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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
Vivi19g00944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00945 Arla1g00418 Armi1g00527 Sain12g00469 Ceso2g01382 Cati3g00580 Ccar2g01980 . Cich4g04448 Lssa7g03419 Laca7g02768 Tako4g04013 Tamo4g02925 Pslu1g21421 Lomi1g00277 Lomi2g04381 Enbr6g01734 Ecan3g02123 Soca5g02745 . . Aary5g02826 Aary13g03299 Aann4g01172 . Chmo13g00740 Chmo14g00731 Chmo15g00615 . Chna2g00598 Cind3g03782 Pdy4g00483 . Hean15g03888 Bial24g02237 Bial12g02380 . . Hetu17g02561 Hetu16g02662 . Amtr02g04052 . . . . . . . . Stre9g01617 . Cobi4g03139 Hean11g00728 Bial4g03421 Bial16g02817 Dapi7g00280 Dapi23g00306 Hetu32g00604 Hetu31g00550 Hetu33g00701 . Smso7g00079 Smso29g00086 Taer1g05530 Fro12g02401 . . Fra11g02540 Fli1g00261
Vivi19g00946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00947 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00950 Arla1g00419 Armi1g00528 Sain12g00473 . Cati3g00581 Ccar2g01979 Cien5g03177 Cich4g04447 Lssa7g03418 Laca7g02767 Tako4g04014 Tamo4g02926 Pslu1g21428 Lomi1g00276 . . Ecan3g02121 Soca5g02539 Glco3g01075 . . . Aann4g01175 Chma7g08164 Chmo13g00738 Chmo14g00728 Chmo15g00613 . Chna2g00596 Cind3g05125 Pdy4g00482 . . . . . . . . . . . . . . . . . . . . Cobi4g03140 Hean11g00727 . . . . . . . . . . Taer1g05531 Fro12g02402 . Ftr4g03697 Fra11g02541 Fli1g00260
Vivi19g00951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivi19g00953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
4 62391903 62402410 + chr4g0777551 Aann4g01172 1172
4 62794722 62796178 - chr4g0777871 Aann4g01175 1175
5 170756343 170766859 + Aargg5g28260.1 Aary5g02826 2826
13 197352400 197362326 + Aargg13g32990.1 Aary13g03299 3299
2 80807589 80813050 - AtrifAMIRv0_Chr02g0136481 Amtr02g04052 4052
1 10511979 10527031 + evm.model.000012F.554 Arla1g00418 418
1 10527873 10533414 - evm.model.000012F.555 Arla1g00419 419
8 8420370 8437351 + evm.model.000043F.410 Arla8g00361 361
1 11196505 11211339 + AmiAMIRv0_Chr01g0005271 Armi1g00527 527
1 11233888 11235303 - AmiAMIRv0_Chr01g0005281 Armi1g00528 528
4 78034282 78040197 + g43260.t1 Bial4g03421 3421
12 54151790 54156178 + g35579.t1 Bial12g02380 2380
16 72314419 72320101 + g127383.t1 Bial16g02817 2817
24 53039398 53043794 + g67903.t1 Bial24g02237 2237
3 5993269 6008607 + CtAH03T0040700.1 Cati3g00580 580
3 6021907 6025335 - CtAH03T0040800.1 Cati3g00581 581
7 68229577 68251046 - CtAH07T0233800.2 Cati7g03162 3162
2 66548324 66549745 + gnl|WGS:LEKV|Ccrd_011026.mRNA.1_mrna Ccar2g01979 1979
2 66553676 66567482 - gnl|WGS:LEKV|Ccrd_011027.mRNA.1_mrna Ccar2g01980 1980
17 3068795 3078310 + gnl|WGS:LEKV|Ccrd_019597.mRNA.1_mrna Ccar17g00275 275
2 28225277 28229755 + >KAJ9560691.1 Ceso2g01382 1382
7 279234207 279237692 + CmaNakai_Chr07g0704661 Chma7g08164 8164
13 34978794 34980420 + evm.model.scaffold_597.98 Chmo13g00738 738
13 35141223 35151205 - evm.model.scaffold_597.109 Chmo13g00740 740
14 33223057 33224448 + evm.model.scaffold_489.59 Chmo14g00728 728
14 33492309 33501443 - evm.model.scaffold_489.71 Chmo14g00731 731
15 32372162 32373915 + evm.model.scaffold_1740.137 Chmo15g00613 613
15 32523938 32539248 - evm.model.scaffold_1740.143 Chmo15g00615 615
2 40784423 40785814 + Cn0067830 Chna2g00596 596
2 40909629 40920445 - Cn0067790 Chna2g00598 598
4 130031056 130032480 + KAI3753582.1 Cich4g04447 4447
4 130056278 130061732 - KAI3753583.1 Cich4g04448 4448
5 76736030 76737463 + KAI3509697.1 Cien5g03177 3177
3 336436617 336445666 + D.indicum_Contig415_G00009.t1 Cind3g03782 3782
3 335793123 335794511 - D.indicum_Contig707_G00011.t1 Cind3g05125 5125
