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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
Vivi19g01084 Arla1g00098 Armi1g00114 Sain12g00113 . Cati3g00152 Ccar2g02303 Cien5g03587 Cich4g04891 Lssa7g03811 Laca7g03114 . Tamo4g02183 Pslu1g20690 . Lomi2g04175 . Ecan3g00176 Soca5g05332 Glco3g01610 Artr3g10701 . . Aann4g00701 Chma7g07221 Chmo13g01176 Chmo14g01074 Chmo15g01019 . Chna2g01010 Cind3g02005 Pdy4g00878 . . . . . . . . . . . . . . . . . . . . Cobi4g02770 Hean11g01493 Bial4g03002 Bial16g02434 Dapi7g00576 Dapi23g00596 Hetu32g01066 Hetu31g01016 Hetu33g01136 Amtr02g06533 Smso7g00523 Smso29g00681 Taer1g05942 Fro12g02148 Fso2g00474 Ftr4g03452 Fra11g02324 Fli1g00538
Vivi19g01085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01086 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01088 Arla1g00097 Armi1g00113 Sain12g00112 Ceso2g03229 Cati3g00149 Ccar2g02304 Cien5g03585 Cich4g04890 Lssa7g03810 Laca7g03113 . Tamo4g02180 Pslu1g20691 . Lomi2g04176 . Ecan3g00177 Soca5g05333 Glco3g01603 . . . Aann4g00705 Chma7g07217 Chmo13g01174 Chmo14g01071 Chmo15g01015 . Chna2g01008 Cind3g02008 Pdy4g00877 . . . . . . . . . . . . . . . . . . . . Cobi4g02771 Hean11g01495 Bial4g03003 Bial16g02435 Dapi7g00575 . Hetu32g01065 . Hetu33g01134 Amtr02g06534 Smso7g00522 Smso29g00680 Taer1g05941 Fro12g02149 Fso2g00473 Ftr4g03455 Fra11g02325 Fli1g00536
Vivi19g01089 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01090 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01091 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 47195132 47201756 - chr4g0764181 Aann4g00701 701
4 47375790 47382817 - chr4g0764321 Aann4g00705 705
2 118349484 118353807 - AtrifAMIRv0_Chr02g0161291 Amtr02g06533 6533
2 118356179 118363865 - AtrifAMIRv0_Chr02g0161301 Amtr02g06534 6534
1 1835210 1842233 + evm.model.000012F.121 Arla1g00097 97
1 1844012 1857246 + evm.model.000012F.122 Arla1g00098 98
8 846284 849904 - evm.model.000077F.404 Arla8g00016 16
1 1821624 1826380 + AmiAMIRv0_Chr01g0001131 Armi1g00113 113
1 1829017 1833219 + AmiAMIRv0_Chr01g0001141 Armi1g00114 114
3 361191886 361195875 - AtridAMIRv0_Chr03g0414371 Artr3g10701 10701
4 68923241 68932458 - g55993.t1 Bial4g03002 3002
4 68935255 68938626 - g55994.t1 Bial4g03003 3003
16 63613067 63622807 - g150148.t1 Bial16g02434 2434
16 63625488 63629416 - g150147.t1 Bial16g02435 2435
3 904015 966106 + CtAH03T0008300.1 Cati3g00149 149
3 969617 976024 + CtAH03T0008500.1 Cati3g00152 152
2 70163763 70168365 - gnl|WGS:LEKV|Ccrd_011354.mRNA.1_mrna Ccar2g02303 2303
2 70173984 70177905 - gnl|WGS:LEKV|Ccrd_011355.mRNA.1_mrna Ccar2g02304 2304
2 81323298 81328186 + >KAJ9562945.1 Ceso2g03229 3229
7 247392825 247393307 + CmaNakai_Chr07g0695191 Chma7g07217 7217
7 247687950 247691825 + CmaNakai_Chr07g0695231 Chma7g07221 7221
13 60416994 60417444 + evm.model.scaffold_10828.7 Chmo13g01174 1174
13 60727386 60731074 + evm.model.scaffold_10828.11 Chmo13g01176 1176
14 54852169 54854496 + evm.model.scaffold_9850.15 Chmo14g01071 1071
14 55289964 55294876 + evm.model.scaffold_9850.31 Chmo14g01074 1074
15 58845394 58851483 + evm.model.scaffold_3415.11 Chmo15g01015 1015
15 59159618 59164571 + evm.model.scaffold_3415.32 Chmo15g01019 1019
2 79298946 79302149 + Cn0814930 Chna2g01008 1008
2 79460934 79466317 + Cn0814960 Chna2g01010 1010
4 138538836 138540799 + KAI3754025.1 Cich4g04890 4890
4 138550526 138553031 + KAI3754026.1 Cich4g04891 4891
5 82116275 82118304 + KAI3510105.1 Cien5g03585 3585
5 82135486 82138005 + KAI3510107.1 Cien5g03587 3587
3 308779064 308783457 - D.indicum_Contig21_G00049.t1 Cind3g02005 2005
3 309096645 309099626 - D.indicum_Contig21_G00052.t1 Cind3g02008 2008
4 75212713 75216206 - h2tg000009l_1.g42509.t1 Cobi4g02770 2770
