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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
Vivi1g00101 Arla3g01115 Armi4g01909 Sain11g02931 Ceso7g01846 Cati8g03125 Ccar1g01798 . . Lssa2g01868 . Tako2g04228 Tamo2g03594 Pslu4g03156 Lomi8g01313 . Enbr3g01168 Ecan6g01187 . . Artr7g04373 Aary2g00893 Aary10g03346 Aann7g00674 Chma2g02654 Chmo7g01430 Chmo8g01743 Chmo9g01687 Chla8g04843 Chna9g02758 Cind7g01804 Pdy8g01435 . . . . . . . . . . . . . . . . . . . . . Hean14g01714 . . Dapi3g01475 Dapi19g01598 . Hetu40g02393 . Amtr01g09522 . . . . . . . .
Vivi1g00102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00109 Arla3g01121 Armi4g01924 Sain11g02926 . . Ccar1g01794 . Cich6g02718 Lssa2g01875 . Tako2g04247 Tamo2g03598 Pslu4g03150 . . . Ecan6g01194 . Glco1g04165 Artr7g04385 Aary2g00897 . Aann7g00681 . Chmo7g01437 Chmo8g01748 Chmo9g01693 Chla8g04837 Chna9g02753 Cind7g01809 Pdy8g01438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
7 44216127 44222775 - chr7g1164181 Aann7g00674 674
7 44292589 44295467 + chr7g1164331 Aann7g00681 681
2 76288432 76294608 - Aargg2g08930.1 Aary2g00893 893
2 76571197 76578408 + Aargg2g08970.1 Aary2g00897 897
10 189405244 189411555 - Aargg10g33460.1 Aary10g03346 3346
1 223311968 223316024 + AtrifAMIRv0_Chr01g0095221 Amtr01g09522 9522
3 77881447 77900784 - evm.model.000025F.165 Arla3g01115 1115
3 78193788 78196453 + evm.model.000025F.175 Arla3g01121 1121
14 8281437 8303924 + evm.model.000059F.282 Arla14g00192 192
14 8336026 8337653 - evm.model.000059F.285 Arla14g00193 193
4 85314521 85333577 - AmiAMIRv0_Chr04g0155721 Armi4g01909 1909
4 85651934 85652842 + AmiAMIRv0_Chr04g0155871 Armi4g01924 1924
13 69371055 69372386 + AmiAMIRv0_Chr13g0396521 Armi13g01587 1587
13 69486075 69508169 - AmiAMIRv0_Chr13g0396541 Armi13g01589 1589
7 168920995 168928189 - AtridAMIRv0_Chr07g0872061 Artr7g04373 4373
7 169386155 169387069 + AtridAMIRv0_Chr07g0872181 Artr7g04385 4385
8 33196091 33206021 + CtAH08T0211000.1 Cati8g03125 3125
12 7894831 7907492 + CtAH12T0029200.2 Cati12g00365 365
12 7949005 7986415 + CtAH12T0029400.1 Cati12g00367 367
1 21994816 22000299 - gnl|WGS:LEKV|Ccrd_013197.mRNA.1_mrna Ccar1g01794 1794
1 22043176 22053355 + gnl|WGS:LEKV|Ccrd_013201.mRNA.1_mrna Ccar1g01798 1798
3 60430040 60441367 - >KAJ9557523.1 Ceso3g02798 2798
7 30664919 30673458 + >KAJ9541415.1 Ceso7g01846 1846
8 162857755 162867791 - ClaG1_Chr08g0560771 Chla8g04837 4837
8 163060914 163067215 + ClaG1_Chr08g0560831 Chla8g04843 4843
2 100195242 100201193 - CmaNakai_Chr02g0169671 Chma2g02654 2654
4 144433701 144438355 - CmaNakai_Chr04g0347181 Chma4g04125 4125
4 136559624 136565730 + evm.model.scaffold_11345.93.1 Chmo4g02017 2017
4 136739393 136740700 - evm.model.scaffold_11345.97 Chmo4g02018 2018
5 133197405 133203599 + evm.model.scaffold_8229.185.2 Chmo5g01890 1890
5 133352393 133353700 - evm.model.scaffold_8229.194 Chmo5g01891 1891
7 119414111 119420050 - evm.model.scaffold_9203.126 Chmo7g01430 1430
7 119646433 119653384 + evm.model.scaffold_9203.111 Chmo7g01437 1437
8 126278871 126285027 - evm.model.scaffold_7954.118 Chmo8g01743 1743
8 126462246 126470162 + evm.model.scaffold_7954.104 Chmo8g01748 1748
9 124278441 124284675 - evm.model.scaffold_118.578 Chmo9g01687 1687
9 124393771 124405741 + evm.model.scaffold_118.586 Chmo9g01693 1693
