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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
Armi1g00189 . Ceso2g03285 Cati3g00228 Ccar2g02244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00190 Sain12g00183 . Cati3g00230 Ccar2g02177 Cien5g03661 . Lssa7g03933 . Tako4g03267 Tamo4g02275 . . . . Ecan3g00104 Soca5g05209 Glco3g01739 . . . . . Chmo13g01290 Chmo14g01179 Chmo15g01127 Chla6g05360 Chna2g01107 Cind3g00445 Pdy4g00965 Cobi10g01772 Hean6g02850 Bial9g01619 Bial21g01603 Dapi16g01710 . Hetu17g02267 . Hetu18g02545 Amtr06g04571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00191 Sain12g00184 Ceso2g03286 Cati3g00233 Ccar2g02176 Cien5g03663 . Lssa7g03937 . Tako4g03273 Tamo4g02279 . . . . Ecan3g00103 Soca5g05208 Glco3g01743 . . . . . . . . . . . Pdy4g00967 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00192 Sain12g00185 . Cati3g00234 Ccar2g02175 Cien5g03666 Cich4g04939 Lssa7g03939 . Tako4g03275 Tamo4g02289 Pslu1g06472 Lomi1g00500 Lomi2g04128 . . . Glco3g01767 . . . . . . . . . Chna2g02173 . . . . . . . . . . . . . . . . . . . . . . Cobi4g02684 Hean11g01389 Bial4g02891 . Dapi7g00637 Dapi23g00648 Hetu32g01163 Hetu31g01121 Hetu33g01233 Amtr02g06447 Smso7g00600 Smso29g00749 . . . . . . Stre6g00816 Mimi17g00858
Armi1g00193 Sain12g00186 Ceso2g03287 Cati3g00235 Ccar2g02174 . Cich4g04941 Lssa7g03940 Laca7g03184 . Tamo4g02290 . . . . . . . . . . . . . . . . . . Pdy4g00971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00194 Sain12g00188 . Cati3g00236 Ccar2g02173 Cien5g03668 Cich4g04942 Lssa7g03941 Laca7g03185 . . Pslu1g06475 Lomi1g00501 Lomi2g04127 . . . Glco3g01768 . . . . Chma7g07377 Chmo13g01309 Chmo14g01198 Chmo15g01133 Chla6g05359 Chna2g01133 Cind3g00452 Pdy4g00973 . . . . . . . . . . . . . . . . . . . . Cobi4g02683 Hean11g01388 Bial4g02890 . Dapi7g00638 Dapi23g00650 Hetu32g01164 . Hetu33g01234 Amtr02g06442 Smso7g00601 Smso29g00750 . . . . . . Stre6g00817 Mimi17g00920
. . . . . . . . . . . . . . . . . . . . . . . . . . Chla6g05358 Chna2g01134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00197 Sain12g00190 Ceso2g03288 Cati3g00237 Ccar2g02171 . . . . . . Pslu1g06486 Lomi1g00504 Lomi2g04125 Enbr6g00602 Ecan3g00093 Soca5g05187 . . . . . Chma7g07374 Chmo13g01313 . Chmo15g01136 . Chna2g01136 Cind3g00458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00198 Sain12g00191 Ceso2g03291 Cati3g00238 . Cien5g03671 Cich4g04943 Lssa7g03943 Laca7g03187 Tako4g03277 Tamo4g02293 Pslu1g06488 Lomi1g00505 . Enbr6g01600 Ecan3g00087 Soca5g05185 Glco3g01778 . . . . Chma7g07367 Chmo13g01316 . Chmo15g01142 Chla6g05355 Chna2g01139 Cind3g00464 Pdy4g00976 . . . . . . . . . . . . . . . . . . . . Cobi4g02679 Hean11g01381 Bial4g02885 . Dapi7g00642 Dapi23g00655 Hetu32g01173 Hetu31g01133 Hetu33g01239 Amtr02g06438 Smso7g00605 Smso29g00754 Taer1g06014 Fro12g02093 . . Fra11g02264 Fli1g00623 Stre6g00819 Mimi17g00916
