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AGRP

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
Armi1g00181 Sain12g00167 Ceso2g03278 Cati3g00219 Ccar2g02252 . . . . . . Pslu1g06461 . Lomi2g04134 Enbr6g01574 Ecan3g00116 Soca5g05234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. Sain12g00169 Ceso2g03279 . . . . . . . . . . . . Ecan3g00115 Soca5g05233 . . . . . . . . Chmo15g01109 Chla6g05380 Chna2g01076 Cind3g00425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00182 Sain12g00170 Ceso2g03280 Cati3g00220 . Cien5g03652 . Lssa7g03924 Laca7g03177 Tako4g03260 Tamo4g02269 Pslu1g06462 . . . . . Glco3g01713 . . . . Chma7g07589 Chmo13g01272 Chmo14g01164 . . Chna2g01098 . . . . . . . . . . . . . . . . . . . . . . Cobi4g02707 Hean11g01406 . . Dapi7g00628 Dapi23g00640 . . . Amtr02g06456 Smso7g00584 Smso29g00740 Taer1g05997 Fro12g02104 Fso2g00517 Ftr4g03399 Fra11g02275 Fli1g00605 Stre6g00803 Mimi17g00936
Armi1g00183 Sain12g00171 Ceso2g03281 . Ccar2g02251 Cien5g03653 . Lssa7g03925 Laca7g03178 . Tamo4g02270 Pslu1g06464 . Lomi2g04133 Enbr6g01571 Ecan3g00113 Soca5g05230 . . . . . Chma7g07590 Chmo13g01273 Chmo14g01165 . . Chna2g01099 . . Cobi10g01770 Hean6g02847 . . Dapi16g01674 . . . . Amtr06g04576 . . . . . . . . . . Cobi4g02705 Hean11g01405 . . . . . . . . . . Taer1g05998 Fro12g02103 Fso2g00520 . Fra11g02274 Fli1g00606 Stre6g00804 .
Armi1g00184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00185 Sain12g00172 Ceso2g03283 Cati3g00222 . Cien5g03654 . Lssa7g03928 . Tako4g03261 Tamo4g02271 Pslu1g06465 . Lomi2g04132 . . . Glco3g01723 . . . . Chma7g07603 Chmo13g01280 Chmo14g01169 . Chla6g05370 Chna2g01101 . . . Hean6g02848 . . . . Hetu17g02265 Hetu16g02381 Hetu18g02543 . . . . . . . . . . . Cobi4g02704 Hean11g01404 Bial4g02922 . Dapi7g00629 Dapi23g00641 Hetu32g01149 Hetu31g01104 Hetu33g01215 Amtr02g06455 Smso7g00585 Smso29g00741 . . . . . . Stre6g00806 Mimi17g00933
Armi1g00186 Sain12g00173 Ceso2g03284 Cati3g00224 Ccar2g02248 Cien5g03655 . Lssa7g03929 Laca7g03179 Tako4g03262 . Pslu1g06466 . Lomi2g04131 . Ecan3g00112 Soca5g05228 Glco3g01725 . . . . Chma7g07604 Chmo13g01282 Chmo14g01171 . Chla6g05369 Chna2g01102 . Pdy4g00955 . Hean6g02849 . . . Dapi32g01586 Hetu17g02266 Hetu16g02382 Hetu18g02544 Amtr06g04573 . . . . . . . . . . Cobi4g02703 Hean11g01403 Bial4g02921 . . . Hetu32g01150 Hetu31g01105 Hetu33g01216 . Smso7g00586 Smso29g00742 . . . . . . Stre6g00808 Mimi17g00932
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00187 Sain12g00174 . Cati3g00226 Ccar2g02247 . . . . . . Pslu1g06468 . Lomi2g04130 . . . . . . . . . Chmo13g01284 Chmo14g01174 . Chla6g05364 Chna2g01103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00188 Sain12g00175 . Cati3g00227 Ccar2g02246 Cien5g03657 Cich4g04935 Lssa7g03930 Laca7g03181 . . Pslu1g06469 . Lomi2g04129 . . . Glco3g01730 . . . . . Chmo13g01285 Chmo14g01176 . Chla6g05362 Chna2g01104 . Pdy4g00956 . . . . . . . . . . . . . . . . . . . . Cobi4g02701 Hean11g01401 Bial4g02919 . Dapi7g00632 . Hetu32g01155 Hetu31g01113 Hetu33g01222 Amtr02g06453 Smso7g00589 Smso29g00744 . . . . . . Stre6g00812 Mimi17g00929
