SinAMIRv0_Chr12g0360571 Sain12g00493 493
12 10978994 10979519 - SinAMIRv0_Chr12g0360601 Sain12g00496 496
5 27869507 27873512 - transfrag11175.t01 Soca5g02548 2548
5 27907481 27908411 - transfrag11177.t01 Soca5g02551 2551
4 90696043 90697118 + TkA04G360060.1 Tako4g04023 4023
4 56088296 56098053 - TbA04G027020.1 Tamo4g02949 2949
4 56450759 56456772 - TbA04G026440.1 Tamo4g02957 2957
       
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