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AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
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
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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. . . . . . . . . . . . . . . . . . . . . . Chma7g07775 . . . . Chna2g00798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . Chmo13g00941 Chmo14g00894 Chmo15g00830 . Chna2g00796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00289 Sain12g00272 Ceso2g03367 Cati3g00322 Ccar2g02109 Cien5g03386 Cich4g04682 Lssa7g03657 Laca7g02973 Tako4g03682 Tamo4g02602 Pslu1g21002 . . . Ecan3g02294 . . . . . Aann4g00951 Chma7g07785 Chmo13g00940 Chmo14g00892 Chmo15g00827 Chla6g05750 Chna2g00794 Cind3g05602 Pdy4g00669 Cobi6g01420 Hean15g04026 Bial24g02159 Bial12g02300 . . . . . Amtr02g04158 . . . . . . . . . . Cobi4g02960 Hean11g01024 Bial4g03236 Bial16g02634 Dapi7g00424 Dapi23g00451 Hetu32g00818 Hetu31g00768 Hetu33g00886 Amtr02g06763 Smso7g00392 Smso29g00439 . . . . . . Stre6g00540 .
Armi1g00290 Sain12g00274 . Cati3g00323 Ccar2g02108 Cien5g03385 Cich4g04681 Lssa7g03656 Laca7g02972 Tako4g03684 Tamo4g02603 Pslu1g21007 . Lomi2g04276 . Ecan3g02293 Soca5g02312 . . . . Aann4g00953 Chma7g07792 Chmo13g00939 Chmo14g00891 Chmo15g00826 Chla6g05751 Chna2g00792 Cind3g05603 Pdy4g00668 . . . . . . . . . . . . . . . . . . . . Cobi4g02448 Hean11g01672 Bial4g02717 . Dapi7g00761 Dapi23g00775 . . . Amtr02g06208 Smso7g00717 Smso29g00852 . . . . . . Stre6g00915 .
Armi1g00291 Sain12g00276 . Cati3g00324 Ccar2g02107 Cien5g03383 Cich4g04680 Lssa7g03655 Laca7g02971 Tako4g03685 Tamo4g02604 Pslu1g21009 Lomi1g00383 Lomi2g04277 . Ecan3g02291 Soca5g02314 . Artr3g11177 . . Aann4g00955 . . . . . . . Pdy4g00667 . . . . . . . . . . . . . . . . . . . . Cobi4g02962 Hean11g01020 Bial12g02301 . Dapi7g00422 Dapi23g00449 Hetu32g00815 . Hetu33g00883 Amtr02g06767 Smso7g00389 Smso29g00436 Taer1g05386 Fro12g02250 . . Fra11g02430 Fli1g00385 Stre6g00538 Mimi17g00561
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 55745234 55750177 - chr4g0771481 Aann4g00951 951
4 55759977 55760726 - chr4g0771501 Aann4g00953 953
4 55775230 55777568 - chr4g0771541 Aann4g00955 955
2 82427533 82430642 + AtrifAMIRv0_Chr02g0137541 Amtr02g04158 4158
2 111572892 111578925 + AtrifAMIRv0_Chr02g0158041 Amtr02g06208 6208
2 122685573 122686304 - AtrifAMIRv0_Chr02g0163591 Amtr02g06763 6763
2 122720997 122722661 - AtrifAMIRv0_Chr02g0163631 Amtr02g06767 6767
1 5188902 5194621 - AmiAMIRv0_Chr01g0002891 Armi1g00289 289
1 5199182 5206813 - AmiAMIRv0_Chr01g0002901 Armi1g00290 290
1 5220538 5222046 - AmiAMIRv0_Chr01g0002911 Armi1g00291 291
3 377206498 377208337 - AtridAMIRv0_Chr03g0419131 Artr3g11177 11177
4 61926346 61931145 + g99972.t1 Bial4g02717 2717
4 74167318 74168037 - g43075.t1 Bial4g03236 3236
12 53328274 53328993 - g35499.t1 Bial12g02300 2300
12 53330517 53331850 - g35500.t1 Bial12g02301 2301
16 68235825 68236535 - g149948.t1 Bial16g02634 2634