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
2 116638997 116649664 + AtrifAMIRv0_Chr02g0160491 Amtr02g06453 6453
2 116680746 116684403 - AtrifAMIRv0_Chr02g0160511 Amtr02g06455 6455
2 116737017 116740238 + AtrifAMIRv0_Chr02g0160521 Amtr02g06456 6456
6 101409383 101412111 + AtrifAMIRv0_Chr06g0433981 Amtr06g04573 4573
6 101630312 101633680 + AtrifAMIRv0_Chr06g0434011 Amtr06g04576 4576
1 3405365 3407952 + AmiAMIRv0_Chr01g0001811 Armi1g00181 181
1 3409412 3420141 - AmiAMIRv0_Chr01g0001821 Armi1g00182 182
1 3427424 3440534 - AmiAMIRv0_Chr01g0001831 Armi1g00183 183
1 3457716 3460962 + AmiAMIRv0_Chr01g0001841 Armi1g00184 184
1 3467149 3472508 + AmiAMIRv0_Chr01g0001851 Armi1g00185 185
1 3475906 3482794 - AmiAMIRv0_Chr01g0001861 Armi1g00186 186
1 3519138 3519452 + AmiAMIRv0_Chr01g0001871 Armi1g00187 187
1 3523412 3536487 - AmiAMIRv0_Chr01g0001881 Armi1g00188 188
4 66876533 66884395 + g55910.t1 Bial4g02919 2919
4 66921413 66925836 + g55912.t1 Bial4g02921 2921
4 66926818 66927258 - g55913.t1 Bial4g02922 2922
3 1739101 1741447 + CtAH03T0013600.1 Cati3g00219 219
3 1743151 1758163 - CtAH03T0013700.1 Cati3g00220 220
3 1767542 1771574 + CtAH03T0013900.1 Cati3g00222 222
3 1772364 1778139 - CtAH03T0013800.4 Cati3g00224 224
3 1784336 1784887 + CtAH03T0014000.1 Cati3g00226 226
3 1786059 1800405 - CtAH03T0014100.1 Cati3g00227 227
2 69521271 69535711 + gnl|WGS:LEKV|Ccrd_011297.mRNA.1_mrna Ccar2g02246 2246
2 69536996 69537406 - gnl|WGS:LEKV|Ccrd_011298.mRNA.1_mrna Ccar2g02247 2247
2 69540100 69546754 + gnl|WGS:LEKV|Ccrd_011299.mRNA.1_mrna Ccar2g02248 2248
2 69561750 69572067 + gnl|WGS:LEKV|Ccrd_011302.mRNA.1_mrna Ccar2g02251 2251
2 69573402 69576235 - gnl|WGS:LEKV|Ccrd_011303.mRNA.1_mrna Ccar2g02252 2252
2 82048665 82050062 + >KAJ9562877.1 Ceso2g03278 3278
2 82049857 82053683 - >KAJ9562880.1 Ceso2g03279 3279
2 82056799 82064613 - >KAJ9562881.1 Ceso2g03280 3280
2 82081153 82088990 - >KAJ9562882.1 Ceso2g03281 3281
2 82185273 82188711 + >KAJ9562662.1 Ceso2g03283 3283
2 82190038 82195582 - >KAJ9562665.1 Ceso2g03284 3284
6 211548172 211557697 + ClaG1_Chr06g0426091 Chla6g05362 5362
6 211561894 211562827 - ClaG1_Chr06g0426111 Chla6g05364 5364
6 211720324 211724887 + ClaG1_Chr06g0426161 Chla6g05369 5369
6 211731224 211736805 - ClaG1_Chr06g0426171 Chla6g05370 5370
6 212091352 212096868 + ClaG1_Chr06g0426271 Chla6g05380 5380
7 260516467 260521193 - CmaNakai_Chr07g0698911 Chma7g07589 7589
7 260522048 260527595 - CmaNakai_Chr07g0698921 Chma7g07590 7590
7 260926448 260929545 + CmaNakai_Chr07g0699051 Chma7g07603 7603
7 260937358 260941455 - CmaNakai_Chr07g0699061 Chma7g07604 7604
13 66169017 66172277 - evm.model.scaffold_184.87 Chmo13g01272 1272
13 66173114 66178038 - evm.model.scaffold_184.86 Chmo13g01273 1273