Armi1g00199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
2 116213336 116220753 - AtrifAMIRv0_Chr02g0160341 Amtr02g06438 6438
2 116396699 116399789 - AtrifAMIRv0_Chr02g0160381 Amtr02g06442 6442
2 116591395 116593786 + AtrifAMIRv0_Chr02g0160451 Amtr02g06447 6447
6 101388543 101389941 + AtrifAMIRv0_Chr06g0433961 Amtr06g04571 4571
1 3591809 3596028 - AmiAMIRv0_Chr01g0001891 Armi1g00189 189
1 3635245 3640231 + AmiAMIRv0_Chr01g0001901 Armi1g00190 190
1 3645643 3648365 - AmiAMIRv0_Chr01g0001911 Armi1g00191 191
1 3650433 3652975 - AmiAMIRv0_Chr01g0001921 Armi1g00192 192
1 3657599 3658471 + AmiAMIRv0_Chr01g0001931 Armi1g00193 193
1 3660450 3663877 + AmiAMIRv0_Chr01g0001941 Armi1g00194 194
1 3712098 3715496 + AmiAMIRv0_Chr01g0001971 Armi1g00197 197
1 3720282 3727800 - AmiAMIRv0_Chr01g0001981 Armi1g00198 198
1 3731334 3734571 - AmiAMIRv0_Chr01g0001991 Armi1g00199 199
4 66359388 66362545 - g100140.t1 Bial4g02885 2885
4 66488668 66493027 - g100145.t1 Bial4g02890 2890
4 66507607 66511721 + g100146.t1 Bial4g02891 2891
9 31219745 31226168 + g132265.t1 Bial9g01619 1619
21 31347252 31349665 + g82088.t1 Bial21g01603 1603
3 1804199 1807725 - CtAH03T0014200.1 Cati3g00228 228
3 1828066 1833638 + CtAH03T0014400.1 Cati3g00230 230
3 1836629 1840835 - CtAH03T0014700.1 Cati3g00233 233
3 1845357 1847755 - CtAH03T0014800.1 Cati3g00234 234
3 1852661 1853524 + CtAH03T0014900.1 Cati3g00235 235
3 1855041 1859478 + CtAH03T0015000.1 Cati3g00236 236
3 1861905 1868481 + CtAH03T0015100.1 Cati3g00237 237
3 1872226 1879507 + CtAH03T0015200.1 Cati3g00238 238
2 68963588 68965716 - gnl|WGS:LEKV|Ccrd_011222.mRNA.1_mrna Ccar2g02171 2171
2 68977342 68981021 - gnl|WGS:LEKV|Ccrd_011224.mRNA.1_mrna Ccar2g02173 2173
2 68982016 68983168 - gnl|WGS:LEKV|Ccrd_011225.mRNA.1_mrna Ccar2g02174 2174
2 68987214 68989944 + gnl|WGS:LEKV|Ccrd_011226.mRNA.1_mrna Ccar2g02175 2175
2 68992587 68995737 + gnl|WGS:LEKV|Ccrd_011227.mRNA.1_mrna Ccar2g02176 2176
2 69001239 69004446 - gnl|WGS:LEKV|Ccrd_011228.mRNA.1_mrna Ccar2g02177 2177
2 69508137 69514886 + gnl|WGS:LEKV|Ccrd_011295.mRNA.1_mrna Ccar2g02244 2244
2 82219020 82221950 - >KAJ9562664.1 Ceso2g03285 3285
2 82375473 82378553 - >KAJ9562506.1 Ceso2g03286 3286
2 82401435 82410153 + >KAJ9562727.1 Ceso2g03287 3287
2 82412015 82415885 + >KAJ9562726.1 Ceso2g03288 3288
2 82422535 82425324 + >KAJ9562729.1 Ceso2g03291 3291
6 211302513 211308370 + ClaG1_Chr06g0426021 Chla6g05355 5355
6 211386478 211389853 + ClaG1_Chr06g0426051 Chla6g05358 5358
