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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
Vivi19g00874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00876 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00877 Arla1g00392 Armi1g00480 Sain12g00437 Ceso2g01361 Cati3g00545 Ccar2g01996 Cien5g03194 Cich4g04483 Lssa7g03451 Laca7g02793 Tako4g03980 . . Lomi1g00293 Lomi2g04364 . Ecan3g02148 Soca5g02514 Glco3g01110 Artr3g11601 Aary5g02807 Aary13g03283 Aann4g01145 Chma7g08122 Chmo13g00768 . Chmo15g00640 Chla6g05965 Chna2g00631 . Pdy4g00503 . Hean15g03926 Bial24g02227 Bial12g02370 . . Hetu17g02522 Hetu16g02634 Hetu18g02791 Amtr02g04077 . Smso13g00209 . . . . . . Stre9g01602 . Cobi4g03112 Hean11g00774 Bial4g03408 Bial16g02802 Dapi7g00303 Dapi23g00334 Hetu32g00625 Hetu31g00577 Hetu33g00726 . . Smso29g00064 . Fro12g02386 Fso2g00243 Ftr4g03685 Fra11g02525 Fli1g00279
Vivi19g00878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00880 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00882 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 71879421 71888335 - chr1g0064741 Aann1g02295 2295
4 61161260 61165029 - chr4g0776601 Aann4g01145 1145
5 167180032 167183325 - Aargg5g28070.1 Aary5g02807 2807
7 216286643 216291290 - Aargg7g25570.1 Aary7g02557 2557
13 194620379 194624236 - Aargg13g32830.1 Aary13g03283 3283
2 81291327 81294030 + AtrifAMIRv0_Chr02g0136731 Amtr02g04077 4077
7 17006294 17009958 - AtrifAMIRv0_Chr07g0463771 Amtr07g01230 1230
1 8837539 8844787 - evm.model.000012F.497 Arla1g00392 392
8 7468621 7474898 + evm.model.000043F.450 Arla8g00345 345
1 9459115 9461671 - AmiAMIRv0_Chr01g0004801 Armi1g00480 480
8 92669764 92675179 - AmiAMIRv0_Chr08g0292821 Armi8g02451 2451
1 54074588 54078286 + AtridAMIRv0_Chr01g0018601 Artr1g01860 1860
3 392700889 392704646 - AtridAMIRv0_Chr03g0423371 Artr3g11601 11601
4 77575308 77578126 - g43247.t1 Bial4g03408 3408
12 54002949 54004428 - g35569.t1 Bial12g02370 2370
16 71825008 71827738 - g127398.t1 Bial16g02802 2802
24 52865174 52866653 - g67893.t1 Bial24g02227 2227
3 5450515 5462230 - CtAH03T0038000.1 Cati3g00545 545
2 66863663 66866507 + gnl|WGS:LEKV|Ccrd_011043.mRNA.1_mrna Ccar2g01996 1996
17 2864414 2871020 + gnl|WGS:LEKV|Ccrd_019585.mRNA.1_mrna Ccar17g00263 263
2 27517938 27520426 - >KAJ9560639.1 Ceso2g01361 1361
4 27895941 27896237 + >KAJ9551525.1 Ceso4g01583 1583
6 240015469 240021035 - ClaG1_Chr06g0432121 Chla6g05965 5965
7 276875823 276878351 - CmaNakai_Chr07g0704241 Chma7g08122 8122
13 37834222 37840171 + evm.model.scaffold_461.90 Chmo13g00768 768
15 35224451 35227415 + evm.model.scaffold_126.91 Chmo15g00640 640
22 294598655 294599050 - evm.model.scaffold_448.496 Chmo22g04883 4883
23 287018722 287023688 - evm.model.scaffold_1107.3 Chmo23g04833 4833
24 291048585 291050686 - evm.model.scaffold_421.313 Chmo24g04837 4837
2 46171589 46175326 + Cn0653190 Chna2g00631 631
5 44084578 44089332 + Cn0367340 Chna5g00894 894
4 130869894 130870874 + KAI3753618.1 Cich4g04483 4483
7 16162365 16166211 + KAI3708227.1 Cich7g00479 479
5 77308430 77309420 + KAI3509714.1 Cien5g03194 3194
1 360368210 360373781 - D.indicum_Contig40_G00056.t1 Cind1g03293 3293
4 80549894 80553344 - h2tg000009l_1.g42167.t1 Cobi4g03112 3112
7 6353798 6355629 + h1tg000030l.g76893.t1 Dapi7g00303 303
12 95827996 95831172 - h2tg000104l.g32321.t1 Dapi12g01344 1344
23 7032135 7033981 + h2tg000284l.g80711.t1 Dapi23g00334 334
3 32324500 32327220 + XM_043766791.1 Ecan3g02148 2148
5 30082123 30086546 - XM_043774863.1 Ecan5g01635 1635