13 66752303 66755817 + evm.model.scaffold_184.57 Chmo13g01280 1280
13 66802984 66804726 - evm.model.scaffold_184.49 Chmo13g01282 1282
13 66848314 66848759 + evm.model.scaffold_184.46 Chmo13g01284 1284
13 66852881 66862432 - evm.model.scaffold_184.45 Chmo13g01285 1285
14 61205540 61208908 - evm.model.scaffold_2680.2 Chmo14g01164 1164
14 61209749 61215198 - evm.model.scaffold_2680.3 Chmo14g01165 1165
14 61637521 61641029 + evm.model.scaffold_2680.21 Chmo14g01169 1169
14 61651038 61652649 - evm.model.scaffold_2680.23 Chmo14g01171 1171
14 61919958 61923702 + evm.model.scaffold_2680.38 Chmo14g01174 1174
14 61953276 61963508 - evm.model.scaffold_2680.41 Chmo14g01176 1176
15 63372200 63377103 - evm.model.scaffold_1478.155 Chmo15g01109 1109
2 85267921 85276773 - Cn0816230 Chna2g01076 1076
2 87208991 87212239 - Cn0225220 Chna2g01098 1098
2 87213065 87219406 - Cn0225230 Chna2g01099 1099
2 87468296 87471750 + Cn0225290 Chna2g01101 1101
2 87505550 87510086 - Cn0225300 Chna2g01102 1102
2 87628903 87629310 + Cn0225370 Chna2g01103 1103
2 87634016 87643609 - Cn0225380 Chna2g01104 1104
4 140153793 140158694 - KAI3754070.1 Cich4g04935 4935
5 83015482 83018546 - KAI3510172.1 Cien5g03652 3652
5 83022433 83025299 - KAI3510173.1 Cien5g03653 3653
5 83030630 83032017 + KAI3510174.1 Cien5g03654 3654
5 83035772 83039681 - KAI3510175.1 Cien5g03655 3655
5 83048202 83052945 - KAI3510177.1 Cien5g03657 3657
3 302078661 302082009 + D.indicum_Contig13_G00036.t1 Cind3g00425 425
4 72891879 72899902 + h2tg000009l_1.g42578.t1 Cobi4g02701 2701
4 72920742 72925107 + h2tg000009l_1.g42576.t1 Cobi4g02703 2703
4 72926507 72929714 - h2tg000009l_1.g42575.t1 Cobi4g02704 2704
4 72938830 72942808 + h2tg000009l_1.g42574.t1 Cobi4g02705 2705
4 72975850 72979933 + h2tg000009l_1.g42572.t1 Cobi4g02707 2707
10 30980582 30984813 - h2tg000027l_1.g15054.t1 Cobi10g01770 1770
7 13827025 13831216 - h1tg000030l.g77218.t1 Dapi7g00628 628
7 13833832 13835867 + h1tg000030l.g77219.t1 Dapi7g00629 629
7 13882737 13891155 - h1tg000030l.g77222.t1 Dapi7g00632 632
16 49142828 49146436 + h1tg000007l.g121025.t1 Dapi16g01674 1674
23 14704845 14710067 - h2tg000020l.g165059.t1 Dapi23g00640 640
23 14714559 14716864 + h2tg000020l.g165058.t1 Dapi23g00641 641
32 48423211 48427859 - h2tg000014l.g158836.t1 Dapi32g01586 1586
3 843550 850568 + XM_043765488.1 Ecan3g00112 112
3 863624 869552 + XM_043765321.1 Ecan3g00113 113
3 902713 905987 + XM_043763542.1 Ecan3g00115 115
3 906072 907585 - XM_043763543.1 Ecan3g00116 116
6 54719535 54721817 + evm.model.ctg5092.4 Enbr6g01571 1571
6 54772696 54773930 - evm.model.ctg7828.1 Enbr6g01574 1574
1 12533862 12537136 + FliAMIRv0_Chr01g0006001 Fli1g00605 605
1 12538241 12541121 + FliAMIRv0_Chr01g0006011 Fli1g00606 606
11 76370689 76373290 - FraAMIRv0_Chr11g0222971 Fra11g02274 2274
11 76374373 76377740 - FraAMIRv0_Chr11g0222981 Fra11g02275 2275
12 28364013 28366955 - FroAMIRv0_Chr12g0216511 Fro12g02103 2103
