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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
Vivi19g01104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01109 Arla1g00094 Armi1g00109 Sain12g00107 Ceso2g03224 Cati3g00146 Ccar2g02307 Cien5g03549 Cich4g04864 Lssa7g03797 Laca7g03097 Tako4g03074 Tamo4g02139 Pslu1g20708 . Lomi2g04179 . Ecan3g00185 Soca5g05352 Glco3g01585 Artr3g10737 . Aary13g03114 Aann4g00711 . . . . . Chna2g01000 Cind3g02017 . . . . . . . . . . . . . . . . . . . . . Cobi4g02789 Hean11g01519 Bial4g03007 Bial16g02438 Dapi7g00570 Dapi23g00590 . Hetu31g00977 Hetu33g01095 Amtr02g06554 Smso7g00508 Smso29g00658 . . . . . .
Vivi19g01110 Arla1g00093 Armi1g00108 Sain12g00106 Ceso2g03223 Cati3g00145 Ccar2g02308 Cien5g03548 Cich4g04861 Lssa7g03791 Laca7g03096 Tako4g03071 Tamo4g02137 Pslu1g20709 . Lomi2g04180 Enbr6g03570 Ecan3g00186 Soca5g05353 Glco3g01581 Artr3g10742 . Aary13g03115 Aann4g00712 Chma7g07193 . . . Chla6g05490 Chna2g00999 Cind3g02018 Pdy4g00863 . . . . . . . . . . . . . . . . . . . . Cobi4g02790 Hean11g01526 Bial4g03008 Bial16g02439 Dapi7g00569 Dapi23g00588 . Hetu31g00973 Hetu33g01092 Amtr02g06555 Smso7g00506 Smso29g00657 Taer1g05935 Fro12g02153 Fso2g00468 Ftr4g03461 Fra11g02330 Fli1g00530
Vivi19g01111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g01113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 47742727 47750300 - chr4g0764571 Aann4g00711 711
4 47801397 47804518 - chr4g0764601 Aann4g00712 712
13 183830169 183838571 - Aargg13g31140.1 Aary13g03114 3114
13 183890030 183891920 - Aargg13g31150.1 Aary13g03115 3115
2 118880802 118887195 - AtrifAMIRv0_Chr02g0161501 Amtr02g06554 6554
2 118953039 118954838 - AtrifAMIRv0_Chr02g0161511 Amtr02g06555 6555
1 1686707 1688653 + evm.model.000012F.116 Arla1g00093 93
1 1728043 1737955 + evm.model.000012F.117 Arla1g00094 94
1 1649750 1651260 + AmiAMIRv0_Chr01g0001081 Armi1g00108 108
1 1686551 1697516 + AmiAMIRv0_Chr01g0001091 Armi1g00109 109
3 362208044 362214508 - AtridAMIRv0_Chr03g0414731 Artr3g10737 10737
3 362377246 362379312 - AtridAMIRv0_Chr03g0414781 Artr3g10742 10742
4 69009207 69013557 - g55998.t1 Bial4g03007 3007
4 69038908 69040998 - g55999.t1 Bial4g03008 3008
16 63714521 63718806 - g150144.t1 Bial16g02438 2438
16 63741776 63743911 - g150143.t1 Bial16g02439 2439
3 834346 836941 + CtAH03T0008000.1 Cati3g00145 145
3 856067 867979 + CtAH03T0008100.1 Cati3g00146 146
2 70228612 70239544 - gnl|WGS:LEKV|Ccrd_011358.mRNA.1_mrna Ccar2g02307 2307
2 70255055 70256738 - gnl|WGS:LEKV|Ccrd_011359.mRNA.1_mrna Ccar2g02308 2308
2 81167734 81169685 + >KAJ9562602.1 Ceso2g03223 3223
2 81193829 81205545 + >KAJ9562603.1 Ceso2g03224 3224
6 216280162 216282300 + ClaG1_Chr06g0427371 Chla6g05490 5490
7 246246106 246247963 - CmaNakai_Chr07g0694951 Chma7g07193 7193
2 78060956 78062956 + Cn0814810 Chna2g00999 999
2 78109064 78116078 + Cn0814820 Chna2g01000 1000
4 137440879 137442193 + KAI3753996.1 Cich4g04861 4861
4 137572983 137577348 + KAI3753999.1 Cich4g04864 4864
5 81355952 81357260 + KAI3510068.1 Cien5g03548 3548
5 81407235 81411482 + KAI3510069.1 Cien5g03549 3549
3 309931019 309937871 - D.indicum_Contig21_G00061.t1 Cind3g02017 2017
3 309998831 310000674 - D.indicum_Contig21_G00062.t1 Cind3g02018 2018
4 75432772 75436938 - h2tg000009l_1.g42490.t1 Cobi4g02789 2789
4 75480612 75482641 - h2tg000009l_1.g42489.t1 Cobi4g02790 2790
7 12115058 12116565 + h1tg000030l.g77159.t1 Dapi7g00569 569