8 20494512 20499134 + evm.model.ctg4863.1 Enbr8g00706 706
1 5571206 5572951 + FliAMIRv0_Chr01g0002741 Fli1g00279 279
4 82601049 82604710 - FliAMIRv0_Chr04g0109591 Fli4g01370 1370
8 9675696 9679343 + FraAMIRv0_Chr08g0144071 Fra8g01008 1008
11 78864967 78866729 - FraAMIRv0_Chr11g0225471 Fra11g02525 2525
9 25499175 25503112 - FroAMIRv0_Chr09g0138141 Fro9g01265 1265
12 31581759 31583534 - FroAMIRv0_Chr12g0219341 Fro12g02386 2386
2 3410431 3412144 + FsoAMIRv0_Chr02g0030621 Fso2g00243 243
11 10693499 10697144 + FsoAMIRv0_Chr11g0268751 Fso11g01047 1047
4 120607251 120608907 - FtrAMIRv0_Chr04g0131191 Ftr4g03685 3685
8 11177955 11181588 + FtrAMIRv0_Chr08g0229871 Ftr8g00910 910
3 67929413 67931284 + GcoAMIRv0_Chr03g0167391 Glco3g01110 1110
7 576637599 576642158 - GcoAMIRv0_Chr07g0516591 Glco7g06874 6874
3 124264981 124269282 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr03g0114101 Hean3g02253 2253
11 17636159 17638395 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474991 Hean11g00774 774
15 150350332 150357728 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0716381 Hean15g03926 3926
7 71473100 71474062 + >Htub.h1tg000735l.g135.t1 Hetu7g01727 1727
8 66659928 66663608 + >Htub.h1tg003382l.g362.t1 Hetu8g01557 1557
16 140247289 140251389 - >Htub.h1tg001448l.g102.t1 Hetu16g02634 2634
17 132614524 132618295 - >Htub.h1tg000886l.g453.t1 Hetu17g02522 2522
18 140463211 140466983 - >Htub.h1tg002759l.g156.t1 Hetu18g02791 2791
31 21813515 21815397 + >Htub.h1tg001429l.g285.t1 Hetu31g00577 577
32 26273849 26275202 + >Htub.h1tg002251l.g267.t1 Hetu32g00625 625
33 27110148 27112029 + >Htub.h1tg001292l.g315.t1 Hetu33g00726 726
7 134643649 134645107 + CAI9294981.1 Laca7g02793 2793
9 132747821 132751890 - CAI9303856.1 Laca9g03263 3263
1 2527018 2528347 + LmiAMIRv0_Chr01g0002931 Lomi1g00293 293
2 48974955 48976222 - LmiAMIRv0_Chr02g0088971 Lomi2g04364 4364
7 182955211 182956594 + >KAJ0197161.1 Lssa7g03451 3451
9 183546182 183549503 - >KAJ0187514.1 Lssa9g03699 3699
14 21030596 21035565 + KAD4179006.1 Mimi14g01069 1069
4 9481984 9483648 + PdyAMIRv0_Chr04g0153101 Pdy4g00503 503
9 41752067 41755548 - PdyAMIRv0_Chr09g0346501 Pdy9g01843 1843
12 9127358 9129444 - SinAMIRv0_Chr12g0360011 Sain12g00437 437
13 131871368 131877010 - SinAMIRv0_Chr13g0398961 Sain13g02340 2340
13 14911632 14919338 + KAI3786466.1 Smso13g00209 209
18 73860302 73863979 - KAI3755710.1 Smso18g01585 1585
29 1320314 1322324 - KAI3675058.1 Smso29g00064 64
5 27153111 27155578 - transfrag11146.t01 Soca5g02514 2514
2 139517624 139523395 - Streb.2G037270.1 Stre2g03727 3727
6 10919689 10921989 + Streb.6G004050.1 Stre6g00405 405
9 28147230 28149454 - Streb.9G016020.1 Stre9g01602 1602
2 29349399 29356767 + TkA02G112160.2 Tako2g01261 1261
4 89561533 89563650 - TkA04G355270.1 Tako4g03980 3980
2 15278634 15282556 + TbA02G017430.1 Tamo2g00834 834
19 14064459 14074173 - GSVIVT01000623001 Vivi19g00874 874
19 14523826 14525599 + GSVIVT01000477001 Vivi19g00875 875
19 14613170 14618041 + GSVIVT01000481001 Vivi19g00876 876
19 14642629 14652553 + GSVIVT01000482001 Vivi19g00877 877
19 14661830 14666329 + GSVIVT01000483001 Vivi19g00878 878
19 14717386 14720889 + GSVIVT01000485001 Vivi19g00879 879
19 14894755 14897484 + GSVIVT01000491001 Vivi19g00880 880
19 14902433 14920509 + GSVIVT01000492001 Vivi19g00881 881
19 14920741 14923863 + GSVIVT01000493001 Vivi19g00882 882
19 14954549 14957701 + GSVIVT01000494001 Vivi19g00883 883
       
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