12 28367633 28371017 - FroAMIRv0_Chr12g0216521 Fro12g02104 2104
2 6861166 6864586 + FsoAMIRv0_Chr02g0033361 Fso2g00517 517
2 6868584 6871295 + FsoAMIRv0_Chr02g0033391 Fso2g00520 520
4 116264646 116267294 - FtrAMIRv0_Chr04g0128331 Ftr4g03399 3399
3 114319287 114324558 - GcoAMIRv0_Chr03g0173421 Glco3g01713 1713
3 115658760 115662646 + GcoAMIRv0_Chr03g0173521 Glco3g01723 1723
3 115668648 115673008 - GcoAMIRv0_Chr03g0173541 Glco3g01725 1725
3 115858049 115867500 - GcoAMIRv0_Chr03g0173591 Glco3g01730 1730
6 101277478 101280506 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0270851 Hean6g02847 2847
6 101356888 101359678 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0270861 Hean6g02848 2848
6 101360198 101364961 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0270871 Hean6g02849 2849
11 40223780 40233927 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482211 Hean11g01401 1401
11 40356949 40360614 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482241 Hean11g01403 1403
11 40362844 40365710 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482251 Hean11g01404 1404
11 40371566 40374492 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482271 Hean11g01405 1405
11 40375673 40379890 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482291 Hean11g01406 1406
16 122473787 122478816 + >Htub.h1tg000461l.g458.t1 Hetu16g02381 2381
16 122480375 122483465 - >Htub.h1tg000461l.g457.t1 Hetu16g02382 2382
17 114883636 114887840 + >Htub.h2tg000417l.g91.t1 Hetu17g02265 2265
17 114888007 114892889 - >Htub.h2tg000417l.g92.t1 Hetu17g02266 2266
18 120900261 120903415 + >Htub.h1tg000740l.g55.t1 Hetu18g02543 2543
18 120903523 120907881 - >Htub.h1tg000740l.g54.t1 Hetu18g02544 2544
31 50960196 50962367 + >Htub.h1tg002927l.g416.t1 Hetu31g01104 1104
31 50964305 50967678 - >Htub.h1tg002927l.g415.t1 Hetu31g01105 1105
31 51554789 51560326 - >Htub.h1tg002927l.g406.t1 Hetu31g01113 1113
32 54751325 54753410 + >Htub.h1tg000795l.g402.t1 Hetu32g01149 1149
32 54755353 54758614 - >Htub.h1tg000795l.g403.t1 Hetu32g01150 1150
32 55271864 55275737 - >Htub.h1tg000795l.g408.t1 Hetu32g01155 1155
33 53698778 53701600 + >Htub.h1tg003380l.g253.t1 Hetu33g01215 1215
33 53712905 53716253 - >Htub.h1tg003380l.g255.t1 Hetu33g01216 1216
33 54191332 54191701 - >Htub.h1tg003380l.g261.t1 Hetu33g01222 1222
7 148769058 148771579 - CAI9295381.1 Laca7g03177 3177
7 148771869 148776328 - CAI9295382.1 Laca7g03178 3178
7 148796525 148799543 - CAI9295383.1 Laca7g03179 3179
7 148825224 148830635 - CAI9295385.1 Laca7g03181 3181
2 46943448 46953028 + LmiAMIRv0_Chr02g0086621 Lomi2g04129 4129
2 46957909 46958322 - LmiAMIRv0_Chr02g0086631 Lomi2g04130 4130
2 46962566 46965957 + LmiAMIRv0_Chr02g0086641 Lomi2g04131 4131
2 46966932 46969663 - LmiAMIRv0_Chr02g0086651 Lomi2g04132 4132
2 46980183 46983514 + LmiAMIRv0_Chr02g0086661 Lomi2g04133 4133
2 46987396 46988642 - LmiAMIRv0_Chr02g0086671 Lomi2g04134 4134
7 205274529 205276860 - >KAJ0197310.1 Lssa7g03924 3924