7 12176574 12183970 + h1tg000030l.g77160.t1 Dapi7g00570 570
23 12980025 12981642 + h2tg000020l.g165111.t1 Dapi23g00588 588
23 13015667 13025632 + h2tg000020l.g165109.t1 Dapi23g00590 590
3 1907981 1916121 - XM_043766759.1 Ecan3g00185 185
3 1929406 1931671 - XM_043765845.1 Ecan3g00186 186
6 132087702 132089751 + evm.model.ctg8310.1 Enbr6g03570 3570
1 10780413 10781950 + FliAMIRv0_Chr01g0005251 Fli1g00530 530
11 77098882 77100442 - FraAMIRv0_Chr11g0223521 Fra11g02330 2330
12 28995754 28997253 - FroAMIRv0_Chr12g0217011 Fro12g02153 2153
2 6130369 6131855 + FsoAMIRv0_Chr02g0032871 Fso2g00468 468
4 117502699 117504259 - FtrAMIRv0_Chr04g0128951 Ftr4g03461 3461
3 102426659 102428456 + GcoAMIRv0_Chr03g0172101 Glco3g01581 1581
3 102652095 102658834 + GcoAMIRv0_Chr03g0172141 Glco3g01585 1585
11 46350847 46358238 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483771 Hean11g01519 1519
11 46625808 46627917 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0483861 Hean11g01526 1526
31 43128361 43130073 + >Htub.h1tg002121l.g205.t1 Hetu31g00973 973
31 43350392 43357309 + >Htub.h1tg002121l.g209.t1 Hetu31g00977 977
33 45570263 45571995 + >Htub.h1tg001052l.g270.t1 Hetu33g01092 1092
33 45773878 45781693 + >Htub.h1tg001052l.g267.t1 Hetu33g01095 1095
7 145973065 145974780 + CAI9295296.1 Laca7g03096 3096
7 146127273 146132267 + CAI9295297.1 Laca7g03097 3097
2 47374707 47380257 - LmiAMIRv0_Chr02g0087121 Lomi2g04179 4179
2 47387307 47389362 - LmiAMIRv0_Chr02g0087131 Lomi2g04180 4180
7 199313708 199315385 + >KAJ0197540.1 Lssa7g03791 3791
7 199665055 199670160 + >KAJ0195898.1 Lssa7g03797 3797
17 44393209 44394523 + KAD3067133.1 Mimi17g00811 811
17 44849078 44856054 + KAD3067137.1 Mimi17g00815 815
4 15733231 15735900 + PdyAMIRv0_Chr04g0156701 Pdy4g00863 863
1 149414429 149420599 - PluAMIRv0_Chr01g0206171 Pslu1g20708 20708
1 149434900 149436512 - PluAMIRv0_Chr01g0206181 Pslu1g20709 20709
12 1435836 1437210 + SinAMIRv0_Chr12g0356711 Sain12g00106 106
12 1470409 1478249 + SinAMIRv0_Chr12g0356721 Sain12g00107 107
7 8385931 8387193 + KAI3810086.1 Smso7g00506 506
7 8426663 8431813 + KAI3810088.1 Smso7g00508 508
29 9280163 9281366 + KAI3675651.1 Smso29g00657 657
29 9311318 9316109 + KAI3675652.1 Smso29g00658 658
5 73549956 73556772 - transfrag23896.t01 Soca5g05352 5352
5 73586466 73588646 - transfrag23897.t01 Soca5g05353 5353
6 20885701 20887371 + Streb.6G007170.1 Stre6g00717 717
6 20993635 20996033 + Streb.6G007200.1 Stre6g00720 720
1 53506437 53509509 + >KAK1440110.1 Taer1g05935 5935
4 59681300 59683224 + TkA04G235070.1 Tako4g03071 3071
4 59855651 59860264 + TkA04G235600.3 Tako4g03074 3074
4 34855011 34857064 + TbA04G052360.1 Tamo4g02137 2137
4 34890588 34896247 + TbA04G052330.1 Tamo4g02139 2139
19 22233245 22235162 - GSVIVT01020253001 Vivi19g01104 1104
19 22237214 22253133 + GSVIVT01020252001 Vivi19g01105 1105
19 22256470 22257340 + GSVIVT01020250001 Vivi19g01106 1106
19 22260502 22262536 - GSVIVT01020249001 Vivi19g01107 1107
19 22279115 22279775 + GSVIVT01036807001 Vivi19g01108 1108
19 22290729 22301684 - GSVIVT01036806001 Vivi19g01109 1109
19 22323046 22329438 - GSVIVT01036804001 Vivi19g01110 1110
19 22340452 22349741 + GSVIVT01036803001 Vivi19g01111 1111
19 22358835 22361459 + GSVIVT01036802001 Vivi19g01112 1112
19 22379272 22383673 - GSVIVT01036801001 Vivi19g01113 1113
       
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