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Asteraceae Genomic Research Platform

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Hierarchical alignments with the Arctium lappa genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Asteraceae genomes. We used Arctium lappa as a reference, and by comparing homologous gene locus maps and Ks values between Arctium lappa and other Asteraceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We constructed a 74×31,441 macro-matrices.


Select 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 Stre_2 Mimi_2
Armi1g00222 Sain12g00212 Ceso2g03304 Cati3g00257 Ccar2g02154 . . . . . . Pslu1g06536 Lomi1g00518 Lomi2g04112 Enbr6g02354 Ecan3g00049 Soca5g05114 . . . . . Chma7g07337 Chmo13g01341 . Chmo15g01163 Chla6g05324 Chna2g01164 Cind3g00495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00223 Sain12g00213 . Cati3g00258 Ccar2g02153 . . . . . . Pslu1g06538 . . . Ecan3g00048 Soca5g05113 . . . . . Chma7g07330 Chmo13g01346 . Chmo15g01167 Chla6g05322 Chna2g01166 Cind3g00498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00224 Sain12g00214 Ceso2g03308 Cati3g00259 Ccar2g02152 Cien5g03693 Cich4g04960 Lssa7g03958 Laca7g03198 . . Pslu1g06539 . Lomi2g04111 . Ecan3g00046 Soca5g05111 Glco3g01829 . . . . . Chmo13g01347 . Chmo15g01168 Chla6g05321 Chna2g01167 Cind3g00499 Pdy4g01001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00225 Sain12g00216 Ceso2g03309 Cati3g00260 Ccar2g02151 Cien5g03694 . Lssa7g03959 Laca7g03201 Tako4g03312 . Pslu1g06543 . Lomi2g04110 Enbr6g02207 Ecan3g00045 Soca5g05110 Glco3g01837 . . . . Chma7g07327 Chmo13g01349 . Chmo15g01170 Chla6g05316 Chna2g01170 Cind3g00503 Pdy4g01011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00226 Sain12g00218 Ceso2g03310 Cati3g00262 Ccar2g02150 Cien5g03697 Cich4g04963 Lssa7g03962 Laca7g03204 Tako4g03313 . Pslu1g06550 Lomi1g00519 Lomi2g04109 . Ecan3g00043 Soca5g05109 Glco3g01846 . . . . Chma7g07318 Chmo13g01351 . Chmo15g01172 Chla6g05311 Chna2g01172 Cind3g00505 Pdy4g01019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00227 Sain12g00219 Ceso2g03311 Cati3g00264 Ccar2g02149 Cien5g03699 Cich4g04964 Lssa7g03965 Laca7g03205 Tako4g03314 Tamo4g02302 Pslu1g06551 . . Enbr6g02209 Ecan3g00042 Soca5g05108 Glco3g01848 . . . . Chma7g07317 Chmo13g01352 . Chmo15g01173 Chla6g05310 Chna2g01173 Cind3g00506 Pdy4g01020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00228 . . . . . . . . . . . . . Enbr6g02210 Ecan3g00041 Soca5g05107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00229 Sain12g00220 . Cati3g00265 Ccar2g02148 Cien5g03702 Cich4g04965 Lssa7g03966 Laca7g03206 Tako4g03316 . Pslu1g06552 . . . . . Glco3g01852 . . . . Chma7g07315 Chmo13g01353 . Chmo15g01174 . Chna2g01174 Cind3g00508 Pdy4g01024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Armi1g00232 Sain12g00221 Ceso2g03312 Cati3g00266 Ccar2g02147 . . Lssa7g03967 Laca7g03207 Tako4g03318 . Pslu1g06553 . . Enbr6g02212 Ecan3g00037 Soca5g05105 Glco3g01853 . . . . Chma7g07311 Chmo13g01355 . Chmo15g01176 Chla6g05309 Chna2g01175 Cind3g00509 Pdy4g01028 . Hean6g02854 . . Dapi16g01721 Dapi31g01431 Hetu17g02276 Hetu43g00492 Hetu18g02555 . . Smso26g01706 . . . . . . Stre7g01686 . . . . . . . . . . . . . . . . . . . . .