24 52183598 52184314 - g67825.t1 Bial24g02159 2159
3 2597716 2598435 - CtAH03T0022400.1 Cati3g00322 322
3 2603456 2611161 - CtAH03T0022500.1 Cati3g00323 323
3 2617999 2619988 - CtAH03T0022600.1 Cati3g00324 324
2 68285723 68286977 + gnl|WGS:LEKV|Ccrd_011156.mRNA.1_mrna Ccar2g02107 2107
2 68293469 68301936 + gnl|WGS:LEKV|Ccrd_011157.mRNA.1_mrna Ccar2g02108 2108
2 68307689 68311527 + gnl|WGS:LEKV|Ccrd_011158.mRNA.1_mrna Ccar2g02109 2109
2 83695011 83700088 - >KAJ9562636.1 Ceso2g03367 3367
6 228563688 228568843 - ClaG1_Chr06g0429971 Chla6g05750 5750
6 228588766 228595737 - ClaG1_Chr06g0429981 Chla6g05751 5751
7 266520849 266522336 + CmaNakai_Chr07g0700771 Chma7g07775 7775
7 266676626 266677354 - CmaNakai_Chr07g0700871 Chma7g07785 7785
7 266779619 266784380 + CmaNakai_Chr07g0700941 Chma7g07792 7792
13 48791390 48795926 + evm.model.scaffold_191.181 Chmo13g00939 939
13 48853475 48858030 + evm.model.scaffold_191.185 Chmo13g00940 940
13 48861761 48865625 + evm.model.scaffold_191.186 Chmo13g00941 941
14 43029079 43033837 + evm.model.scaffold_25.301 Chmo14g00891 891
14 43136198 43138041 + evm.model.scaffold_25.299 Chmo14g00892 892
14 43167335 43170956 + evm.model.scaffold_25.296 Chmo14g00894 894
15 47043243 47048494 + evm.model.scaffold_1806.437 Chmo15g00826 826
15 47115127 47116253 + evm.model.scaffold_1806.433 Chmo15g00827 827
15 47221150 47224588 + evm.model.scaffold_1806.430 Chmo15g00830 830
2 60173043 60177077 + Cn0026040 Chna2g00792 792
2 60220238 60220966 + Cn0026060 Chna2g00794 794
2 60505241 60508061 + Cn0026110 Chna2g00796 796
2 60599810 60602926 - Cn0026130 Chna2g00798 798
4 134457271 134458985 + KAI3753815.1 Cich4g04680 4680
4 134480196 134484006 + KAI3753816.1 Cich4g04681 4681
4 134494897 134495604 + KAI3753817.1 Cich4g04682 4682
5 79695723 79696818 + KAI3509903.1 Cien5g03383 3383
5 79723249 79727147 + KAI3509905.1 Cien5g03385 3385
5 79734839 79735911 + KAI3509906.1 Cien5g03386 3386
3 320382090 320382818 - D.indicum_Contig84_G00034.t1 Cind3g05602 5602
3 320404452 320408889 - D.indicum_Contig84_G00035.t1 Cind3g05603 5603
4 65301913 65306428 + h2tg000009l_1.g42831.t1 Cobi4g02448 2448
4 78604991 78608062 - h2tg000009l_1.g42319.t1 Cobi4g02960 2960
4 78630259 78632070 - h2tg000009l_1.g42317.t1 Cobi4g02962 2962
6 11507488 11509917 + h2tg000021l_1.g11256.t1 Cobi6g01420 1420
7 9166169 9167378 + h1tg000030l.g77012.t1 Dapi7g00422 422
7 9176811 9177527 + h1tg000030l.g77014.t1 Dapi7g00424 424
7 18238798 18245989 - h1tg000030l.g77351.t1 Dapi7g00761 761
23 9876972 9878457 + h2tg000020l.g165250.t1 Dapi23g00449 449
23 9915462 9916181 + h2tg000020l.g165248.t1 Dapi23g00451 451
23 19648092 19655244 - h2tg000020l.g164924.t1 Dapi23g00775 775
3 33666654 33668222 + XM_043766768.1 Ecan3g02291 2291
3 33687801 33693201 + XM_043765053.1 Ecan3g02293 2293
3 33699049 33704057 + XM_043765744.1 Ecan3g02294 2294
1 7874230 7875800 + FliAMIRv0_Chr01g0003801 Fli1g00385 385
11 78047501 78049296 - FraAMIRv0_Chr11g0224521 Fra11g02430 2430
