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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
Vivi1g00131 Arla3g01145 Armi4g01960 Sain11g02893 Ceso7g01795 Cati8g03077 . Cien2g00945 Cich6g02692 Lssa2g01906 Laca2g01470 Tako2g04288 Tamo2g03624 Pslu4g03112 . Lomi10g01431 . Ecan6g01219 . Glco1g04074 Artr7g04460 Aary2g00915 Aary10g03359 Aann7g00707 Chma2g02592 . . . Chla8g04811 Chna9g02721 Cind7g01838 Pdy8g01454 . . . . . . . . . . . . . . . . . . . . Cobi9g01827 Hean14g01761 Bial7g01013 . . . . . . Amtr01g09447 Smso11g01334 Smso12g01726 Taer10g01807 Fro15g01054 . . . Fli6g00939
Vivi1g00132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00134 Arla3g01146 Armi4g01961 Sain11g02892 Ceso7g01794 Cati8g03075 . . . Lssa2g01907 Laca2g01471 Tako2g04289 Tamo2g03628 Pslu4g03111 . Lomi10g01430 . Ecan6g01220 . Glco1g04073 Artr7g04468 Aary2g00916 Aary10g03361 Aann7g00710 Chma2g02234 Chmo7g01466 Chmo8g01789 . Chla8g04810 Chna9g02720 Cind7g01839 Pdy8g01455 . . . . . . . . . . . . . . . . . . . . Cobi9g01828 Hean14g01762 . . Dapi3g01453 Dapi19g01572 . . . Amtr01g09446 Smso11g01335 Smso12g01723 . . . . . .
Vivi1g00135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
7 44911235 44921583 - chr7g1164941 Aann7g00707 707
7 45091382 45106939 - chr7g1165061 Aann7g00710 710
2 77613355 77618742 - Aargg2g09150.1 Aary2g00915 915
2 77817668 77823091 - Aargg2g09160.1 Aary2g00916 916
10 190555485 190563745 - Aargg10g33590.1 Aary10g03359 3359
10 190722575 190730904 - Aargg10g33610.1 Aary10g03361 3361
1 221486722 221491867 + AtrifAMIRv0_Chr01g0094461 Amtr01g09446 9446
1 221497483 221504642 + AtrifAMIRv0_Chr01g0094471 Amtr01g09447 9447
3 79228914 79239929 - evm.model.000025F.217 Arla3g01145 1145
3 79251761 79259544 - evm.model.000025F.218 Arla3g01146 1146
14 2560679 2571239 - evm.model.000059F.33 Arla14g00084 84
14 6934624 6959519 + evm.model.000059F.219 Arla14g00169 169
4 86788610 86797875 - AmiAMIRv0_Chr04g0156231 Armi4g01960 1960
4 86811558 86818611 - AmiAMIRv0_Chr04g0156241 Armi4g01961 1961
13 71109918 71115020 - AmiAMIRv0_Chr13g0396931 Armi13g01628 1628
13 75230038 75239618 + AmiAMIRv0_Chr13g0398191 Armi13g01754 1754
7 171855008 171863038 - AtridAMIRv0_Chr07g0872931 Artr7g04460 4460
7 172105758 172111944 - AtridAMIRv0_Chr07g0873011 Artr7g04468 4468
7 41233336 41241906 - g95617.t1 Bial7g01013 1013
8 32234857 32240470 + CtAH08T0207400.1 Cati8g03075 3075
8 32242450 32255249 + CtAH08T0207500.1 Cati8g03077 3077
12 2056527 2065252 - CtAH12T0011400.1 Cati12g00152 152
12 6041137 6055454 + CtAH12T0025200.1 Cati12g00319 319
3 65746506 65755654 + >KAJ9557589.1 Ceso3g03006 3006
7 29548157 29555330 + >KAJ9541304.1 Ceso7g01794 1794
7 29558732 29566885 + >KAJ9541303.1 Ceso7g01795 1795
8 161767358 161773843 + ClaG1_Chr08g0560501 Chla8g04810 4810
8 161828238 161836236 + ClaG1_Chr08g0560511 Chla8g04811 4811
2 88441813 88443945 - CmaNakai_Chr02g0165471 Chma2g02234 2234
2 98385509 98393486 + CmaNakai_Chr02g0169051 Chma2g02592 2592
4 135907658 135912190 + evm.model.scaffold_11345.59 Chmo4g02006 2006
5 132459166 132463729 + evm.model.scaffold_8229.143 Chmo5g01880 1880
7 120973645 120979738 - evm.model.scaffold_9203.46 Chmo7g01466 1466
8 128844241 128863253 - evm.model.scaffold_7880.13 Chmo8g01789 1789
4 158014863 158019429 - Cn0080880 Chna4g02298 2298
9 141865608 141872011 + Cn0994890 Chna9g02720 2720
9 141974785 141986286 + Cn0994900 Chna9g02721 2721
2 122707704 122712001 + KAI3781207.1 Cich2g03259 3259
6 45708551 45716580 + KAI3723178.1 Cich6g02692 2692
2 48738637 48746523 - KAI3518860.1 Cien2g00945 945
3 26394589 26398691 - KAI3515122.1 Cien3g01382 1382
4 154809147 154813703 + D.indicum_Contig1042_G00001.t1 Cind4g00056 56
7 152919876 152928883 + D.indicum_Contig22_G00140.t1 Cind7g01838 1838
7 152865989 152871920 + D.indicum_Contig22_G00141.t1 Cind7g01839 1839
