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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
Vivi19g01034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01040 Arla1g00103 Armi1g00118 . Ceso2g03235 Cati3g00161 . Cien5g03590 Cich4g04894 Lssa7g03818 Laca7g03120 . . . . . . Ecan3g00171 Soca5g05327 Glco3g01615 Artr3g10679 Aary5g02671 . Aann4g00697 . . . . . . . Pdy4g00883 . . . . . . . . . . . . . . . . . . . . Cobi4g02767 Hean11g01484 Bial4g02996 Bial16g02431 Dapi7g00580 Dapi23g00600 Hetu32g01076 Hetu31g01028 Hetu33g01139 . Smso7g00528 Smso29g00685 Taer1g05946 Fro12g02145 Fso2g00477 . Fra11g02321 Fli1g00545
Vivi19g01041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01042 Arla1g00100 Armi1g00117 Sain12g00116 Ceso2g03231 Cati3g00153 Ccar2g02301 Cien5g03589 Cich4g04893 Lssa7g03814 Laca7g03116 . . Pslu1g20683 . Lomi2g04173 . Ecan3g00174 Soca5g05330 Glco3g01613 . . . Aann4g00698 Chma7g07223 Chmo13g01179 Chmo14g01078 Chmo15g01026 . Chna2g01012 Cind3g02001 Pdy4g00881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01043 Arla1g00099 Armi1g00115 Sain12g00115 Ceso2g03230 . Ccar2g02302 Cien5g03588 Cich4g04892 Lssa7g03812 Laca7g03115 . Tamo4g02184 Pslu1g20684 . Lomi2g04174 . Ecan3g00175 Soca5g05331 Glco3g01611 Artr3g10700 . . Aann4g00700 Chma7g07220 Chmo13g01177 Chmo14g01075 Chmo15g01020 . Chna2g01011 Cind3g02004 . . . . . . . . . . . . . . . . . . . . . Cobi4g02769 Hean11g01491 Bial4g03001 Bial16g02433 Dapi7g00577 Dapi23g00597 Hetu32g01067 Hetu31g01021 Hetu33g01137 Amtr02g06532 Smso7g00525 Smso29g00682 Taer1g05943 Fro12g02147 Fso2g00475 Ftr4g03451 Fra11g02323 Fli1g00540
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 46960261 46971299 - chr4g0764011 Aann4g00697 697
4 47091052 47093660 + chr4g0764141 Aann4g00698 698
4 47187799 47194205 - chr4g0764171 Aann4g00700 700
5 154644681 154656205 + Aargg5g26710.1 Aary5g02671 2671
2 118315010 118316783 - AtrifAMIRv0_Chr02g0161281 Amtr02g06532 6532
1 1860050 1862999 + evm.model.000012F.123 Arla1g00099 99
1 2067351 2071702 - evm.model.000012F.126 Arla1g00100 100
1 2249232 2253743 + evm.model.000012F.135 Arla1g00103 103
1 1845575 1848742 + AmiAMIRv0_Chr01g0001151 Armi1g00115 115
1 2280797 2284833 - AmiAMIRv0_Chr01g0001171 Armi1g00117 117
1 2365863 2382591 + AmiAMIRv0_Chr01g0001181 Armi1g00118 118
3 360449914 360459928 - AtridAMIRv0_Chr03g0414151 Artr3g10679 10679
3 361164758 361166054 - AtridAMIRv0_Chr03g0414361 Artr3g10700 10700
4 68821108 68823150 - g55987.t1 Bial4g02996 2996
4 68890824 68892340 - g55992.t1 Bial4g03001 3001
16 63515763 63522982 - g150151.t1 Bial16g02431 2431
16 63579983 63581499 - g150149.t1 Bial16g02433 2433
3 1112870 1117208 - CtAH03T0008600.1 Cati3g00153 153
3 1133416 1152936 + CtAH03T0008700.8 Cati3g00161 161
