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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
Vivi1g00061 Arla4g01970 Armi3g04275 Sain4g00798 Ceso4g04259 Cati7g00447 Ccar13g00303 Cien3g02834 Cich2g01194 Lssa8g01718 Laca8g01432 Tako5g02527 Tamo5g03348 Pslu5g12966 Lomi3g01853 Lomi4g01644 Enbr1g05998 Ecan1g02763 Soca1g02953 Glco1g01681 Artr1g07589 . Aary17g00898 Aann5g04649 . Chmo16g03276 Chmo17g03426 Chmo18g02917 Chla5g04195 Chna6g01808 Cind2g04055 Pdy1g05460 . . . . . . . . . . . . . . . . . . . . Cobi12g00179 Hean12g01049 Bial1g00162 Bial13g00211 Dapi8g00195 Dapi24g00150 Hetu47g03406 Hetu48g03149 Hetu46g03362 Amtr02g01423 Smso5g02220 Smso26g02849 Taer7g03584 Fro3g00188 Fso8g02035 . Fra14g01131 Fli15g01659
Vivi1g00062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
5 145701643 145708857 + chr5g0331181 Aann5g04649 4649
17 79963829 79969797 - Aargg17g08980.1 Aary17g00898 898
2 34673816 34681437 - AtrifAMIRv0_Chr02g0110191 Amtr02g01423 1423
4 105684700 105695997 - evm.model.000240F.35 Arla4g01970 1970
3 155422263 155431772 - AmiAMIRv0_Chr03g0132081 Armi3g04275 4275
1 221425294 221431201 + AtridAMIRv0_Chr01g0075891 Artr1g07589 7589
1 1622776 1629508 + g146489.t1 Bial1g00162 162
13 2404999 2411734 + g63990.t1 Bial13g00211 211
7 4160135 4168931 + CtAH07T0033300.2 Cati7g00447 447
13 3596284 3604783 + gnl|WGS:LEKV|Ccrd_016184.mRNA.1_mrna Ccar13g00303 303
4 95852750 95861270 - >KAJ9554239.1 Ceso4g04259 4259
5 179943679 179945881 - ClaG1_Chr05g0339051 Chla5g04195 4195
16 214899573 214904913 - evm.model.scaffold_1509.74 Chmo16g03276 3276
17 232869569 232875151 - evm.model.scaffold_1419.212 Chmo17g03426 3426
18 235508852 235514202 - evm.model.scaffold_611.11 Chmo18g02917 2917
6 112212314 112217914 + Cn0690800 Chna6g01808 1808
2 40121125 40132199 - KAI3779142.1 Cich2g01194 1194
3 75497530 75506691 + KAI3516574.1 Cien3g02834 2834
2 115737986 115743393 + D.indicum_Contig494_G00010.t1 Cind2g04055 4055
12 1801129 1807684 + h2tg000030l_1.g18135.t1 Cobi12g00179 179
8 3483258 3491511 + h1tg000025l.g56596.t1 Dapi8g00195 195
24 2099615 2106224 + h1tg000067l.g106457.t1 Dapi24g00150 150
1 41932770 41939113 - XM_043771279.1 Ecan1g02763 2763
1 182634274 182640207 + evm.model.ctg5528.1 Enbr1g05998 5998
15 59396833 59403195 - FliAMIRv0_Chr15g0347651 Fli15g01659 1659
14 42108232 42114675 + FraAMIRv0_Chr14g0282741 Fra14g01131 1131
3 2004902 2011292 + FroAMIRv0_Chr03g0031911 Fro3g00188 188
8 50723619 50729987 - FsoAMIRv0_Chr08g0195311 Fso8g02035 2035
1 84079612 84085043 - GcoAMIRv0_Chr01g0016811 Glco1g01681 1681
12 22616073 22629193 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr12g0532591 Hean12g01049 1049
46 198740011 198748418 - >Htub.h1tg000449l.g183.t1 Hetu46g03362 3362
47 213402465 213410860 - >Htub.h1tg001680l.g375.t1 Hetu47g03406 3406
48 187215550 187223957 + >Htub.h2tg000112l.g321.t1 Hetu48g03149 3149
8 49727573 49732641 - CAI9296985.1 Laca8g01432 1432
3 15746717 15753519 + LmiAMIRv0_Chr03g0110411 Lomi3g01853 1853
4 24488776 24490301 - LmiAMIRv0_Chr04g0141141 Lomi4g01644 1644
8 71083823 71090434 - >KAJ0190144.1 Lssa8g01718 1718
19 57146042 57152618 - KAD2393626.1 Mimi19g00929 929
1 115621272 115628603 + PdyAMIRv0_Chr01g0054561 Pdy1g05460 5460
5 96147617 96153472 - PluAMIRv0_Chr05g0878231 Pslu5g12966 12966
4 22485660 22492694 - SinAMIRv0_Chr04g0091321 Sain4g00798 798
5 110215771 110222225 - KAI3816640.1 Smso5g02220 2220
26 63206141 63212601 - KAI3696334.1 Smso26g02849 2849
1 32855427 32862258 + transfrag2495.t01 Soca1g02953 2953
5 7503498 7512754 + Streb.5G002940.1 Stre5g00294 294
7 42464925 42470613 - >KAK1419897.1 Taer7g03584 3584
5 88198518 88200189 + TkA05G355800.1 Tako5g02527 2527
5 78037532 78043911 + TbA05G096670.1 Tamo5g03348 3348
1 649077 654363 - GSVIVT01012194001 Vivi1g00061 61
1 656270 666920 + GSVIVT01012193001 Vivi1g00062 62
1 667767 679204 - GSVIVT01012192001 Vivi1g00063 63
1 679483 685333 - GSVIVT01012191001 Vivi1g00064 64
1 688228 696254 + GSVIVT01012190001 Vivi1g00065 65
1 697863 701409 - GSVIVT01012189001 Vivi1g00066 66
1 701419 707690 - GSVIVT01012188001 Vivi1g00067 67
1 710556 714160 - GSVIVT01012187001 Vivi1g00068 68
1 715659 718644 - GSVIVT01012185001 Vivi1g00069 69
1 721721 725418 + GSVIVT01012184001 Vivi1g00070 70
       
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