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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
Vivi19g00914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00915 Arla1g00119 Armi1g00147 Sain12g00138 . Cati3g00183 Ccar2g02278 . . . . . . Pslu1g06429 . . . . . . . . . . Chma7g07517 Chmo13g01210 Chmo14g01113 Chmo15g01062 Chla6g05424 Chna2g01035 Cind3g01963 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00916 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00920 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 2665771 2672808 + evm.model.000012F.153 Arla1g00119 119
1 2839750 2845405 + AmiAMIRv0_Chr01g0001471 Armi1g00147 147
3 1423836 1431596 + CtAH03T0010600.1 Cati3g00183 183
2 69840205 69846128 - gnl|WGS:LEKV|Ccrd_011329.mRNA.1_mrna Ccar2g02278 2278
6 213571454 213574487 - ClaG1_Chr06g0426711 Chla6g05424 5424
7 258294187 258296213 + CmaNakai_Chr07g0698191 Chma7g07517 7517
13 63702623 63706279 + evm.model.scaffold_4060.90 Chmo13g01210 1210
14 58827582 58830449 + evm.model.scaffold_948.75 Chmo14g01113 1113
15 61153026 61156386 + evm.model.scaffold_1478.15 Chmo15g01062 1062
2 82329700 82335915 + Cn0815480 Chna2g01035 1035
3 306027835 306031533 - D.indicum_Contig21_G00007.t1 Cind3g01963 1963
1 44078736 44082428 + PluAMIRv0_Chr01g0064051 Pslu1g06429 6429
12 2443222 2448712 + SinAMIRv0_Chr12g0357031 Sain12g00138 138
19 16401287 16406784 + GSVIVT01038022001 Vivi19g00914 914
19 16413689 16414795 + GSVIVT01038023001 Vivi19g00915 915
19 16448662 16459547 - GSVIVT01038025001 Vivi19g00916 916
19 16531632 16532867 + GSVIVT01038031001 Vivi19g00917 917
19 16533381 16545164 + GSVIVT01038032001 Vivi19g00918 918
19 16545942 16556452 + GSVIVT01038033001 Vivi19g00919 919
19 16557000 16569957 - GSVIVT01038034001 Vivi19g00920 920
19 16570451 16572001 + GSVIVT01038035001 Vivi19g00921 921
19 16593568 16595273 + GSVIVT01038037001 Vivi19g00922 922
19 16609679 16610200 + GSVIVT01038038001 Vivi19g00923 923
       
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