6 211391534 211396245 - ClaG1_Chr06g0426061 Chla6g05359 5359
6 211445776 211448233 + ClaG1_Chr06g0426071 Chla6g05360 5360
7 253343155 253349384 - CmaNakai_Chr07g0696691 Chma7g07367 7367
7 253480772 253484732 - CmaNakai_Chr07g0696761 Chma7g07374 7374
7 253554101 253558784 - CmaNakai_Chr07g0696791 Chma7g07377 7377
13 67046484 67048926 - evm.model.scaffold_184.35 Chmo13g01290 1290
13 67713655 67725434 + evm.model.scaffold_10346.331 Chmo13g01309 1309
13 67858111 67862110 + evm.model.scaffold_10346.323 Chmo13g01313 1313
13 68108818 68115939 + evm.model.scaffold_10346.307 Chmo13g01316 1316
14 62122292 62124489 - evm.model.scaffold_2680.46 Chmo14g01179 1179
14 62984940 62985934 + evm.model.scaffold_1828.8 Chmo14g01198 1198
15 64078822 64081256 - evm.model.scaffold_1478.199 Chmo15g01127 1127
15 64564465 64569595 + evm.model.scaffold_1478.223 Chmo15g01133 1133
15 64792284 64796399 + evm.model.scaffold_1478.240 Chmo15g01136 1136
15 64977492 64983253 + evm.model.scaffold_1478.258 Chmo15g01142 1142
2 87840809 87843201 - Cn0225410 Chna2g01107 1107
2 92005574 92010320 + Cn0679510 Chna2g01133 1133
2 92011691 92015255 - Cn0679500 Chna2g01134 1134
2 92241132 92244751 + Cn0679440 Chna2g01136 1136
2 92459678 92465459 + Cn0679380 Chna2g01139 1139
2 228780783 228782797 + Cn0816810 Chna2g02173 2173
4 140265305 140266559 - KAI3754074.1 Cich4g04939 4939
4 140294085 140294954 + KAI3754076.1 Cich4g04941 4941
4 140295215 140296804 + KAI3754077.1 Cich4g04942 4942
4 140369041 140372504 + KAI3754078.1 Cich4g04943 4943
5 83099846 83102016 + KAI3510181.1 Cien5g03661 3661
5 83108528 83110593 - KAI3510183.1 Cien5g03663 3663
5 83129905 83131159 - KAI3510186.1 Cien5g03666 3666
5 83145718 83148472 + KAI3510188.1 Cien5g03668 3668
5 83159457 83163555 + KAI3510191.1 Cien5g03671 3671
3 301351800 301354050 + D.indicum_Contig13_G00056.t1 Cind3g00445 445
3 300953523 300957858 - D.indicum_Contig13_G00063.t1 Cind3g00452 452
3 300845674 300849108 - D.indicum_Contig13_G00069.t1 Cind3g00458 458
3 300698366 300705261 - D.indicum_Contig13_G00075.t1 Cind3g00464 464
4 71740125 71744966 - h2tg000009l_1.g42600.t1 Cobi4g02679 2679
4 71927423 71931305 - h2tg000009l_1.g42596.t1 Cobi4g02683 2683
4 71935379 71937671 + h2tg000009l_1.g42595.t1 Cobi4g02684 2684
10 31336870 31339820 - h2tg000027l_1.g15052.t1 Cobi10g01772 1772
7 14067260 14069739 - h1tg000030l.g77227.t1 Dapi7g00637 637
7 14072372 14074394 + h1tg000030l.g77228.t1 Dapi7g00638 638
7 14246752 14252136 + h1tg000030l.g77232.t1 Dapi7g00642 642
16 53497634 53499960 - h1tg000026l.g56663.t1 Dapi16g01710 1710
23 14920935 14923804 - h2tg000020l.g165051.t1 Dapi23g00648 648
23 14948801 14951230 + h2tg000020l.g165049.t1 Dapi23g00650 650
