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AGRP

Asteraceae Genomic Research Platform

Gene Search

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Example:

Hierarchical alignments with the Vitis vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Vitis vinifera as a reference, and by comparing homologous gene locus maps and Ks values between Vitis vinifera and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 219×23,647 macro-matrices.
Select Vivi_1 Arla_1 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
Vivi19g00964 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00965 Arla1g00117 Armi1g00144 Sain12g00136 Ceso2g03258 Cati3g00181 Ccar2g02281 . . . . . . Pslu1g06427 . Lomi2g04154 . Ecan3g00149 Soca5g05276 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00966 Arla1g00116 Armi1g00143 Sain12g00135 Ceso2g03256 Cati3g00180 Ccar2g02282 . . . . . . Pslu1g06426 . Lomi2g04155 . Ecan3g00151 Soca5g05277 . . . . . Chma7g07516 Chmo13g01208 Chmo14g01111 Chmo15g01059 Chla6g05427 Chna2g01033 Cind3g01966 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00967 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00968 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 2625207 2639777 + evm.model.000012F.150 Arla1g00116 116
1 2641547 2643510 - evm.model.000012F.151 Arla1g00117 117
1 2774263 2788895 + AmiAMIRv0_Chr01g0001431 Armi1g00143 143
1 2791177 2792571 - AmiAMIRv0_Chr01g0001441 Armi1g00144 144
3 1392312 1398400 + CtAH03T0010300.1 Cati3g00180 180
3 1400055 1402229 - CtAH03T0010400.1 Cati3g00181 181
2 69866900 69868806 + gnl|WGS:LEKV|Ccrd_011332.mRNA.1_mrna Ccar2g02281 2281
2 69870559 69885208 - gnl|WGS:LEKV|Ccrd_011333.mRNA.1_mrna Ccar2g02282 2282
2 81703264 81713517 + >KAJ9562782.1 Ceso2g03256 3256
2 81715632 81718361 - >KAJ9562785.1 Ceso2g03258 3258
6 213636529 213641198 - ClaG1_Chr06g0426741 Chla6g05427 5427
7 258226967 258233408 + CmaNakai_Chr07g0698181 Chma7g07516 7516
13 63637430 63642476 + evm.model.scaffold_4060.93 Chmo13g01208 1208
14 58719030 58724118 + evm.model.scaffold_948.71 Chmo14g01111 1111
15 61029105 61034658 + evm.model.scaffold_1478.8 Chmo15g01059 1059
2 82052544 82057810 + Cn0815450 Chna2g01033 1033
3 306256006 306261219 - D.indicum_Contig21_G00010.t1 Cind3g01966 1966
3 1320445 1323206 + XM_043765837.1 Ecan3g00149 149
3 1393666 1400152 - XM_043764633.1 Ecan3g00151 151
2 47162337 47164043 + LmiAMIRv0_Chr02g0086871 Lomi2g04154 4154
2 47164910 47170419 - LmiAMIRv0_Chr02g0086881 Lomi2g04155 4155
1 44058276 44063771 + PluAMIRv0_Chr01g0064021 Pslu1g06426 6426
1 44065801 44067104 - PluAMIRv0_Chr01g0064031 Pslu1g06427 6427
12 2401868 2413779 + SinAMIRv0_Chr12g0357001 Sain12g00135 135
12 2420578 2422760 - SinAMIRv0_Chr12g0357011 Sain12g00136 136
5 71724585 71726939 + transfrag23834.t01 Soca5g05276 5276
5 71735431 71741779 - augustus35854.t01 Soca5g05277 5277
19 18679154 18679264 - GSVIVT01020485001 Vivi19g00964 964
19 18708699 18709996 + GSVIVT01020484001 Vivi19g00965 965
19 18712458 18722886 - GSVIVT01020482001 Vivi19g00966 966
19 18754506 18762882 + GSVIVT01020479001 Vivi19g00967 967
19 18785290 18790280 - GSVIVT01020478001 Vivi19g00968 968
19 18803652 18822202 - GSVIVT01020477001 Vivi19g00969 969
19 18872620 18880961 - GSVIVT01020475001 Vivi19g00970 970
19 18966010 18966189 - GSVIVT01020470001 Vivi19g00971 971
19 18967468 18968195 - GSVIVT01020468001 Vivi19g00972 972
19 18990270 19006513 - GSVIVT01020466001 Vivi19g00973 973
       
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