2 70136928 70140959 + gnl|WGS:LEKV|Ccrd_011352.mRNA.1_mrna Ccar2g02301 2301
2 70148884 70151235 - gnl|WGS:LEKV|Ccrd_011353.mRNA.1_mrna Ccar2g02302 2302
2 81351385 81353801 + >KAJ9562944.1 Ceso2g03230 3230
2 81362305 81365676 - >KAJ9562950.1 Ceso2g03231 3231
2 81407991 81421170 + >KAJ9562674.1 Ceso2g03235 3235
7 247583535 247584831 - CmaNakai_Chr07g0695221 Chma7g07220 7220
7 247786737 247787414 - CmaNakai_Chr07g0695251 Chma7g07223 7223
13 60767026 60768434 + evm.model.scaffold_10828.12 Chmo13g01177 1177
13 61075995 61080420 - evm.model.scaffold_10828.22 Chmo13g01179 1179
14 55324805 55326157 + evm.model.scaffold_9850.33.1 Chmo14g01075 1075
14 55540665 55544711 - evm.model.scaffold_9850.38 Chmo14g01078 1078
15 59183037 59184389 + evm.model.scaffold_3415.34.1 Chmo15g01020 1020
15 59345978 59349779 - evm.model.scaffold_3415.43 Chmo15g01026 1026
2 79484704 79486081 + Cn0814970 Chna2g01011 1011
2 79674902 79678980 - Cn0815030 Chna2g01012 1012
4 138574053 138575334 + KAI3754027.1 Cich4g04892 4892
4 138660754 138664428 - KAI3754028.1 Cich4g04893 4893
4 138761072 138763381 + KAI3754029.1 Cich4g04894 4894
5 82149934 82151225 + KAI3510108.1 Cien5g03588 3588
5 82184644 82187934 - KAI3510109.1 Cien5g03589 3589
5 82228062 82234164 + KAI3510110.1 Cien5g03590 3590
3 308618784 308620517 + D.indicum_Contig21_G00045.t1 Cind3g02001 2001
3 308767134 308768314 - D.indicum_Contig21_G00048.t1 Cind3g02004 2004
4 75028282 75034826 - h2tg000009l_1.g42512.t1 Cobi4g02767 2767
4 75180814 75182261 - h2tg000009l_1.g42510.t1 Cobi4g02769 2769
7 12313326 12315765 + h1tg000030l.g77167.t1 Dapi7g00577 577
7 12429082 12431422 + h1tg000030l.g77170.t1 Dapi7g00580 580
23 13145432 13147874 + h2tg000020l.g165102.t1 Dapi23g00597 597
23 13302311 13310422 + h2tg000020l.g165099.t1 Dapi23g00600 600
3 1663245 1675830 - XM_043763064.1 Ecan3g00171 171
3 1691753 1694971 + XM_043766205.1 Ecan3g00174 174
3 1701429 1703187 - XM_043766854.1 Ecan3g00175 175
1 11065705 11067075 + FliAMIRv0_Chr01g0005351 Fli1g00540 540
1 11216516 11218432 + FliAMIRv0_Chr01g0005401 Fli1g00545 545
11 76919784 76926851 - FraAMIRv0_Chr11g0223431 Fra11g02321 2321
11 76978465 76979802 - FraAMIRv0_Chr11g0223451 Fra11g02323 2323
12 28831417 28845007 - FroAMIRv0_Chr12g0216931 Fro12g02145 2145
12 28890128 28892304 - FroAMIRv0_Chr12g0216951 Fro12g02147 2147
2 6280452 6281799 + FsoAMIRv0_Chr02g0032941 Fso2g00475 475
2 6352262 6360540 + FsoAMIRv0_Chr02g0032961 Fso2g00477 477
4 117257194 117258529 - FtrAMIRv0_Chr04g0128851 Ftr4g03451 3451
3 105014940 105016219 + GcoAMIRv0_Chr03g0172401 Glco3g01611 1611
3 105180787 105184665 - GcoAMIRv0_Chr03g0172421 Glco3g01613 1613
3 105492972 105501466 + GcoAMIRv0_Chr03g0172441 Glco3g01615 1615
11 44667224 44689650 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483311 Hean11g01484 1484
