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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
Vivi1g00051 Arla4g01962 Armi3g00280 Sain4g00790 Ceso4g04253 Cati7g00456 Ccar13g00309 Cien3g02851 Cich2g01184 Lssa8g01706 Laca8g01418 Tako5g02564 Tamo5g03369 Pslu5g12953 Lomi3g01862 Lomi4g01635 Enbr1g05978 Ecan1g02753 Soca1g02962 . . Aary9g02684 Aary17g00893 Aann5g04664 . Chmo16g03264 Chmo17g03407 Chmo18g02899 Chla5g04182 Chna6g01817 . Pdy1g05470 Cobi2g00624 Hean8g00400 Bial8g00361 Bial20g00126 Dapi18g02915 Dapi2g03741 . . . Amtr09g02805 . Smso21g00501 Taer8g02253 Fro18g01561 . Ftr1g02451 Fra1g01590 Fli5g00495 . . Cobi12g00185 Hean12g01059 Bial1g00167 Bial13g00219 Dapi8g00201 Dapi24g00157 . . . . Smso5g02214 Smso26g02843 . . . . . .
Vivi1g00052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00059 Arla4g01968 Armi3g00277 Sain4g00796 . Cati7g00451 . . . . . . . Pslu5g12963 Lomi3g01855 Lomi4g01640 . Ecan1g02760 Soca1g02955 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00060 Arla4g01969 Armi3g00276 Sain4g00797 . Cati7g00449 Ccar13g00304 Cien3g02836 . Lssa8g01717 . . . Pslu5g12964 Lomi3g01854 Lomi4g01641 . Ecan1g02762 . Glco1g01679 . . . . . Chmo16g03275 Chmo17g03424 Chmo18g02916 Chla5g04191 Chna6g01810 Cind2g04053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
5 146277113 146280939 + chr5g0331701 Aann5g04664 4664
8 43841565 43846177 + chr8g1064401 Aann8g00789 789
4 194651925 194657609 - Aargg4g28920.1 Aary4g02892 2892
9 158527450 158531010 - Aargg9g26840.1 Aary9g02684 2684
12 194040558 194044914 - Aargg12g28840.1 Aary12g02884 2884
17 79490040 79494870 - Aargg17g08930.1 Aary17g00893 893
9 74136570 74141034 + AtrifAMIRv0_Chr09g0599901 Amtr09g02805 2805
4 105510719 105514551 - evm.model.000240F.44 Arla4g01962 1962
4 105628945 105631608 + evm.model.000240F.37 Arla4g01968 1968
4 105645918 105655783 - evm.model.000240F.36 Arla4g01969 1969
5 5299615 5301357 - evm.model.000113F.252 Arla5g00257 257
5 5381568 5385097 + evm.model.000113F.255 Arla5g00260 260
14 11421624 11431501 - evm.model.000197F.76 Arla14g00232 232
3 6053053 6057041 + AmiAMIRv0_Chr03g0092091 Armi3g00276 276
3 6069135 6070595 - AmiAMIRv0_Chr03g0092101 Armi3g00277 277
3 6144262 6147492 + AmiAMIRv0_Chr03g0092131 Armi3g00280 280
13 65891713 65901239 + AmiAMIRv0_Chr13g0395761 Armi13g01511 1511
4 58191619 58192666 + AtridAMIRv0_Chr04g0461211 Artr4g01866 1866
1 1684953 1690009 + g146484.t1 Bial1g00167 167
8 4010881 4014077 + g30784.t1 Bial8g00361 361
13 2469331 2476274 + g63998.t1 Bial13g00219 219
20 1436282 1440337 + g139555.t1 Bial20g00126 126
3 37483534 37491569 + CtAH03T0122600.1 Cati3g01684 1684
4 89509273 89513752 - CtAH04T0236000.1 Cati4g03134 3134
7 4185449 4195914 + CtAH07T0033400.1 Cati7g00449 449
7 4205113 4206660 - CtAH07T0033500.1 Cati7g00451 451
7 4263639 4268137 + CtAH07T0034000.1 Cati7g00456 456
