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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
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00150 Sain12g00141 Ceso2g03261 Cati3g00185 Ccar2g02276 . . . . . . Pslu1g06431 . Lomi2g04152 . Ecan3g00146 Soca5g05272 . . . . . Chma7g07521 Chmo13g01212 Chmo14g01115 Chmo15g01064 . Chna2g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. Sain12g00142 . . Ccar2g02275 . . . . . . Pslu1g06432 . . . Ecan3g00145 Soca5g05271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00154 Sain12g00143 . Cati3g00186 Ccar2g02274 . . . . . . Pslu1g06433 . Lomi2g04151 . Ecan3g00143 Soca5g05269 . . . . . Chma7g07523 Chmo13g01213 Chmo14g01116 Chmo15g01065 . Chna2g01039 Cind3g01960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00155 Sain12g00144 Ceso2g03262 Cati3g00187 Ccar2g02272 . . . . . . Pslu1g06435 . . Enbr6g03573 Ecan3g00137 Soca5g05266 . . . . . Chma7g07525 Chmo13g01215 Chmo14g01118 Chmo15g01067 . Chna2g01041 Cind3g01958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00156 Sain12g00145 . Cati3g00189 Ccar2g02271 . . . . . . Pslu1g06436 . Lomi2g04150 . Ecan3g00135 . . . . . . Chma7g07526 Chmo13g01217 Chmo14g01119 Chmo15g01068 Chla6g05419 Chna2g01042 Cind3g05811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 2906816 2911642 + AmiAMIRv0_Chr01g0001501 Armi1g00150 150
1 2973558 2981787 + AmiAMIRv0_Chr01g0001541 Armi1g00154 154
1 2985410 2988596 - AmiAMIRv0_Chr01g0001551 Armi1g00155 155
1 2990460 2990960 - AmiAMIRv0_Chr01g0001561 Armi1g00156 156
3 1442246 1448237 + CtAH03T0010800.1 Cati3g00185 185
3 1449447 1462046 + CtAH03T0010900.1 Cati3g00186 186
3 1454658 1466315 - CtAH03T0011000.1 Cati3g00187 187
3 1467464 1470018 - CtAH03T0011100.2 Cati3g00189 189
2 69786639 69792158 + gnl|WGS:LEKV|Ccrd_011322.mRNA.1_mrna Ccar2g02271 2271
2 69793085 69812562 + gnl|WGS:LEKV|Ccrd_011323.mRNA.1_mrna Ccar2g02272 2272
2 69803719 69813661 - gnl|WGS:LEKV|Ccrd_011325.mRNA.1_mrna Ccar2g02274 2274
2 69823632 69824876 - gnl|WGS:LEKV|Ccrd_011326.mRNA.1_mrna Ccar2g02275 2275
2 69828990 69833409 - gnl|WGS:LEKV|Ccrd_011327.mRNA.1_mrna Ccar2g02276 2276
2 81754137 81758903 + >KAJ9562780.1 Ceso2g03261 3261
2 81770943 81774947 - >KAJ9562784.1 Ceso2g03262 3262
6 213459410 213462312 + ClaG1_Chr06g0426661 Chla6g05419 5419
7 258588767 258592998 + CmaNakai_Chr07g0698231 Chma7g07521 7521
7 258610145 258613950 + CmaNakai_Chr07g0698251 Chma7g07523 7523
7 258643336 258647175 + CmaNakai_Chr07g0698271 Chma7g07525 7525
7 258647779 258648283 - CmaNakai_Chr07g0698281 Chma7g07526 7526
13 63943219 63947687 + evm.model.scaffold_4060.84 Chmo13g01212 1212
13 63948488 63953108 + evm.model.scaffold_4060.83 Chmo13g01213 1213
13 64120282 64122302 + evm.model.scaffold_4060.80 Chmo13g01215 1215
13 64123451 64123930 - evm.model.scaffold_4060.78 Chmo13g01217 1217
14 59176147 59180801 + evm.model.scaffold_948.92 Chmo14g01115 1115
14 59181112 59186203 + evm.model.scaffold_948.93 Chmo14g01116 1116
14 59221504 59225213 + evm.model.scaffold_948.96 Chmo14g01118 1118
14 59225305 59228024 - evm.model.scaffold_948.97 Chmo14g01119 1119
15 61430849 61434187 + evm.model.scaffold_1478.29 Chmo15g01064 1064
15 61435403 61457500 + evm.model.scaffold_1478.30 Chmo15g01065 1065
15 61464241 61467755 + evm.model.scaffold_1478.32 Chmo15g01067 1067
15 61467873 61470643 - evm.model.scaffold_1478.33 Chmo15g01068 1068
2 82537554 82540509 + Cn0815520 Chna2g01038 1038
2 82541130 82546225 + Cn0815530 Chna2g01039 1039
2 82853787 82859267 + Cn0815550 Chna2g01041 1041
2 82859893 82860393 - Cn0815570 Chna2g01042 1042
3 305687309 305690485 - D.indicum_Contig21_G00002.t1 Cind3g01958 1958
3 305816698 305820478 - D.indicum_Contig21_G00004.t1 Cind3g01960 1960
3 304904674 304905174 + D.indicum_Contig902_G00006.t1 Cind3g05811 5811
3 1203587 1206964 + XM_043764886.1 Ecan3g00135 135
3 1220176 1223447 + XM_043762819.1 Ecan3g00137 137
3 1273384 1276438 - XM_043765005.1 Ecan3g00143 143
3 1277198 1279133 + XM_043762932.1 Ecan3g00145 145
3 1291003 1294790 - XM_043766152.1 Ecan3g00146 146
6 132227211 132230395 - evm.model.ctg2429.2 Enbr6g03573 3573
2 47125954 47126454 + LmiAMIRv0_Chr02g0086831 Lomi2g04150 4150
2 47129688 47133266 - LmiAMIRv0_Chr02g0086841 Lomi2g04151 4151
2 47141567 47144782 - LmiAMIRv0_Chr02g0086851 Lomi2g04152 4152
1 44090517 44093708 + PluAMIRv0_Chr01g0064071 Pslu1g06431 6431
1 44094446 44096257 + PluAMIRv0_Chr01g0064081 Pslu1g06432 6432
1 44112842 44116401 + PluAMIRv0_Chr01g0064091 Pslu1g06433 6433
1 44137498 44142500 - PluAMIRv0_Chr01g0064111 Pslu1g06435 6435
1 44143086 44143586 - PluAMIRv0_Chr01g0064121 Pslu1g06436 6436
12 2481689 2487523 + SinAMIRv0_Chr12g0357061 Sain12g00141 141
12 2500232 2501911 + SinAMIRv0_Chr12g0357071 Sain12g00142 142
12 2556333 2562923 + SinAMIRv0_Chr12g0357081 Sain12g00143 143
12 2582679 2586103 - SinAMIRv0_Chr12g0357091 Sain12g00144 144
12 2586510 2587010 - SinAMIRv0_Chr12g0357101 Sain12g00145 145
5 71600840 71603940 + augustus35841.t02 Soca5g05266 5266
5 71628240 71634826 - augustus35845.t02 Soca5g05269 5269
5 71639940 71641794 + augustus35846.t01 Soca5g05271 5271
5 71677658 71682382 - transfrag23829.t01 Soca5g05272 5272
       
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