Armi1g00233 Sain12g00222 Ceso2g03313 Cati3g00267 . Cien5g03704 Cich4g04967 Lssa7g03968 Laca7g03208 Tako4g03319 . Pslu1g06555 . . . . . . . . . . . . . . . . . Pdy4g01030 . . . . . . . . . . . . . . . . . . . . . Hean11g01312 . . . . . . . . . . . . . . . . . .
   
Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
1 4075153 4089476 + AmiAMIRv0_Chr01g0002221 Armi1g00222 222
1 4093217 4093627 + AmiAMIRv0_Chr01g0002231 Armi1g00223 223
1 4097448 4102697 + AmiAMIRv0_Chr01g0002241 Armi1g00224 224
1 4106475 4110754 + AmiAMIRv0_Chr01g0002251 Armi1g00225 225
1 4123311 4127603 + AmiAMIRv0_Chr01g0002261 Armi1g00226 226
1 4133216 4136422 + AmiAMIRv0_Chr01g0002271 Armi1g00227 227
1 4138447 4140955 - AmiAMIRv0_Chr01g0002281 Armi1g00228 228
1 4149997 4150671 + AmiAMIRv0_Chr01g0002291 Armi1g00229 229
1 4175642 4179015 + AmiAMIRv0_Chr01g0002321 Armi1g00232 232
1 4180860 4184654 + AmiAMIRv0_Chr01g0002331 Armi1g00233 233
3 2067548 2082618 + CtAH03T0016800.1 Cati3g00257 257
3 2084242 2099752 + CtAH03T0016900.1 Cati3g00258 258
3 2102647 2109530 + CtAH03T0017000.1 Cati3g00259 259
3 2114660 2125423 + CtAH03T0017100.1 Cati3g00260 260
3 2136708 2141513 + CtAH03T0017200.1 Cati3g00262 262
3 2144069 2148852 + CtAH03T0017400.1 Cati3g00264 264
3 2160044 2160706 + CtAH03T0017500.1 Cati3g00265 265
3 2170652 2176777 + CtAH03T0017600.1 Cati3g00266 266
3 2178412 2186919 + CtAH03T0017700.1 Cati3g00267 267
2 68671608 68678453 - gnl|WGS:LEKV|Ccrd_011196.mRNA.1_mrna Ccar2g02147 2147
2 68684984 68685640 - gnl|WGS:LEKV|Ccrd_011197.mRNA.1_mrna Ccar2g02148 2148
2 68689337 68693268 - gnl|WGS:LEKV|Ccrd_011198.mRNA.1_mrna Ccar2g02149 2149
2 68696003 68699914 - gnl|WGS:LEKV|Ccrd_011199.mRNA.1_mrna Ccar2g02150 2150
2 68712566 68717736 - gnl|WGS:LEKV|Ccrd_011200.mRNA.1_mrna Ccar2g02151 2151
2 68719309 68722934 - gnl|WGS:LEKV|Ccrd_011201.mRNA.1_mrna Ccar2g02152 2152
2 68725149 68730824 - gnl|WGS:LEKV|Ccrd_011202.mRNA.1_mrna Ccar2g02153 2153
2 68736502 68748601 - gnl|WGS:LEKV|Ccrd_011203.mRNA.1_mrna Ccar2g02154 2154
2 82598527 82615052 + >KAJ9562589.1 Ceso2g03304 3304
2 82810745 82826233 + >KAJ9563012.1 Ceso2g03308 3308
2 82827603 82831504 + >KAJ9563011.1 Ceso2g03309 3309
2 82858417 82862649 + >KAJ9563010.1 Ceso2g03310 3310
2 82866666 82869816 + >KAJ9563009.1 Ceso2g03311 3311
2 82911873 82914030 + >KAJ9562666.1 Ceso2g03312 3312
2 82917336 82925380 + >KAJ9562669.1 Ceso2g03313 3313
6 209018653 209021203 - ClaG1_Chr06g0425561 Chla6g05309 5309
6 209147519 209149826 - ClaG1_Chr06g0425571 Chla6g05310 5310
6 209150424 209153556 - ClaG1_Chr06g0425581 Chla6g05311 5311
6 209454367 209457119 - ClaG1_Chr06g0425631 Chla6g05316 5316
6 209756598 209759433 - ClaG1_Chr06g0425681 Chla6g05321 5321
6 209776755 209794893 - ClaG1_Chr06g0425691 Chla6g05322 5322
6 209888563 209900496 - ClaG1_Chr06g0425711 Chla6g05324 5324