12 2190431 2191783 - gnl|WGS:LEKV|Ccrd_000179.mRNA.1_mrna Ccar12g00175 175
12 2218415 2222320 + gnl|WGS:LEKV|Ccrd_000182.mRNA.1_mrna Ccar12g00178 178
13 3628887 3635653 + gnl|WGS:LEKV|Ccrd_016185.mRNA.1_mrna Ccar13g00304 304
13 3709582 3713191 + gnl|WGS:LEKV|Ccrd_016190.mRNA.1_mrna Ccar13g00309 309
2 104878765 104881670 - >KAJ9563858.1 Ceso2g04383 4383
4 95706947 95709031 - >KAJ9554192.1 Ceso4g04253 4253
5 179204651 179207132 - ClaG1_Chr05g0338921 Chla5g04182 4182
5 179778313 179792266 - ClaG1_Chr05g0339011 Chla5g04191 4191
5 111273133 111292956 + evm.model.scaffold_1519.227 Chmo5g01705 1705
16 213446888 213448926 - evm.model.scaffold_226.15 Chmo16g03264 3264
16 214684654 214695728 - evm.model.scaffold_1509.80 Chmo16g03275 3275
17 231476389 231478478 - evm.model.scaffold_1419.147 Chmo17g03407 3407
17 232520642 232529957 - evm.model.scaffold_1419.194 Chmo17g03424 3424
18 234348671 234350702 - evm.model.scaffold_6071.26 Chmo18g02899 2899
18 235204234 235218415 - evm.model.scaffold_611.5 Chmo18g02916 2916
4 177792641 177793574 - Cn0959860 Chna4g02446 2446
6 112560976 112564013 + Cn0690750 Chna6g01810 1810
6 113340035 113342255 + Cn0690640 Chna6g01817 1817
2 39619018 39621575 - KAI3779132.1 Cich2g01184 1184
3 6947052 6948831 + KAI3763689.1 Cich3g00249 249
3 75550650 75552812 + KAI3516576.1 Cien3g02836 2836
3 75750366 75755333 + KAI3516591.1 Cien3g02851 2851
8 4557422 4559845 + KAI3497800.1 Cien8g00217 217
2 116069892 116072797 + D.indicum_Contig494_G00008.t1 Cind2g04053 4053
2 7737294 7741018 - h2tg000034l_1.g20730.t1 Cobi2g00624 624
12 1841893 1844597 + h2tg000030l_1.g18129.t1 Cobi12g00185 185
2 141430879 141434501 - h2tg000149l.g52068.t1 Dapi2g03741 3741
8 3531343 3534195 + h1tg000025l.g56602.t1 Dapi8g00201 201
18 131389658 131393226 - h1tg000021l.g26566.t1 Dapi18g02915 2915
24 2173892 2176915 + h1tg000067l.g106450.t1 Dapi24g00157 157
1 41849421 41852583 - XM_043781783.1 Ecan1g02753 2753
1 41907554 41909285 + XM_043757718.1 Ecan1g02760 2760
1 41924253 41927796 - XM_043755716.1 Ecan1g02762 2762
4 31378170 31380978 - XM_043767891.1 Ecan4g02026 2026
4 31406432 31408033 + XM_043771260.1 Ecan4g02029 2029
1 182195666 182198045 - evm.model.ctg228.6 Enbr1g05978 5978
4 98274549 98285705 - evm.model.ctg771.4 Enbr4g02835 2835
5 8356327 8358905 - FliAMIRv0_Chr05g0125161 Fli5g00495 495
1 76667340 76670184 + FraAMIRv0_Chr01g0015871 Fra1g01590 1590
18 22511072 22514149 + FroAMIRv0_Chr18g0343201 Fro18g01561 1561
1 85383674 85385407 + FtrAMIRv0_Chr01g0024481 Ftr1g02451 2451
1 83873492 83876122 - GcoAMIRv0_Chr01g0016791 Glco1g01679 1679
6 579640515 579644475 - GcoAMIRv0_Chr06g0439851 Glco6g05886 5886
8 6821126 6827185 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr08g0322171 Hean8g00400 400
12 22778613 22784300 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr12g0532691 Hean12g01059 1059
4 12130903 12133441 + CAI9278443.1 Laca4g00295 295