11 45210077 45212345 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483411 Hean11g01491 1491
31 45224543 45226035 + >Htub.h1tg000660l.g375.t1 Hetu31g01021 1021
31 45692410 45712459 + >Htub.h1tg000660l.g382.t1 Hetu31g01028 1028
32 49964390 49965894 + >Htub.h1tg000795l.g316.t1 Hetu32g01067 1067
32 50374676 50377875 + >Htub.h1tg000795l.g325.t1 Hetu32g01076 1076
33 47653157 47654660 + >Htub.h1tg001052l.g224.t1 Hetu33g01137 1137
33 48044147 48058293 + >Htub.h1tg001052l.g222.t1 Hetu33g01139 1139
7 146654187 146655683 + CAI9295316.1 Laca7g03115 3115
7 146807352 146811317 - CAI9295317.1 Laca7g03116 3116
7 147057550 147062586 + CAI9295322.1 Laca7g03120 3120
2 47303331 47306979 + LmiAMIRv0_Chr02g0087061 Lomi2g04173 4173
2 47314279 47315641 - LmiAMIRv0_Chr02g0087071 Lomi2g04174 4174
7 200599663 200601125 + >KAJ0195980.1 Lssa7g03812 3812
7 200898147 200898601 - >KAJ0198081.1 Lssa7g03814 3814
7 202180220 202185233 + >KAJ0197645.1 Lssa7g03818 3818
17 45427347 45429062 + KAD3067146.1 Mimi17g00824 824
17 46250837 46263096 + KAD3067149.1 Mimi17g00827 827
4 16548874 16552524 - PdyAMIRv0_Chr04g0156881 Pdy4g00881 881
4 16629371 16635770 + PdyAMIRv0_Chr04g0156901 Pdy4g00883 883
1 149246358 149249491 + PluAMIRv0_Chr01g0205921 Pslu1g20683 20683
1 149254695 149256776 - PluAMIRv0_Chr01g0205931 Pslu1g20684 20684
12 1690388 1692477 + SinAMIRv0_Chr12g0356801 Sain12g00115 115
12 1706530 1710436 - SinAMIRv0_Chr12g0356811 Sain12g00116 116
7 8670089 8671665 + KAI3810105.1 Smso7g00525 525
7 8817308 8833658 + KAI3810108.1 Smso7g00528 528
29 9909905 9911516 + KAI3675676.1 Smso29g00682 682
29 9982078 9983690 + KAI3675679.1 Smso29g00685 685
5 73242583 73253386 - transfrag23870.t04 Soca5g05327 5327
5 73269980 73273872 + transfrag23871.t01 Soca5g05330 5330
5 73282826 73284588 - transfrag23872.t01 Soca5g05331 5331
6 21315735 21317532 + Streb.6G007270.1 Stre6g00727 727
6 21558006 21565724 + Streb.6G007300.1 Stre6g00730 730
1 53592522 53595096 + >KAK1440118.1 Taer1g05943 5943
1 53636000 53638465 + >KAK1440121.1 Taer1g05946 5946
4 35991450 35993051 + TbA04G050960.1 Tamo4g02184 2184
19 20534127 20535179 - GSVIVT01020363001 Vivi19g01034 1034
19 20535309 20537409 + GSVIVT01020362001 Vivi19g01035 1035
19 20583944 20587021 - GSVIVT01020361001 Vivi19g01036 1036
19 20593527 20595940 - GSVIVT01020360001 Vivi19g01037 1037
19 20595962 20596458 - GSVIVT01020359001 Vivi19g01038 1038
19 20596644 20609026 - GSVIVT01020358001 Vivi19g01039 1039
19 20683310 20804352 - GSVIVT01020355001 Vivi19g01040 1040
19 20810625 20819467 - GSVIVT01020354001 Vivi19g01041 1041
19 20862597 20865868 + GSVIVT01020353001 Vivi19g01042 1042
19 20911181 20912549 - GSVIVT01020352001 Vivi19g01043 1043
       
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