7 251322211 251324373 - CmaNakai_Chr07g0696131 Chma7g07311 7311
7 251422210 251422860 - CmaNakai_Chr07g0696171 Chma7g07315 7315
7 251515444 251517669 - CmaNakai_Chr07g0696191 Chma7g07317 7317
7 251518440 251520664 - CmaNakai_Chr07g0696201 Chma7g07318 7318
7 251827654 251830308 - CmaNakai_Chr07g0696291 Chma7g07327 7327
7 252125417 252125824 - CmaNakai_Chr07g0696321 Chma7g07330 7330
7 252203283 252211770 - CmaNakai_Chr07g0696391 Chma7g07337 7337
13 69374471 69385930 + evm.model.scaffold_10346.236 Chmo13g01341 1341
13 69458345 69459016 + evm.model.scaffold_10346.226 Chmo13g01346 1346
13 69471515 69474810 + evm.model.scaffold_10346.224 Chmo13g01347 1347
13 69788215 69791153 + evm.model.scaffold_10346.200 Chmo13g01349 1349
13 70199693 70202912 + evm.model.scaffold_10346.188_evm.model.scaffold_10346.189 Chmo13g01351 1351
13 70203948 70205858 + evm.model.scaffold_10346.187 Chmo13g01352 1352
13 70305573 70306677 + evm.model.scaffold_10346.177 Chmo13g01353 1353
13 70375564 70377979 + evm.model.scaffold_10346.173 Chmo13g01355 1355
15 65877152 65889130 + evm.model.scaffold_1478.318 Chmo15g01163 1163
15 66029252 66029924 + evm.model.scaffold_4331.5 Chmo15g01167 1167
15 66110817 66114218 + evm.model.scaffold_4331.7 Chmo15g01168 1168
15 66784468 66787406 + evm.model.scaffold_4331.42 Chmo15g01170 1170
15 67287272 67290482 + evm.model.scaffold_4331.62 Chmo15g01172 1172
15 67291031 67293314 + evm.model.scaffold_4331.63 Chmo15g01173 1173
15 67408188 67409138 + evm.model.scaffold_4331.65 Chmo15g01174 1174
15 67573954 67576367 + evm.model.scaffold_4331.77 Chmo15g01176 1176
2 94652688 94665898 + Cn0678930 Chna2g01164 1164
2 94892390 94892821 + Cn0678890 Chna2g01166 1166
2 94908267 94912084 + Cn0678880 Chna2g01167 1167
2 95192950 95195647 + Cn0678810 Chna2g01170 1170
2 95423611 95426616 + Cn0678740 Chna2g01172 1172
2 95435688 95437683 + Cn0678730 Chna2g01173 1173
2 95620154 95620819 + Cn0678710 Chna2g01174 1174
2 95666297 95668734 + Cn0678700 Chna2g01175 1175
4 140854685 140855937 + KAI3754095.1 Cich4g04960 4960
4 140958894 140960666 + KAI3754098.1 Cich4g04963 4963
4 140962908 140964293 + KAI3754099.1 Cich4g04964 4964
4 140980882 140981592 + KAI3754100.1 Cich4g04965 4965
4 141044585 141047342 + KAI3754102.1 Cich4g04967 4967
5 83339371 83341191 + KAI3510213.1 Cien5g03693 3693
5 83344811 83347821 + KAI3510214.1 Cien5g03694 3694
5 83383371 83385124 + KAI3510217.1 Cien5g03697 3697
5 83388503 83389918 + KAI3510219.1 Cien5g03699 3699
5 83412641 83413351 + KAI3510222.1 Cien5g03702 3702
5 83435588 83440598 + KAI3510224.1 Cien5g03704 3704
3 298699448 298706289 - D.indicum_Contig13_G00106.t1 Cind3g00495 495
3 298564468 298564899 - D.indicum_Contig13_G00109.t1 Cind3g00498 498
3 298520741 298523603 - D.indicum_Contig13_G00110.t1 Cind3g00499 499