12 29923948 29925796 - FroAMIRv0_Chr12g0217981 Fro12g02250 2250
11 26253523 26255881 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0477771 Hean11g01020 1020
11 26531266 26535153 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0477821 Hean11g01024 1024
11 51354446 51359452 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0485601 Hean11g01672 1672
15 157066996 157070661 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0717591 Hean15g04026 4026
31 32892177 32892884 + >Htub.h1tg000667l.g29.t1 Hetu31g00768 768
32 35790432 35791351 + >Htub.h1tg002251l.g70.t1 Hetu32g00815 815
32 35915810 35916517 + >Htub.h1tg002251l.g67.t1 Hetu32g00818 818
33 35990294 35991207 + >Htub.h1tg001856l.g125.t1 Hetu33g00883 883
33 36085811 36086518 + >Htub.h1tg001856l.g122.t1 Hetu33g00886 886
7 141340433 141342158 + CAI9295164.1 Laca7g02971 2971
7 141346255 141349833 + CAI9295165.1 Laca7g02972 2972
7 141353097 141353807 + CAI9295166.1 Laca7g02973 2973
1 3399581 3401653 + LmiAMIRv0_Chr01g0003831 Lomi1g00383 383
2 48229168 48233855 - LmiAMIRv0_Chr02g0088091 Lomi2g04276 4276
2 48237954 48239257 - LmiAMIRv0_Chr02g0088101 Lomi2g04277 4277
7 192725747 192727534 + >KAJ0195592.1 Lssa7g03655 3655
7 192745625 192749472 + >KAJ0197963.1 Lssa7g03656 3656
7 192752593 192753961 + >KAJ0196488.1 Lssa7g03657 3657
17 21178527 21179845 + KAD3066883.1 Mimi17g00561 561
4 12047431 12048820 + PdyAMIRv0_Chr04g0154741 Pdy4g00667 667
4 12054766 12059082 + PdyAMIRv0_Chr04g0154751 Pdy4g00668 668
4 12088562 12091771 + PdyAMIRv0_Chr04g0154761 Pdy4g00669 669
1 151220408 151221124 - PluAMIRv0_Chr01g0209101 Pslu1g21002 21002
1 151265481 151270207 - PluAMIRv0_Chr01g0209151 Pslu1g21007 21007
1 151282496 151283882 - PluAMIRv0_Chr01g0209171 Pslu1g21009 21009
12 4931339 4933114 - SinAMIRv0_Chr12g0358371 Sain12g00272 272
12 4942242 4947761 - SinAMIRv0_Chr12g0358391 Sain12g00274 274
12 4968299 4969756 - SinAMIRv0_Chr12g0358411 Sain12g00276 276
7 6351194 6352645 + KAI3809969.1 Smso7g00389 389
7 6443862 6452156 + KAI3809972.1 Smso7g00392 392
7 13326243 13333072 - KAI3810297.1 Smso7g00717 717
29 6453536 6455097 + KAI3675430.1 Smso29g00436 436
29 6525069 6525785 + KAI3675433.1 Smso29g00439 439
29 12830540 12836040 - KAI3675846.1 Smso29g00852 852
5 24623453 24628852 - augustus16562.t01 Soca5g02312 2312
5 24646529 24648042 - transfrag10998.t01 Soca5g02314 2314
6 14766525 14768210 + Streb.6G005380.1 Stre6g00538 538
6 14817679 14820855 + Streb.6G005400.1 Stre6g00540 540
6 30818461 30823414 - Streb.6G009150.1 Stre6g00915 915
1 49440882 49442000 - >KAK1439566.1 Taer1g05386 5386
4 82168758 82170204 - TkA04G325040.1 Tako4g03682 3682
4 82186078 82190719 - TkA04G325090.1 Tako4g03684 3684
4 82282761 82284879 - TkA04G325500.1 Tako4g03685 3685
4 48580540 48581935 - TbA04G035760.1 Tamo4g02602 2602
4 48586729 48589966 - TbA04G035750.1 Tamo4g02603 2603
4 48601928 48604005 - TbA04G035740.1 Tamo4g02604 2604
       
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