23 15260042 15265083 + h2tg000020l.g165044.t1 Dapi23g00655 655
3 621129 626112 - XM_043765337.1 Ecan3g00087 87
3 655981 659531 - XM_043765614.1 Ecan3g00093 93
3 757820 761011 - XM_043766696.1 Ecan3g00103 103
3 774565 777342 - XM_043762907.1 Ecan3g00104 104
6 22115373 22117645 + evm.model.ctg1272.4 Enbr6g00602 602
6 55611268 55612226 + evm.model.ctg3082.5 Enbr6g01600 1600
1 13029022 13034445 + FliAMIRv0_Chr01g0006181 Fli1g00623 623
11 76197258 76202136 - FraAMIRv0_Chr11g0222871 Fra11g02264 2264
12 28226140 28230940 - FroAMIRv0_Chr12g0216411 Fro12g02093 2093
3 116209606 116210470 - GcoAMIRv0_Chr03g0173681 Glco3g01739 1739
3 116512546 116515597 - GcoAMIRv0_Chr03g0173721 Glco3g01743 1743
3 117328148 117329773 - GcoAMIRv0_Chr03g0173961 Glco3g01767 1767
3 117421271 117426219 + GcoAMIRv0_Chr03g0173971 Glco3g01768 1768
3 118071801 118078923 + GcoAMIRv0_Chr03g0174071 Glco3g01778 1778
6 101452105 101453785 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0270881 Hean6g02850 2850
11 39690597 39696379 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0481961 Hean11g01381 1381
11 40006075 40008600 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482051 Hean11g01388 1388
11 40045704 40048304 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0482061 Hean11g01389 1389
17 114950830 114952404 - >Htub.h2tg000417l.g93.t1 Hetu17g02267 2267
18 120966286 120967860 - >Htub.h1tg000740l.g53.t1 Hetu18g02545 2545
31 51964080 51968910 - >Htub.h1tg002927l.g398.t1 Hetu31g01121 1121
31 52724367 52729640 + >Htub.h1tg002927l.g385.t1 Hetu31g01133 1133
32 55674628 55676955 - >Htub.h1tg000795l.g416.t1 Hetu32g01163 1163
32 55751881 55753160 + >Htub.h1tg000795l.g417.t1 Hetu32g01164 1164
32 56539623 56543518 + >Htub.h1tg000795l.g426.t1 Hetu32g01173 1173
33 54735210 54737894 - >Htub.h1tg003380l.g273.t1 Hetu33g01233 1233
33 54831096 54835993 + >Htub.h1tg003380l.g275.t1 Hetu33g01234 1234
33 55541488 55546833 + >Htub.h1tg003380l.g280.t1 Hetu33g01239 1239
7 148939631 148940515 + CAI9295389.1 Laca7g03184 3184
7 148941322 148943047 + CAI9295390.1 Laca7g03185 3185
7 148955071 148959788 + CAI9295392.1 Laca7g03187 3187
1 4735956 4737768 - LmiAMIRv0_Chr01g0005001 Lomi1g00500 500
1 4740689 4743478 + LmiAMIRv0_Chr01g0005011 Lomi1g00501 501
1 4767082 4770297 + LmiAMIRv0_Chr01g0005041 Lomi1g00504 504
1 4781153 4786245 + LmiAMIRv0_Chr01g0005051 Lomi1g00505 505
2 46898445 46901775 - LmiAMIRv0_Chr02g0086581 Lomi2g04125 4125
2 46921523 46924677 - LmiAMIRv0_Chr02g0086601 Lomi2g04127 4127
2 46927270 46929071 + LmiAMIRv0_Chr02g0086611 Lomi2g04128 4128
7 205507999 205509816 - >KAJ0197360.1 Lssa7g03933 3933
7 205551574 205552991 - >KAJ0195281.1 Lssa7g03937 3937
