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Asteraceae Genomic Research Platform

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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
Vivi1g00121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00124 Arla3g01142 Armi4g01957 Sain11g02896 Ceso7g01800 Cati8g03089 . Cien2g00943 Cich6g02694 Lssa2g01902 Laca2g01465 Tako2g04280 Tamo2g03616 Pslu4g03115 Lomi8g01300 . . Ecan6g01214 . Glco1g04083 Artr7g04448 Aary2g00912 Aary10g03356 Aann7g00701 . . . . . . . Pdy8g01451 . . . . . . . . . . . . . . . . . . . . Cobi9g01823 Hean14g01750 Bial7g01010 . Dapi3g01457 Dapi19g01575 Hetu42g02238 Hetu40g02353 Hetu41g02504 Amtr01g09452 Smso11g01329 Smso12g01732 . . . . . .
Vivi1g00125 Arla3g01144 Armi4g01959 Sain11g02894 Ceso7g01796 Cati8g03078 . . . Lssa2g01905 Laca2g01469 Tako2g04287 Tamo2g03623 Pslu4g03113 Lomi8g01298 Lomi10g01432 . Ecan6g01217 . Glco1g04075 . Aary2g00914 Aary10g03358 Aann7g00706 Chma2g02593 Chmo7g01464 Chmo8g01785 . Chla8g04812 Chna9g02722 Cind7g01837 Pdy8g01453 . . . . . . . . . . . . . . . . . . . . . Hean14g01760 Bial7g01012 . Dapi3g01456 Dapi19g01574 Hetu42g02236 Hetu40g02349 Hetu41g02500 Amtr01g09448 Smso11g01333 Smso12g01727 Taer10g01808 Fro15g01053 Fso18g01630 . Fra12g01592 Fli6g00938
Vivi1g00126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi1g00130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
7 44814777 44818768 - chr7g1164821 Aann7g00701 701
7 44905847 44911233 + chr7g1164931 Aann7g00706 706
2 77404168 77409184 - Aargg2g09120.1 Aary2g00912 912
2 77605918 77610374 + Aargg2g09140.1 Aary2g00914 914
10 190360820 190364181 - Aargg10g33560.1 Aary10g03356 3356
10 190550035 190555189 + Aargg10g33580.1 Aary10g03358 3358
1 221505164 221508883 - AtrifAMIRv0_Chr01g0094481 Amtr01g09448 9448
1 221585868 221588749 + AtrifAMIRv0_Chr01g0094521 Amtr01g09452 9452
3 79143287 79145605 - evm.model.000025F.212 Arla3g01142 1142
3 79216793 79228867 + evm.model.000025F.216 Arla3g01144 1144
4 86695876 86697894 - AmiAMIRv0_Chr04g0156201 Armi4g01957 1957
4 86777253 86788186 + AmiAMIRv0_Chr04g0156221 Armi4g01959 1959
7 171204662 171208805 - AtridAMIRv0_Chr07g0872811 Artr7g04448 4448
7 41186380 41188893 - g95614.t1 Bial7g01010 1010
7 41229545 41232901 + g95616.t1 Bial7g01012 1012
8 32251971 32261957 - CtAH08T0207600.1 Cati8g03078 3078
8 32351280 32354490 + CtAH08T0208000.1 Cati8g03089 3089
7 29567251 29572771 - >KAJ9541309.1 Ceso7g01796 1796
7 29661570 29663698 + >KAJ9541341.1 Ceso7g01800 1800
8 161836536 161841255 - ClaG1_Chr08g0560521 Chla8g04812 4812
2 98393990 98398416 - CmaNakai_Chr02g0169061 Chma2g02593 2593
7 120920835 120925778 + evm.model.scaffold_9203.48 Chmo7g01464 1464
8 128690518 128693008 + evm.model.scaffold_7880.8 Chmo8g01785 1785
9 141986803 141991247 - Cn0994910 Chna9g02722 2722
6 45784589 45787183 + KAI3723180.1 Cich6g02694 2694
2 48676608 48679188 - KAI3518858.1 Cien2g00943 943
7 152929400 152946370 - D.indicum_Contig22_G00139.t1 Cind7g01837 1837
9 62424221 62425890 - h2tg000008l_1.g41264.t1 Cobi9g01823 1823
3 29871816 29875254 - h2tg000226l.g72897.t1 Dapi3g01456 1456
3 29928791 29931224 + h2tg000226l.g72898.t1 Dapi3g01457 1457
19 28198709 28202454 - h2tg000072l.g15155.t1 Dapi19g01574 1574