4 75219204 75222202 - h2tg000009l_1.g42508.t1 Cobi4g02771 2771
7 12298377 12301560 + h1tg000030l.g77165.t1 Dapi7g00575 575
7 12304179 12307119 + h1tg000030l.g77166.t1 Dapi7g00576 576
23 13129840 13138696 + h2tg000020l.g165103.t1 Dapi23g00596 596
3 1709770 1714923 - XM_043765720.1 Ecan3g00176 176
3 1727778 1730967 - XM_043766304.1 Ecan3g00177 177
1 10983256 10987079 + FliAMIRv0_Chr01g0005311 Fli1g00536 536
1 11010367 11014403 + FliAMIRv0_Chr01g0005331 Fli1g00538 538
11 76999069 77002387 - FraAMIRv0_Chr11g0223461 Fra11g02324 2324
11 77011801 77015144 - FraAMIRv0_Chr11g0223471 Fra11g02325 2325
12 28904321 28907685 - FroAMIRv0_Chr12g0216961 Fro12g02148 2148
12 28915361 28918530 - FroAMIRv0_Chr12g0216971 Fro12g02149 2149
2 6251071 6254864 + FsoAMIRv0_Chr02g0032921 Fso2g00473 473
2 6265514 6268849 + FsoAMIRv0_Chr02g0032931 Fso2g00474 474
4 117268759 117271993 - FtrAMIRv0_Chr04g0128861 Ftr4g03452 3452
4 117331355 117334756 - FtrAMIRv0_Chr04g0128891 Ftr4g03455 3455
3 104565637 104569058 + GcoAMIRv0_Chr03g0172321 Glco3g01603 1603
3 105004808 105009729 + GcoAMIRv0_Chr03g0172391 Glco3g01610 1610
11 45252176 45261061 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483431 Hean11g01493 1493
11 45268127 45271760 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483451 Hean11g01495 1495
31 45062898 45070980 + >Htub.h1tg000660l.g370.t1 Hetu31g01016 1016
32 49793150 49796369 + >Htub.h1tg000795l.g314.t1 Hetu32g01065 1065
32 49823650 49831726 + >Htub.h1tg000795l.g315.t1 Hetu32g01066 1066
33 47473268 47474884 + >Htub.h1tg001052l.g227.t1 Hetu33g01134 1134
33 47500224 47508359 + >Htub.h1tg001052l.g225.t1 Hetu33g01136 1136
7 146591564 146595180 + CAI9295314.1 Laca7g03113 3113
7 146612700 146616046 + CAI9295315.1 Laca7g03114 3114
2 47322718 47326131 - LmiAMIRv0_Chr02g0087081 Lomi2g04175 4175
2 47331505 47333870 - LmiAMIRv0_Chr02g0087091 Lomi2g04176 4176
7 200441192 200443313 + >KAJ0194914.1 Lssa7g03810 3810
7 200477961 200481288 + >KAJ0197445.1 Lssa7g03811 3811
17 45258196 45262527 + KAD3067144.1 Mimi17g00822 822
4 16486421 16489336 + PdyAMIRv0_Chr04g0156841 Pdy4g00877 877
4 16497642 16501033 + PdyAMIRv0_Chr04g0156851 Pdy4g00878 878
1 149300197 149303500 - PluAMIRv0_Chr01g0205991 Pslu1g20690 20690
1 149305137 149307637 - PluAMIRv0_Chr01g0206001 Pslu1g20691 20691
12 1615171 1619100 + SinAMIRv0_Chr12g0356771 Sain12g00112 112
12 1644556 1649300 + SinAMIRv0_Chr12g0356781 Sain12g00113 113
7 8651817 8657196 + KAI3810102.1 Smso7g00522 522
7 8657221 8661340 + KAI3810103.1 Smso7g00523 523
29 9888678 9891688 + KAI3675674.1 Smso29g00680 680
29 9895362 9899806 + KAI3675675.1 Smso29g00681 681
5 73294131 73299068 - transfrag23873.t01 Soca5g05332 5332
5 73312673 73316288 - transfrag23874.t01 Soca5g05333 5333
6 21295311 21299536 + Streb.6G007260.1 Stre6g00726 726
1 53574088 53577564 + >KAK1440116.1 Taer1g05941 5941
1 53581562 53584680 + >KAK1440117.1 Taer1g05942 5942
4 35912834 35915851 + TbA04G051040.1 Tamo4g02180 2180
4 35979415 35983092 + TbA04G050980.1 Tamo4g02183 2183
19 21901990 21911420 - GSVIVT01020284001 Vivi19g01084 1084
19 21916038 21918539 - GSVIVT01020282001 Vivi19g01085 1085
19 21920857 21934724 + GSVIVT01020281001 Vivi19g01086 1086
19 21934772 21952939 - GSVIVT01020280001 Vivi19g01087 1087
19 21954863 21962081 - GSVIVT01020279001 Vivi19g01088 1088
19 21964515 21967349 - GSVIVT01020278001 Vivi19g01089 1089
19 22008383 22021510 + GSVIVT01020274001 Vivi19g01090 1090
19 22021511 22044521 - GSVIVT01020273001 Vivi19g01091 1091
19 22065409 22070479 - GSVIVT01020269001 Vivi19g01092 1092
19 22070987 22071806 + GSVIVT01020268001 Vivi19g01093 1093
       
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