3 298091629 298094325 - D.indicum_Contig13_G00114.t1 Cind3g00503 503
3 297781187 297783472 - D.indicum_Contig13_G00116.t1 Cind3g00505 505
3 297778318 297779864 - D.indicum_Contig13_G00117.t1 Cind3g00506 506
3 297556976 297557638 - D.indicum_Contig13_G00119.t1 Cind3g00508 508
3 297469675 297479565 - D.indicum_Contig13_G00120.t1 Cind3g00509 509
16 54613624 54616035 + h1tg000026l.g56674.t1 Dapi16g01721 1721
31 57434516 57444230 + h2tg000177l.g62871.t1 Dapi31g01431 1431
3 285635 287959 - XM_043762872.1 Ecan3g00037 37
3 307081 308330 + XM_043764607.1 Ecan3g00041 41
3 310016 312358 - XM_043766000.1 Ecan3g00042 42
3 313012 315800 - XM_043762844.1 Ecan3g00043 43
3 323880 328490 - XM_043762829.1 Ecan3g00045 45
3 329326 332894 - XM_043764054.1 Ecan3g00046 46
3 389556 390038 - XM_043762778.1 Ecan3g00048 48
3 390933 405095 - XM_043763684.1 Ecan3g00049 49
6 78519035 78522574 - evm.model.ctg8288.3 Enbr6g02207 2207
6 78594529 78599550 + evm.model.ctg3526.1 Enbr6g02209 2209
6 78602045 78602982 - evm.model.ctg3526.2 Enbr6g02210 2210
6 78663461 78665642 + evm.model.ctg3526.4 Enbr6g02212 2212
6 84040253 84042840 - evm.model.ctg6186.3 Enbr6g02354 2354
3 121203309 121206318 + GcoAMIRv0_Chr03g0174581 Glco3g01829 1829
3 121828626 121831159 + GcoAMIRv0_Chr03g0174661 Glco3g01837 1837
3 122919847 122922438 + GcoAMIRv0_Chr03g0174751 Glco3g01846 1846
3 122933911 122934747 + GcoAMIRv0_Chr03g0174771 Glco3g01848 1848
3 123329923 123330603 + GcoAMIRv0_Chr03g0174811 Glco3g01852 1852
3 123437549 123439648 + GcoAMIRv0_Chr03g0174821 Glco3g01853 1853
6 101645378 101647332 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr06g0270921 Hean6g02854 2854
11 37400232 37404469 + gnl|WGS:MNCJ|mrna.Hean1vXRQr2_Chr11g0481161 Hean11g01312 1312
17 115463803 115465269 + >Htub.h2tg000417l.g102.t1 Hetu17g02276 2276
18 121472207 121473683 + >Htub.h1tg000740l.g43.t1 Hetu18g02555 2555
43 37250144 37253888 - >Htub.h1tg001422l.g489.t1 Hetu43g00492 492
7 149553986 149558044 + CAI9295403.1 Laca7g03198 3198
7 149575493 149579058 + CAI9295406.1 Laca7g03201 3201
7 149683812 149686125 + CAI9295409.1 Laca7g03204 3204
7 149710710 149713214 + CAI9295410.1 Laca7g03205 3205
7 149794247 149794948 + CAI9295411.1 Laca7g03206 3206
7 149827687 149829702 + CAI9295412.1 Laca7g03207 3207
7 149829910 149833454 + CAI9295413.1 Laca7g03208 3208
1 4913966 4922670 + LmiAMIRv0_Chr01g0005181 Lomi1g00518 518
1 4946030 4947920 + LmiAMIRv0_Chr01g0005191 Lomi1g00519 519
2 46721647 46723525 - LmiAMIRv0_Chr02g0086421 Lomi2g04109 4109
2 46735595 46737938 - LmiAMIRv0_Chr02g0086431 Lomi2g04110 4110
2 46743653 46747072 - LmiAMIRv0_Chr02g0086441 Lomi2g04111 4111
2 46766109 46774682 - LmiAMIRv0_Chr02g0086451 Lomi2g04112 4112
7 206764475 206766352 + >KAJ0197995.1 Lssa7g03958 3958
7 206784706 206789476 + >KAJ0195486.1 Lssa7g03959 3959
7 206974202 206976881 + >KAJ0196190.1 Lssa7g03962 3962