7 205629577 205631338 - >KAJ0196185.1 Lssa7g03939 3939
7 205925981 205926865 + >KAJ0197659.1 Lssa7g03940 3940
7 205927187 205928838 + >KAJ0195075.1 Lssa7g03941 3941
7 205982709 205987957 + >KAJ0198045.1 Lssa7g03943 3943
17 48231029 48233141 + KAD3067180.1 Mimi17g00858 858
17 51139758 51149076 + KAD3067238.1 Mimi17g00916 916
17 51620213 51622797 - KAD3067242.1 Mimi17g00920 920
4 18158556 18160601 - PdyAMIRv0_Chr04g0157721 Pdy4g00965 965
4 18207118 18208910 - PdyAMIRv0_Chr04g0157741 Pdy4g00967 967
4 18361911 18362774 + PdyAMIRv0_Chr04g0157781 Pdy4g00971 971
4 18366665 18369893 + PdyAMIRv0_Chr04g0157801 Pdy4g00973 973
4 18425977 18431583 + PdyAMIRv0_Chr04g0157831 Pdy4g00976 976
1 44457452 44459171 - PluAMIRv0_Chr01g0064481 Pslu1g06472 6472
1 44465288 44467186 + PluAMIRv0_Chr01g0064511 Pslu1g06475 6475
1 44582910 44586304 + PluAMIRv0_Chr01g0064621 Pslu1g06486 6486
1 44594518 44598805 + PluAMIRv0_Chr01g0064641 Pslu1g06488 6488
12 3292878 3295891 + SinAMIRv0_Chr12g0357481 Sain12g00183 183
12 3299348 3302165 - SinAMIRv0_Chr12g0357491 Sain12g00184 184
12 3311545 3314445 - SinAMIRv0_Chr12g0357501 Sain12g00185 185
12 3317522 3318394 + SinAMIRv0_Chr12g0357511 Sain12g00186 186
12 3324148 3328036 + SinAMIRv0_Chr12g0357531 Sain12g00188 188
12 3391160 3394889 - SinAMIRv0_Chr12g0357551 Sain12g00190 190
12 3396731 3405011 + SinAMIRv0_Chr12g0357561 Sain12g00191 191
7 10363462 10365536 - KAI3810180.1 Smso7g00600 600
7 10401702 10403877 + KAI3810181.1 Smso7g00601 601
7 10538940 10542346 + KAI3810185.1 Smso7g00605 605
29 11053898 11056325 - KAI3675743.1 Smso29g00749 749
29 11059178 11061705 + KAI3675744.1 Smso29g00750 750
29 11218253 11222820 + KAI3675748.1 Smso29g00754 754
5 70167833 70174758 - transfrag7959.t02 Soca5g05185 5185
5 70186616 70189977 - augustus11782.t01 Soca5g05187 5187
5 70586668 70597314 + transfrag7941.t03 Soca5g05208 5208
5 70586668 70597314 + transfrag7941.t02 Soca5g05209 5209
6 25052798 25054940 - Streb.6G008160.1 Stre6g00816 816
6 25129870 25132673 + Streb.6G008170.1 Stre6g00817 817
6 25302934 25308374 + Streb.6G008190.1 Stre6g00819 819
1 54153786 54154601 + >KAK1440189.1 Taer1g06014 6014
4 66972178 66974024 - TkA04G264740.1 Tako4g03267 3267
4 67131479 67134197 - TkA04G265480.2 Tako4g03273 3273
4 67334103 67335898 - TkA04G266420.1 Tako4g03275 3275
4 67345842 67349852 + TkA04G266460.1 Tako4g03277 3277
4 38280267 38282196 - TbA04G048280.1 Tamo4g02275 2275
4 38353738 38356234 + TbA04G048210.1 Tamo4g02279 2279
4 38547281 38549156 - TbA04G047950.1 Tamo4g02289 2289
4 38550427 38551053 + TbA04G047940.1 Tamo4g02290 2290
4 38566785 38570270 + TbA04G047900.1 Tamo4g02293 2293
       
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