7 205279786 205280321 - >KAJ0198347.1 Lssa7g03925 3925
7 205300698 205301904 + >KAJ0197889.1 Lssa7g03928 3928
7 205304944 205307985 - >KAJ0196136.1 Lssa7g03929 3929
7 205331286 205336615 - >KAJ0194640.1 Lssa7g03930 3930
17 51874703 51899844 + KAD3067251.1 Mimi17g00929 929
17 52024127 52032378 + KAD3067254.1 Mimi17g00932 932
17 52034401 52034866 - KAD3067255.1 Mimi17g00933 933
17 52122158 52125563 + KAD3067258.1 Mimi17g00936 936
4 17964042 17968169 - PdyAMIRv0_Chr04g0157621 Pdy4g00955 955
4 17976185 17984610 - PdyAMIRv0_Chr04g0157631 Pdy4g00956 956
1 44365498 44366743 + PluAMIRv0_Chr01g0064371 Pslu1g06461 6461
1 44367145 44370346 - PluAMIRv0_Chr01g0064381 Pslu1g06462 6462
1 44374761 44378010 - PluAMIRv0_Chr01g0064401 Pslu1g06464 6464
1 44382753 44385222 + PluAMIRv0_Chr01g0064411 Pslu1g06465 6465
1 44386260 44389488 - PluAMIRv0_Chr01g0064421 Pslu1g06466 6466
1 44417252 44417677 + PluAMIRv0_Chr01g0064441 Pslu1g06468 6468
1 44419223 44426857 - PluAMIRv0_Chr01g0064451 Pslu1g06469 6469
12 2984586 2987015 + SinAMIRv0_Chr12g0357321 Sain12g00167 167
12 2997556 3001606 - SinAMIRv0_Chr12g0357341 Sain12g00169 169
12 3007811 3009486 - SinAMIRv0_Chr12g0357351 Sain12g00170 170
12 3009523 3013635 - SinAMIRv0_Chr12g0357361 Sain12g00171 171
12 3060983 3064034 + SinAMIRv0_Chr12g0357371 Sain12g00172 172
12 3064890 3072124 - SinAMIRv0_Chr12g0357381 Sain12g00173 173
12 3097323 3097781 + SinAMIRv0_Chr12g0357391 Sain12g00174 174
12 3110401 3126686 - SinAMIRv0_Chr12g0357401 Sain12g00175 175
7 10139908 10143882 - KAI3810164.1 Smso7g00584 584
7 10174870 10178108 + KAI3810165.1 Smso7g00585 585
7 10181064 10185417 - KAI3810166.1 Smso7g00586 586
7 10243852 10269880 - KAI3810169.1 Smso7g00589 589
29 10923638 10930484 - KAI3675734.1 Smso29g00740 740
29 10943606 10947681 + KAI3675735.1 Smso29g00741 741
29 10949071 10953635 - KAI3675736.1 Smso29g00742 742
29 10975056 10985133 - KAI3675738.1 Smso29g00744 744
5 71041726 71049454 + augustus59628.t01 Soca5g05228 5228
5 71062122 71068356 + transfrag40184.t01 Soca5g05230 5230
5 71080128 71084048 + transfrag40182.t01 Soca5g05233 5233
5 71084185 71085615 - transfrag40181.t01 Soca5g05234 5234
6 24594879 24599407 - Streb.6G008030.1 Stre6g00803 803
6 24601542 24605175 - Streb.6G008040.1 Stre6g00804 804
6 24704282 24706621 + Streb.6G008060.1 Stre6g00806 806
6 24731563 24736157 - Streb.6G008080.1 Stre6g00808 808
6 24920744 24931066 - Streb.6G008120.1 Stre6g00812 812
1 54027988 54030127 - >KAK1440172.1 Taer1g05997 5997
1 54030849 54035125 - >KAK1440173.1 Taer1g05998 5998
4 66808850 66812885 - TkA04G264100.2 Tako4g03260 3260
4 66828596 66829844 + TkA04G264120.1 Tako4g03261 3261
4 66830261 66834472 - TkA04G264130.1 Tako4g03262 3262
4 38165245 38174190 - TbA04G048420.1 Tamo4g02269 2269
4 38177027 38180576 - TbA04G048410.1 Tamo4g02270 2270
4 38185975 38186911 + TbA04G048400.1 Tamo4g02271 2271
       
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