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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
Vivi1g00081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00082 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00083 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00086 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00089 Arla3g01111 Armi4g01903 Sain11g02936 Ceso7g01849 . . Cien2g00913 Cich6g02724 Lssa2g01864 Laca2g01422 Tako2g04222 Tamo2g03590 Pslu4g03160 Lomi8g01314 Lomi10g01448 . Ecan6g01185 . Glco1g04174 Artr7g04357 Aary2g00890 Aary10g03342 Aann7g00671 . Chmo7g01426 Chmo8g01738 Chmo9g01683 Chla8g04846 Chna9g02760 Cind7g01801 Pdy8g01430 . . . . . . . . . . . . . . . . . . . . . Hean14g02510 . . . . . . . . . . . . . . . .
Vivi1g00090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
7 43294513 43302372 - chr7g1163711 Aann7g00671 671
2 76109926 76137811 - Aargg2g08900.1 Aary2g00890 890
10 189082839 189090380 - Aargg10g33420.1 Aary10g03342 3342
3 77476310 77480193 - evm.model.000025F.155 Arla3g01111 1111
14 8361263 8363371 - evm.model.000059F.286 Arla14g00194 194
4 84891393 84895342 - AmiAMIRv0_Chr04g0155661 Armi4g01903 1903
7 168488250 168494456 - AtridAMIRv0_Chr07g0871901 Artr7g04357 4357
7 30820098 30824800 + >KAJ9541296.1 Ceso7g01849 1849
8 163287315 163294548 - ClaG1_Chr08g0560861 Chla8g04846 4846
7 119132207 119140133 - evm.model.scaffold_9203.133 Chmo7g01426 1426
8 126036212 126044744 - evm.model.scaffold_7954.127 Chmo8g01738 1738
9 124044874 124051307 - evm.model.scaffold_118.572 Chmo9g01683 1683
9 144752060 144755213 + Cn0066890 Chna9g02760 2760
6 46690833 46697632 + KAI3723210.1 Cich6g02724 2724
2 48157382 48164673 - KAI3518828.1 Cien2g00913 913
7 154855029 154859625 + D.indicum_Contig22_G00103.t1 Cind7g01801 1801
6 22807484 22811645 - XM_043776041.1 Ecan6g01185 1185
1 296905623 296925999 + GcoAMIRv0_Chr01g0041741 Glco1g04174 4174
14 131175415 131178177 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0649841 Hean14g02510 2510
2 98050608 98057420 - CAI9271745.1 Laca2g01422 1422
8 12806065 12810280 + LmiAMIRv0_Chr08g0253361 Lomi8g01314 1314
10 12217706 12221770 + LmiAMIRv0_Chr10g0304401 Lomi10g01448 1448
2 141952903 141960916 - >KAJ0223242.1 Lssa2g01864 1864
8 46840918 46845493 - PdyAMIRv0_Chr08g0307531 Pdy8g01430 1430
4 20571214 20575230 + PluAMIRv0_Chr04g0611131 Pslu4g03160 3160
5 20007088 20008416 - SinAMIRv0_Chr05g0120401 Sain5g00361 361
11 78488604 78493073 + SinAMIRv0_Chr11g0337351 Sain11g02936 2936
2 112063379 112069439 - TkA02G440920.1 Tako2g04222 4222
2 81735048 81742450 - TbA02G099260.1 Tamo2g03590 3590
1 785438 792711 + GSVIVT01012172001 Vivi1g00081 81
1 793753 796574 + GSVIVT01012171001 Vivi1g00082 82
1 797708 800133 + GSVIVT01012170001 Vivi1g00083 83
1 806983 839693 + GSVIVT01012169001 Vivi1g00084 84
1 850561 867482 + GSVIVT01012168001 Vivi1g00085 85
1 867583 888643 + GSVIVT01012167001 Vivi1g00086 86
1 888711 895574 - GSVIVT01012166001 Vivi1g00087 87
1 901077 903566 + GSVIVT01012165001 Vivi1g00088 88
1 903666 929421 + GSVIVT01012164001 Vivi1g00089 89
1 930401 945147 - GSVIVT01012163001 Vivi1g00090 90
       
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