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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
Vivi1g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00072 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00075 Arla4g01975 Armi3g04280 . Ceso4g04262 Cati7g00441 . Cien3g02804 . Lssa8g01753 . Tako5g02508 . Pslu5g12973 Lomi3g01849 Lomi4g01648 Enbr1g05991 Ecan1g02767 Soca1g02949 . . . . . . Chmo16g03280 Chmo17g03430 Chmo18g02921 Chla5g04204 Chna6g01805 Cind2g04060 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00076 Arla4g01976 Armi3g04281 . Ceso4g04263 Cati7g00440 . . . . . . . Pslu5g12974 Lomi3g01848 Lomi4g01649 Enbr1g05990 Ecan1g02768 Soca1g02948 . . . . . . . . Chmo18g02922 . Chna6g01804 Cind2g04061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00077 Arla4g01977 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00079 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00080 Arla4g01979 Armi3g04283 . Ceso4g04264 Cati7g00437 Ccar13g00299 . . . . . . Pslu5g12999 Lomi3g01845 Lomi4g01652 Enbr1g05989 Ecan1g02772 Soca1g02945 . . . . . . . . Chmo18g02927 . Chna6g01803 Cind2g04064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
8 43532165 43533908 - chr8g1064041 Aann8g00771 771
4 195293636 195295663 + Aargg4g29050.1 Aary4g02905 2905
4 105749299 105760675 + evm.model.000240F.29 Arla4g01975 1975
4 105761033 105766465 + evm.model.000240F.28 Arla4g01976 1976
4 105768265 105771164 + evm.model.000240F.27 Arla4g01977 1977
4 105774309 105780766 - evm.model.000240F.25 Arla4g01979 1979
5 5109749 5112029 - evm.model.000113F.243 Arla5g00249 249
3 5865926 5867970 - AmiAMIRv0_Chr03g0092011 Armi3g00268 268
3 155485007 155495225 + AmiAMIRv0_Chr03g0132131 Armi3g04280 4280
3 155496895 155500976 + AmiAMIRv0_Chr03g0132141 Armi3g04281 4281
3 155508421 155512757 - AmiAMIRv0_Chr03g0132161 Armi3g04283 4283
4 89661849 89664451 + CtAH04T0236600.1 Cati4g03142 3142
7 4097827 4104266 + CtAH07T0032500.1 Cati7g00437 437
7 4111164 4115145 - CtAH07T0032800.1 Cati7g00440 440
7 4116451 4127855 - CtAH07T0032900.1 Cati7g00441 441
12 2092275 2093565 - gnl|WGS:LEKV|Ccrd_000173.mRNA.1_mrna Ccar12g00169 169
13 3533309 3540463 + gnl|WGS:LEKV|Ccrd_016180.mRNA.1_mrna Ccar13g00299 299
2 105017593 105019220 + >KAJ9563797.1 Ceso2g04387 4387
4 95888558 95894598 + >KAJ9554161.1 Ceso4g04262 4262
4 95896784 95899829 + >KAJ9554162.1 Ceso4g04263 4263
4 95909603 95913800 - >KAJ9554163.1 Ceso4g04264 4264
5 180310949 180316518 - ClaG1_Chr05g0339141 Chla5g04204 4204
16 215109039 215114555 + evm.model.scaffold_1509.66 Chmo16g03280 3280
17 232988376 232993512 + evm.model.scaffold_1419.219.2 Chmo17g03430 3430
18 235567319 235572251 + evm.model.scaffold_611.19.2 Chmo18g02921 2921
18 235690969 235694625 + evm.model.scaffold_611.24 Chmo18g02922 2922
18 235755629 235761168 - evm.model.scaffold_611.31 Chmo18g02927 2927
6 112034874 112040102 + Cn0690850 Chna6g01803 1803