7 207075190 207077746 + >KAJ0195594.1 Lssa7g03965 3965
7 207181189 207181890 + >KAJ0198096.1 Lssa7g03966 3966
7 207236705 207238748 + >KAJ0196788.1 Lssa7g03967 3967
7 207239157 207242276 + >KAJ0195285.1 Lssa7g03968 3968
4 18794637 18798611 + PdyAMIRv0_Chr04g0158081 Pdy4g01001 1001
4 19041039 19043401 + PdyAMIRv0_Chr04g0158181 Pdy4g01011 1011
4 19176436 19178311 + PdyAMIRv0_Chr04g0158261 Pdy4g01019 1019
4 19180185 19181766 + PdyAMIRv0_Chr04g0158271 Pdy4g01020 1020
4 19241866 19242579 + PdyAMIRv0_Chr04g0158311 Pdy4g01024 1024
4 19467360 19470005 + PdyAMIRv0_Chr04g0158351 Pdy4g01028 1028
4 19481785 19485970 + PdyAMIRv0_Chr04g0158371 Pdy4g01030 1030
1 44835730 44844357 + PluAMIRv0_Chr01g0065121 Pslu1g06536 6536
1 44848932 44849378 + PluAMIRv0_Chr01g0065141 Pslu1g06538 6538
1 44857444 44860769 + PluAMIRv0_Chr01g0065151 Pslu1g06539 6539
1 44875217 44878354 + PluAMIRv0_Chr01g0065191 Pslu1g06543 6543
1 44901094 44902994 + PluAMIRv0_Chr01g0065261 Pslu1g06550 6550
1 44904279 44905900 + PluAMIRv0_Chr01g0065271 Pslu1g06551 6551
1 44924195 44924833 + PluAMIRv0_Chr01g0065281 Pslu1g06552 6552
1 44930377 44932286 + PluAMIRv0_Chr01g0065291 Pslu1g06553 6553
1 44943335 44947096 + PluAMIRv0_Chr01g0065311 Pslu1g06555 6555
12 3801436 3815454 + SinAMIRv0_Chr12g0357771 Sain12g00212 212
12 3826100 3826534 + SinAMIRv0_Chr12g0357781 Sain12g00213 213
12 3843981 3848592 + SinAMIRv0_Chr12g0357791 Sain12g00214 214
12 3875733 3880863 + SinAMIRv0_Chr12g0357811 Sain12g00216 216
12 3961252 3965475 + SinAMIRv0_Chr12g0357831 Sain12g00218 218
12 3969005 3971983 + SinAMIRv0_Chr12g0357841 Sain12g00219 219
12 4003932 4004612 + SinAMIRv0_Chr12g0357851 Sain12g00220 220
12 4013504 4017305 + SinAMIRv0_Chr12g0357861 Sain12g00221 221
12 4018671 4022778 + SinAMIRv0_Chr12g0357871 Sain12g00222 222
26 27438719 27441158 + KAI3695191.1 Smso26g01706 1706
5 69269587 69271808 - transfrag8007.t01 Soca5g05105 5105
5 69289732 69290566 + augustus11858.t01 Soca5g05107 5107
5 69293678 69297243 - augustus11857.t01 Soca5g05108 5108
5 69297465 69300425 - asmbl_1496.p1 Soca5g05109 5109
5 69356318 69360776 - augustus11853.t01 Soca5g05110 5110
5 69368308 69371761 - asmbl_1495.p1 Soca5g05111 5111
5 69419073 69419513 - genewise10234.t01 Soca5g05113 5113
5 69420229 69431742 - asmbl_1494.p1 Soca5g05114 5114
7 80347045 80349540 + Streb.7G016860.1 Stre7g01686 1686
4 67881845 67884347 + TkA04G268630.2 Tako4g03312 3312
4 67887555 67890043 + TkA04G268640.1 Tako4g03313 3313
4 67890299 67892500 + TkA04G268650.1 Tako4g03314 3314
4 67920964 67921608 + TkA04G268820.1 Tako4g03316 3316
4 68186973 68188855 + TkA04G269890.1 Tako4g03318 3318
4 68189151 68192114 + TkA04G269900.1 Tako4g03319 3319
4 38912098 38914502 + TbA04G047740.1 Tamo4g02302 2302
       
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