8 49219939 49223198 - CAI9296971.1 Laca8g01418 1418
3 15758285 15760646 + LmiAMIRv0_Chr03g0110421 Lomi3g01854 1854
3 15773247 15774680 - LmiAMIRv0_Chr03g0110431 Lomi3g01855 1855
3 15822763 15826233 + LmiAMIRv0_Chr03g0110501 Lomi3g01862 1862
4 24411431 24414576 - LmiAMIRv0_Chr04g0141051 Lomi4g01635 1635
4 24459307 24460740 + LmiAMIRv0_Chr04g0141101 Lomi4g01640 1640
4 24474810 24477229 - LmiAMIRv0_Chr04g0141111 Lomi4g01641 1641
8 13488082 13490809 + LmiAMIRv0_Chr08g0253851 Lomi8g01363 1363
10 12898268 12899701 - LmiAMIRv0_Chr10g0305181 Lomi10g01526 1526
10 12918165 12920914 + LmiAMIRv0_Chr10g0305211 Lomi10g01529 1529
4 20073686 20075968 + >KAJ0212733.1 Lssa4g00459 459
8 70561986 70564619 - >KAJ0191683.1 Lssa8g01706 1706
8 71013754 71021995 - >KAJ0193448.1 Lssa8g01717 1717
19 57072716 57088713 - KAD2393621.1 Mimi19g00924 924
1 115758891 115762137 + PdyAMIRv0_Chr01g0054661 Pdy1g05470 5470
2 3961711 3964808 - PdyAMIRv0_Chr02g0058261 Pdy2g00209 209
4 21746069 21747520 - PluAMIRv0_Chr04g0612811 Pslu4g03328 3328
4 21774159 21778251 + PluAMIRv0_Chr04g0612851 Pslu4g03332 3332
5 96054258 96057812 - PluAMIRv0_Chr05g0878101 Pslu5g12953 12953
5 96123584 96125008 + PluAMIRv0_Chr05g0878201 Pslu5g12963 12963
5 96138554 96141027 - PluAMIRv0_Chr05g0878211 Pslu5g12964 12964
4 22096901 22100434 - SinAMIRv0_Chr04g0091241 Sain4g00790 790
4 22387386 22388861 + SinAMIRv0_Chr04g0091301 Sain4g00796 796
4 22437420 22439992 - SinAMIRv0_Chr04g0091311 Sain4g00797 797
5 27671453 27689522 - SinAMIRv0_Chr05g0121161 Sain5g00437 437
9 215774370 215775809 - SinAMIRv0_Chr09g0250041 Sain9g04110 4110
9 215866854 215870220 + SinAMIRv0_Chr09g0250081 Sain9g04114 4114
5 110164202 110169608 - KAI3816634.1 Smso5g02214 2214
21 5086015 5088591 - KAI3730707.1 Smso21g00501 501
26 63158423 63161837 - KAI3696328.1 Smso26g02843 2843
1 32920231 32922711 - transfrag2497.t01 Soca1g02955 2955
1 33055164 33058254 + transfrag2505.t01 Soca1g02962 2962
9 21716299 21717750 - augustus54003.t01 Soca9g01926 1926
9 21776507 21779602 + transfrag2014.t01 Soca9g01929 1929
5 7568434 7572505 + Streb.5G002980.1 Stre5g00298 298
8 62703862 62706809 + >KAK1416010.1 Taer8g02253 2253
5 88804042 88806587 + TkA05G357930.1 Tako5g02564 2564
3 105815734 105820759 - TbA03G004360.1 Tamo3g05012 5012
5 78365918 78369955 + TbA05G097010.1 Tamo5g03369 3369
1 563211 566736 - GSVIVT01012207001 Vivi1g00051 51
1 572047 573055 + GSVIVT01012206001 Vivi1g00052 52
1 573526 579404 - GSVIVT01012205001 Vivi1g00053 53
1 586453 588903 + GSVIVT01012203001 Vivi1g00054 54
1 590869 593407 + GSVIVT01012201001 Vivi1g00055 55
1 593578 596330 - GSVIVT01012200001 Vivi1g00056 56
1 599213 602915 + GSVIVT01012199001 Vivi1g00057 57
1 605267 607892 + GSVIVT01012198001 Vivi1g00058 58
1 609375 618213 + GSVIVT01012197001 Vivi1g00059 59
1 628682 633595 - GSVIVT01012196001 Vivi1g00060 60
       
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