4 80941115 80947624 + h2tg000009l_1.g42140.t1 Cobi4g03139 3139
4 80951777 80953111 - h2tg000009l_1.g42139.t1 Cobi4g03140 3140
7 5592189 5605259 - h1tg000030l.g76870.t1 Dapi7g00280 280
23 6230000 6235716 - h2tg000284l.g80739.t1 Dapi23g00306 306
3 32018936 32020528 + XM_043766578.1 Ecan3g02121 2121
3 32022562 32029827 - XM_043766704.1 Ecan3g02123 2123
6 61232811 61240010 - evm.model.ctg5390.6 Enbr6g01734 1734
1 5212780 5214144 + FliAMIRv0_Chr01g0002551 Fli1g00260 260
1 5216989 5227246 - FliAMIRv0_Chr01g0002561 Fli1g00261 261
11 79060023 79064274 + FraAMIRv0_Chr11g0225621 Fra11g02540 2540
11 79066600 79067967 - FraAMIRv0_Chr11g0225631 Fra11g02541 2541
12 31848146 31853431 + FroAMIRv0_Chr12g0219491 Fro12g02401 2401
12 31855817 31857178 - FroAMIRv0_Chr12g0219501 Fro12g02402 2402
4 120890630 120891988 - FtrAMIRv0_Chr04g0131311 Ftr4g03697 3697
3 63982295 63983689 - GcoAMIRv0_Chr03g0167041 Glco3g01075 1075
11 15556964 15558319 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474381 Hean11g00727 727
11 15561477 15573526 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0474391 Hean11g00728 728
15 147632045 147638775 - gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr15g0715941 Hean15g03888 3888
16 143805292 143809500 + >Htub.h1tg002434l.g118.t1 Hetu16g02662 2662
17 135965507 135969720 + >Htub.h1tg000886l.g413.t1 Hetu17g02561 2561
31 20300134 20309111 - >Htub.h1tg001429l.g313.t1 Hetu31g00550 550
32 24411800 24420777 - >Htub.h1tg001952l.g161.t1 Hetu32g00604 604
33 24810621 24819124 - >Htub.h1tg000986l.g372.t1 Hetu33g00701 701
7 132212466 132213650 + CAI9294955.1 Laca7g02767 2767
7 132218618 132221519 - CAI9294956.1 Laca7g02768 2768
1 2324583 2326028 + LmiAMIRv0_Chr01g0002761 Lomi1g00276 276
1 2328740 2334807 - LmiAMIRv0_Chr01g0002771 Lomi1g00277 277
2 49185742 49193025 + LmiAMIRv0_Chr02g0089141 Lomi2g04381 4381
7 179423027 179424454 + >KAJ0197251.1 Lssa7g03418 3418
7 179427631 179432161 - >KAJ0194728.1 Lssa7g03419 3419
17 12550367 12551758 + KAD3066709.1 Mimi17g00387 387
4 8959369 8960823 + PdyAMIRv0_Chr04g0152901 Pdy4g00482 482
4 8978943 8985172 - PdyAMIRv0_Chr04g0152911 Pdy4g00483 483
1 153904484 153911286 + PluAMIRv0_Chr01g0213271 Pslu1g21421 21421
1 153953574 153955004 - PluAMIRv0_Chr01g0213341 Pslu1g21428 21428
12 10323354 10334515 + SinAMIRv0_Chr12g0360331 Sain12g00469 469
12 10347919 10349334 - SinAMIRv0_Chr12g0360371 Sain12g00473 473
7 1643433 1653115 + KAI3809659.1 Smso7g00079 79
29 1746261 1753052 + KAI3675080.1 Smso29g00086 86
5 27645961 27647385 - augustus16795.t01 Soca5g02539 2539
5 30429233 30437349 + transfrag32063.t01 Soca5g02745 2745
6 10034697 10036280 + Streb.6G003760.1 Stre6g00376 376
9 28541818 28546426 + Streb.9G016170.1 Stre9g01617 1617
1 50559712 50564077 + >KAK1439710.1 Taer1g05530 5530
1 50569810 50571198 - >KAK1439711.1 Taer1g05531 5531
4 90321123 90325779 + TkA04G358450.1 Tako4g04013 4013
4 90327702 90329009 - TkA04G358460.1 Tako4g04014 4014
4 55877888 55883216 + TbA04G027350.1 Tamo4g02925 2925
4 55885565 55886848 - TbA04G027340.1 Tamo4g02926 2926
19 17645200 17647650 + GSVIVT01038080001 Vivi19g00944 944
19 17668878 17700404 - GSVIVT01038082001 Vivi19g00945 945
19 17731446 17757520 + GSVIVT01038085001 Vivi19g00946 946
19 17767658 17774586 - GSVIVT01038086001 Vivi19g00947 947
19 17849972 17876784 - GSVIVT01038087001 Vivi19g00948 948
19 18056453 18061495 + GSVIVT01020514001 Vivi19g00949 949
19 18129430 18130854 - GSVIVT01020511001 Vivi19g00950 950
19 18194905 18198944 + GSVIVT01020509001 Vivi19g00951 951
19 18220089 18220624 - GSVIVT01020508001 Vivi19g00952 952
19 18235216 18236248 - GSVIVT01020507001 Vivi19g00953 953
       
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