6 112117029 112119749 - Cn0690840 Chna6g01804 1804
6 112129709 112133805 - Cn0690830 Chna6g01805 1805
3 6655703 6656601 - KAI3763672.1 Cich3g00232 232
3 75056613 75059604 + KAI3516544.1 Cien3g02804 2804
2 115548655 115553236 - D.indicum_Contig494_G00015.t1 Cind2g04060 4060
2 115529725 115532244 - D.indicum_Contig494_G00016.t1 Cind2g04061 4061
2 115448610 115452283 + D.indicum_Contig494_G00019.t1 Cind2g04064 4064
1 41993806 42000259 + XM_043751138.1 Ecan1g02767 2767
1 42005341 42009662 + XM_043753142.1 Ecan1g02768 2768
1 42047557 42053403 - XM_043755798.1 Ecan1g02772 2772
4 31524687 31526277 + XM_043767539.1 Ecan4g02036 2036
1 182440392 182444217 + evm.model.ctg185.10 Enbr1g05989 5989
1 182503298 182507792 - evm.model.ctg185.13 Enbr1g05990 5990
1 182517146 182522514 - evm.model.ctg185.14 Enbr1g05991 5991
6 580985767 580986742 + GcoAMIRv0_Chr06g0440091 Glco6g05910 5910
3 15659098 15663023 + LmiAMIRv0_Chr03g0110331 Lomi3g01845 1845
3 15675837 15680145 - LmiAMIRv0_Chr03g0110361 Lomi3g01848 1848
3 15682464 15687444 - LmiAMIRv0_Chr03g0110371 Lomi3g01849 1849
4 24513845 24518768 + LmiAMIRv0_Chr04g0141181 Lomi4g01648 1648
4 24520869 24524851 + LmiAMIRv0_Chr04g0141191 Lomi4g01649 1649
4 24547377 24551305 - LmiAMIRv0_Chr04g0141221 Lomi4g01652 1652
8 35961916 35963152 - LmiAMIRv0_Chr08g0266121 Lomi8g02590 2590
10 34189352 34190693 - LmiAMIRv0_Chr10g0319331 Lomi10g02941 2941
4 19262796 19263768 - >KAJ0212319.1 Lssa4g00441 441
8 71828109 71831945 - >KAJ0189590.1 Lssa8g01753 1753
2 4158886 4160259 + PdyAMIRv0_Chr02g0058411 Pdy2g00224 224
4 119542253 119543791 - PluAMIRv0_Chr04g0745611 Pslu4g16651 16651
5 96203089 96208195 + PluAMIRv0_Chr05g0878301 Pslu5g12973 12973
5 96212472 96216092 + PluAMIRv0_Chr05g0878311 Pslu5g12974 12974
5 96313645 96317401 - PluAMIRv0_Chr05g0878561 Pslu5g12999 12999
9 215468051 215475952 - SinAMIRv0_Chr09g0249911 Sain9g04097 4097
1 32722022 32728326 + transfrag2485.t01 Soca1g02945 2945
1 32777298 32781358 - augustus03393.t01 Soca1g02948 2948
1 32782683 32789670 - transfrag2490.t01 Soca1g02949 2949
9 21514259 21515892 - transfrag36113.t01 Soca9g01911 1911
3 149130478 149131675 + TkA03G586860.1 Tako3g06088 6088
5 88053129 88057611 + TkA05G355300.2 Tako5g02508 2508
3 105923160 105924484 + TbA03G004220.1 Tamo3g05023 5023
1 726650 729085 + GSVIVT01012183001 Vivi1g00071 71
1 729267 731550 - GSVIVT01012182001 Vivi1g00072 72
1 731577 733548 + GSVIVT01012181001 Vivi1g00073 73
1 736946 738532 + GSVIVT01012179001 Vivi1g00074 74
1 741222 751123 + GSVIVT01012178001 Vivi1g00075 75
1 751779 759740 + GSVIVT01012177001 Vivi1g00076 76
1 760231 762137 + GSVIVT01012176001 Vivi1g00077 77
1 762706 763140 + GSVIVT01012175001 Vivi1g00078 78
1 763145 767420 - GSVIVT01012174001 Vivi1g00079 79
1 770020 779392 - GSVIVT01012173001 Vivi1g00080 80
       
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