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Asteraceae Genomic Research Platform

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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
Vivi1g00091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00094 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00095 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00097 Arla3g01113 . Sain11g02932 . . Ccar1g01799 Cien2g00915 Cich6g02722 Lssa2g01866 Laca2g01428 Tako2g04225 Tamo2g03593 Pslu4g03157 . Lomi10g01447 . Ecan6g01186 . . Artr7g04372 Aary2g00892 Aary10g03345 Aann7g00673 . Chmo7g01429 Chmo8g01742 Chmo9g01686 Chla8g04844 Chna9g02759 Cind7g01803 Pdy8g01434 . . . . . . . . . . . . . . . . . . . . Cobi9g01803 Hean14g01710 Bial7g00983 . Dapi3g01480 Dapi19g01604 Hetu42g02261 Hetu40g02395 Hetu41g02529 Amtr01g09528 Smso11g01297 Smso12g01769 Taer10g01848 Fro15g01033 Fso18g01599 Ftr10g01387 Fra12g01619 Fli6g00909
Vivi1g00098 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
7 44212319 44214724 - chr7g1164171 Aann7g00673 673
2 76265678 76267456 - Aargg2g08920.1 Aary2g00892 892
10 189381014 189391171 - Aargg10g33450.1 Aary10g03345 3345
1 223347623 223348765 + AtrifAMIRv0_Chr01g0095281 Amtr01g09528 9528
3 77704058 77706095 - evm.model.000025F.159 Arla3g01113 1113
7 168829752 168830918 - AtridAMIRv0_Chr07g0872051 Artr7g04372 4372
7 40706536 40708281 - g95587.t1 Bial7g00983 983
1 22065850 22067622 + gnl|WGS:LEKV|Ccrd_013202.mRNA.1_mrna Ccar1g01799 1799
8 163086637 163088390 + ClaG1_Chr08g0560841 Chla8g04844 4844
7 119323669 119324424 - evm.model.scaffold_9203.128 Chmo7g01429 1429
8 126251337 126253509 - evm.model.scaffold_7954.120 Chmo8g01742 1742
9 124247954 124249931 - evm.model.scaffold_118.577 Chmo9g01686 1686
9 144603274 144605031 + Cn0995430 Chna9g02759 2759
6 46553960 46555708 + KAI3723208.1 Cich6g02722 2722
2 48222458 48224206 - KAI3518830.1 Cien2g00915 915
7 154643747 154645504 + D.indicum_Contig22_G00105.t1 Cind7g01803 1803
9 62125182 62126909 - h2tg000008l_1.g41244.t1 Cobi9g01803 1803
3 30601112 30602086 + h2tg000226l.g72921.t1 Dapi3g01480 1480
19 28785902 28787074 + h2tg000072l.g15125.t1 Dapi19g01604 1604
6 22825196 22827268 - XM_043776685.1 Ecan6g01186 1186
6 60477047 60478795 - FliAMIRv0_Chr06g0154691 Fli6g00909 909
12 20504095 20505843 + FraAMIRv0_Chr12g0244441 Fra12g01619 1619
15 24390278 24392038 - FroAMIRv0_Chr15g0271381 Fro15g01033 1033
18 61018447 61019223 - FsoAMIRv0_Chr18g0450621 Fso18g01599 1599
10 19500774 19502522 + FtrAMIRv0_Chr10g0290991 Ftr10g01387 1387
14 102579484 102581211 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0640411 Hean14g01710 1710
40 91447613 91449340 + >Htub.h1tg003701l.g52.t1 Hetu40g02395 2395
41 99880582 99882309 + >Htub.h1tg000457l.g259.t1 Hetu41g02529 2529
42 95920041 95921165 + >Htub.h1tg002359l.g400.t1 Hetu42g02261 2261
2 98171279 98173055 - CAI9271751.1 Laca2g01428 1428
10 12206196 12206450 + LmiAMIRv0_Chr10g0304391 Lomi10g01447 1447
2 142263732 142265480 - >KAJ0223732.1 Lssa2g01866 1866
1 80264112 80265845 - KAD7478266.1 Mimi1g01402 1402
8 46873655 46875403 - PdyAMIRv0_Chr08g0307571 Pdy8g01434 1434
4 20526348 20528120 + PluAMIRv0_Chr04g0611101 Pslu4g03157 3157
11 78337798 78340126 + SinAMIRv0_Chr11g0337311 Sain11g02932 2932
11 71975338 71975808 - KAI3798415.1 Smso11g01297 1297
12 21827946 21829673 + KAI3794718.1 Smso12g01769 1769
1 17749566 17751456 - Streb.1G008810.1 Stre1g00881 881
10 14393880 14395613 + >KAK1410899.1 Taer10g01848 1848
2 112081073 112082176 - TkA02G440970.1 Tako2g04225 4225
2 81759688 81761445 - TbA02G099290.1 Tamo2g03593 3593
1 949657 957893 + GSVIVT01012161001 Vivi1g00091 91
1 958551 959737 + GSVIVT01012160001 Vivi1g00092 92
1 961115 963805 - GSVIVT01012159001 Vivi1g00093 93
1 965815 971269 + GSVIVT01012158001 Vivi1g00094 94
1 972356 975005 - GSVIVT01012157001 Vivi1g00095 95
1 979380 981773 + GSVIVT01012156001 Vivi1g00096 96
1 984735 987272 - GSVIVT01012155001 Vivi1g00097 97
1 989103 993721 - GSVIVT01012154001 Vivi1g00098 98
1 995577 997132 - GSVIVT01012153001 Vivi1g00099 99
1 997178 1000812 - GSVIVT01012152001 Vivi1g00100 100
       
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