19 28264259 28266688 + h2tg000072l.g15154.t1 Dapi19g01575 1575
6 23121713 23128719 - XM_043778934.1 Ecan6g01214 1214
6 23166212 23170750 + XM_043775996.1 Ecan6g01217 1217
6 61674225 61677608 + FliAMIRv0_Chr06g0154981 Fli6g00938 938
12 19952609 19955994 - FraAMIRv0_Chr12g0244171 Fra12g01592 1592
15 24662030 24665394 + FroAMIRv0_Chr15g0271581 Fro15g01053 1053
18 61487082 61490468 + FsoAMIRv0_Chr18g0450931 Fso18g01630 1630
1 281810295 281814898 - GcoAMIRv0_Chr01g0040751 Glco1g04075 4075
1 283263019 283265991 + GcoAMIRv0_Chr01g0040831 Glco1g04083 4083
14 105263719 105267855 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0640881 Hean14g01750 1750
14 105585508 105590277 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr14g0640991 Hean14g01760 1760
40 88277691 88281616 - >Htub.h1tg000723l.g13.t1 Hetu40g02349 2349
40 88575038 88579104 + >Htub.h1tg000723l.g17.t1 Hetu40g02353 2353
41 97763405 97767327 - >Htub.h1tg000457l.g230.t1 Hetu41g02500 2500
41 98123593 98127217 + >Htub.h1tg000457l.g234.t1 Hetu41g02504 2504
42 94143733 94147631 - >Htub.h1tg002359l.g375.t1 Hetu42g02236 2236
42 94377707 94381313 + >Htub.h1tg002359l.g377.t1 Hetu42g02238 2238
2 99304877 99308200 + CAI9271790.1 Laca2g01465 1465
2 99577113 99581898 + CAI9271794.1 Laca2g01469 1469
8 12635474 12639321 - LmiAMIRv0_Chr08g0253201 Lomi8g01298 1298
8 12654499 12657631 + LmiAMIRv0_Chr08g0253221 Lomi8g01300 1300
10 12084679 12088506 - LmiAMIRv0_Chr10g0304241 Lomi10g01432 1432
2 143848176 143849404 + >KAJ0222411.1 Lssa2g01902 1902
2 144099421 144104114 + >KAJ0221669.1 Lssa2g01905 1905
1 80703635 80708399 - KAD7478291.1 Mimi1g01427 1427
1 80783226 80786782 + KAD7478295.1 Mimi1g01431 1431
8 47057623 47060291 - PdyAMIRv0_Chr08g0307741 Pdy8g01451 1451
8 47080631 47084367 + PdyAMIRv0_Chr08g0307761 Pdy8g01453 1453
4 20289223 20292980 - PluAMIRv0_Chr04g0610661 Pslu4g03113 3113
4 20308215 20311418 + PluAMIRv0_Chr04g0610681 Pslu4g03115 3115
11 76674788 76679709 - SinAMIRv0_Chr11g0336931 Sain11g02894 2894
11 76720832 76722763 + SinAMIRv0_Chr11g0336951 Sain11g02896 2896
11 72390775 72393425 - KAI3798447.1 Smso11g01329 1329
11 72457213 72460516 + KAI3798451.1 Smso11g01333 1333
12 21028501 21033247 - KAI3794676.1 Smso12g01727 1727
12 21084821 21087430 + KAI3794681.1 Smso12g01732 1732
1 19307609 19312111 - Streb.1G009390.1 Stre1g00939 939
1 19341965 19345929 + Streb.1G009420.1 Stre1g00942 942
10 14012625 14016025 - >KAK1410860.1 Taer10g01808 1808
2 112836586 112839783 - TkA02G444040.1 Tako2g04280 4280
2 112969919 112974473 + TkA02G444640.1 Tako2g04287 4287
2 82077456 82080459 - TbA02G099740.1 Tamo2g03616 3616
2 82185856 82192534 + TbA02G099850.1 Tamo2g03623 3623
1 1198056 1206373 + GSVIVT01012128001 Vivi1g00121 121
1 1209657 1211146 + GSVIVT01012127001 Vivi1g00122 122
1 1211163 1211513 + GSVIVT01012126001 Vivi1g00123 123
1 1219790 1221546 - GSVIVT01012125001 Vivi1g00124 124
1 1226337 1240986 + GSVIVT01012124001 Vivi1g00125 125
1 1241082 1242515 - GSVIVT01012123001 Vivi1g00126 126
1 1242559 1244964 - GSVIVT01012122001 Vivi1g00127 127
1 1245113 1248294 + GSVIVT01012121001 Vivi1g00128 128
1 1248327 1254994 - GSVIVT01012120001 Vivi1g00129 129
1 1256060 1261111 - GSVIVT01012119001 Vivi1g00130 130
       
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