4 157371958 157373265 + Cn0081810 Chna4g02286 2286
4 157531411 157537677 - Cn0081800 Chna4g02287 2287
9 144304136 144307070 - Cn0995350 Chna9g02753 2753
9 144454980 144461410 + Cn0995410 Chna9g02758 2758
2 130519150 130522307 - KAI3781491.1 Cich2g03543 3543
6 46368534 46370248 - KAI3723204.1 Cich6g02718 2718
3 23351296 23354843 + KAI3514896.1 Cien3g01156 1156
4 156769253 156774803 + D.indicum_Contig797_G00009.t1 Cind4g05320 5320
4 156949684 156950705 - D.indicum_Contig797_G00011.t1 Cind4g05322 5322
7 154412055 154417886 + D.indicum_Contig22_G00106.t1 Cind7g01804 1804
7 154246272 154247186 - D.indicum_Contig22_G00111.t1 Cind7g01809 1809
3 30524133 30525441 + h2tg000226l.g72916.t1 Dapi3g01475 1475
19 28678243 28679962 + h2tg000072l.g15131.t1 Dapi19g01598 1598
2 10575854 10577343 + XM_043762457.1 Ecan2g00857 857
2 10580764 10590317 - XM_043758913.1 Ecan2g00859 859
6 22846533 22852326 - XM_043778191.1 Ecan6g01187 1187
6 22901702 22904426 + XM_043778413.1 Ecan6g01194 1194
2 75219274 75224940 - evm.model.ctg1370.2 Enbr2g02325 2325
3 34862899 34867522 - evm.model.ctg747.7 Enbr3g01168 1168
1 295053461 295054375 - GcoAMIRv0_Chr01g0041651 Glco1g04165 4165
14 102878630 102879825 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0640461 Hean14g01714 1714
40 91248057 91249820 + >Htub.h1tg003701l.g50.t1 Hetu40g02393 2393
8 12788748 12792705 + LmiAMIRv0_Chr08g0253351 Lomi8g01313 1313
9 20553517 20560918 - LmiAMIRv0_Chr09g0277251 Lomi9g01074 1074
2 142338957 142343045 - >KAJ0222848.1 Lssa2g01868 1868
2 142460291 142461205 - >KAJ0222193.1 Lssa2g01875 1875
8 172126404 172131488 + >KAJ0189366.1 Lssa8g03770 3770
6 54754445 54761241 + PdyAMIRv0_Chr06g0245501 Pdy6g01843 1843
8 46878459 46884214 - PdyAMIRv0_Chr08g0307581 Pdy8g01435 1435
8 46895622 46896536 + PdyAMIRv0_Chr08g0307611 Pdy8g01438 1438
4 20484935 20485834 - PluAMIRv0_Chr04g0611031 Pslu4g03150 3150
4 20517795 20521741 + PluAMIRv0_Chr04g0611091 Pslu4g03156 3156
5 19613169 19629851 + SinAMIRv0_Chr05g0120371 Sain5g00358 358
5 19835181 19836476 + SinAMIRv0_Chr05g0120391 Sain5g00360 360
11 78130202 78131110 - SinAMIRv0_Chr11g0337251 Sain11g02926 2926
11 78332050 78337377 + SinAMIRv0_Chr11g0337301 Sain11g02931 2931
7 25211973 25213322 + augustus25345.t01 Soca7g01303 1303
7 25233250 25241969 - transfrag16760.t02 Soca7g01305 1305
2 112100746 112104366 - TkA02G441020.2 Tako2g04228 4228
2 112169323 112171169 + TkA02G441260.2 Tako2g04247 4247
5 9215601 9218384 + TkA05G034160.3 Tako5g00580 580
2 81768083 81771101 - TbA02G099300.1 Tamo2g03594 3594
2 81808396 81810910 + TbA02G099360.1 Tamo2g03598 3598
5 19696212 19699939 + TbA05G024010.1 Tamo5g01417 1417
1 1002540 1009582 - GSVIVT01012151001 Vivi1g00101 101
1 1017874 1019921 + GSVIVT01012150001 Vivi1g00102 102
1 1030308 1032374 + GSVIVT01012149001 Vivi1g00103 103
1 1049293 1049640 - GSVIVT01012148001 Vivi1g00104 104
1 1060701 1062011 + GSVIVT01012147001 Vivi1g00105 105
1 1063042 1070438 - GSVIVT01012146001 Vivi1g00106 106
1 1071686 1078368 - GSVIVT01012145001 Vivi1g00107 107
1 1079054 1081341 + GSVIVT01012144001 Vivi1g00108 108
1 1082207 1082935 + GSVIVT01012143001 Vivi1g00109 109
1 1082989 1085765 - GSVIVT01012142001 Vivi1g00110 110
       
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