9 62501313 62508400 - h2tg000008l_1.g41268.t1 Cobi9g01827 1827
9 62511268 62515873 - h2tg000008l_1.g41269.t1 Cobi9g01828 1828
3 29798485 29803158 + h2tg000226l.g72894.t1 Dapi3g01453 1453
19 28152308 28157232 + h2tg000072l.g15157.t1 Dapi19g01572 1572
2 11112034 11116571 - XM_043762241.1 Ecan2g00889 889
6 23171589 23182560 - XM_043775491.1 Ecan6g01219 1219
6 23194379 23200561 - XM_043779294.1 Ecan6g01220 1220
2 74501930 74506364 + evm.model.ctg4506.2 Enbr2g02309 2309
6 61678188 61685013 - FliAMIRv0_Chr06g0154991 Fli6g00939 939
15 24666068 24672857 - FroAMIRv0_Chr15g0271591 Fro15g01054 1054
1 281509822 281521269 + GcoAMIRv0_Chr01g0040731 Glco1g04073 4073
1 281801381 281809411 + GcoAMIRv0_Chr01g0040741 Glco1g04074 4074
14 105590382 105600376 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0641001 Hean14g01761 1761
14 105653978 105661018 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0641011 Hean14g01762 1762
2 99582064 99589579 - CAI9271795.1 Laca2g01470 1470
2 99649361 99655016 - CAI9271796.1 Laca2g01471 1471
8 138659050 138663289 - CAI9299072.1 Laca8g03405 3405
8 141226513 141231519 + CAI9299147.1 Laca8g03479 3479
9 21330244 21335864 + LmiAMIRv0_Chr09g0277641 Lomi9g01113 1113
10 12068173 12073785 + LmiAMIRv0_Chr10g0304221 Lomi10g01430 1430
10 12077394 12084197 + LmiAMIRv0_Chr10g0304231 Lomi10g01431 1431
12 13631234 13637087 - LmiAMIRv0_Chr12g0358111 Lomi12g01112 1112
2 144104083 144113843 - >KAJ0220489.1 Lssa2g01906 1906
2 144169134 144174769 - >KAJ0220499.1 Lssa2g01907 1907
8 190420839 190425543 - >KAJ0192243.1 Lssa8g04045 4045
8 194855284 194860216 + >KAJ0189951.1 Lssa8g04155 4155
1 80787340 80794113 - KAD7478296.1 Mimi1g01432 1432
1 80842559 80847564 - KAD7478298.1 Mimi1g01434 1434
6 54172308 54176526 + PdyAMIRv0_Chr06g0245341 Pdy6g01827 1827
8 47084811 47091691 - PdyAMIRv0_Chr08g0307771 Pdy8g01454 1454
8 47100614 47104276 - PdyAMIRv0_Chr08g0307781 Pdy8g01455 1455
4 20273990 20278869 + PluAMIRv0_Chr04g0610641 Pslu4g03111 3111
4 20281962 20288709 + PluAMIRv0_Chr04g0610651 Pslu4g03112 3112
6 35634666 35639634 - PluAMIRv0_Chr06g0967871 Pslu6g05150 5150
5 5234894 5242011 - SinAMIRv0_Chr05g0117971 Sain5g00118 118
5 13423322 13427756 + SinAMIRv0_Chr05g0119761 Sain5g00297 297
11 76658834 76664509 + SinAMIRv0_Chr11g0336911 Sain11g02892 2892
11 76667252 76674365 + SinAMIRv0_Chr11g0336921 Sain11g02893 2893
11 72461039 72467746 - KAI3798452.1 Smso11g01334 1334
11 72484790 72489949 - KAI3798453.1 Smso11g01335 1335
12 21009322 21014090 + KAI3794672.1 Smso12g01723 1723
12 21021057 21027960 + KAI3794675.1 Smso12g01726 1726
7 27501564 27507410 - augustus25237.t01 Soca7g01375 1375
1 19351188 19354473 - Streb.1G009440.1 Stre1g00944 944
1 19358043 19363732 - Streb.1G009460.1 Stre1g00946 946
10 14003586 14011999 + >KAK1410859.1 Taer10g01807 1807
2 112974009 112983149 - TkA02G444650.1 Tako2g04288 4288
2 112991311 112996326 - TkA02G444690.1 Tako2g04289 4289
5 14192470 14195811 - TkA05G053360.1 Tako5g00837 837
5 15450294 15451703 + TkA05G058020.1 Tako5g00918 918
2 82193685 82194353 - TbA02G099860.1 Tamo2g03624 3624
2 82203409 82207888 - TbA02G099900.1 Tamo2g03628 3628
5 22075481 22079034 - TbA05G026900.1 Tamo5g01595 1595
5 23071282 23075695 + TbA05G028160.1 Tamo5g01668 1668
1 1272689 1293994 - GSVIVT01012117001 Vivi1g00131 131
1 1303636 1315494 + GSVIVT01012116001 Vivi1g00132 132
1 1315728 1316069 - GSVIVT01012115001 Vivi1g00133 133
1 1316104 1326207 - GSVIVT01012114001 Vivi1g00134 134
1 1336618 1340485 + GSVIVT01012113001 Vivi1g00135 135
1 1340900 1343491 - GSVIVT01012112001 Vivi1g00136 136
1 1343520 1344663 - GSVIVT01012111001 Vivi1g00137 137
1 1353272 1355920 + GSVIVT01012110001 Vivi1g00138 138
1 1360444 1369503 + GSVIVT01012108001 Vivi1g00139 139
1 1386743 1417789 + GSVIVT01012107001 Vivi1g00140 140
       
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