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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
Armi18g00002 Sain8g01973 . . . . . Lssa3g03684 Laca3g02901 . Tamo6g02693 Pslu2g13579 Lomi6g01914 Lomi7g01686 . Ecan8g02721 Soca4g03452 Glco7g02175 . . . . Chma3g03764 Chmo25g01542 Chmo26g01667 . Chla9g03238 Chna8g01076 Cind9g03628 Pdy3g03141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF
Select Chromosome Start End Strand Old_gene Gene Num
18 141320 161452 - AmiAMIRv0_Chr18g0469351 Armi18g00002 2
9 111411038 111420545 - ClaG1_Chr09g0611991 Chla9g03238 3238
3 155418992 155429265 + CmaNakai_Chr03g0267241 Chma3g03764 3764
25 128207562 128217112 + evm.model.scaffold_1102.129 Chmo25g01542 1542
26 137073910 137083756 + evm.model.scaffold_517.42 Chmo26g01667 1667
8 102705932 102715458 + Cn0734560 Chna8g01076 1076
9 154456896 154465842 + D.indicum_Contig59_G00055.t1 Cind9g03628 3628
8 38049162 38056507 + XM_043751063.1 Ecan8g02721 2721
7 351164969 351174363 + GcoAMIRv0_Chr07g0469601 Glco7g02175 2175
3 124887284 124893786 + CAI9277269.1 Laca3g02901 2901
6 27024327 27034207 - LmiAMIRv0_Chr06g0205521 Lomi6g01914 1914
7 27183676 27192653 - LmiAMIRv0_Chr07g0231561 Lomi7g01686 1686
3 217644078 217650402 + >KAJ0218754.1 Lssa3g03684 3684
3 89299620 89310372 + PdyAMIRv0_Chr03g0129801 Pdy3g03141 3141
2 101325031 101334747 - PluAMIRv0_Chr02g0356261 Pslu2g13579 13579
8 131899487 131917461 - SinAMIRv0_Chr08g0197061 Sain8g01973 1973
4 65070440 65079796 + transfrag37557.t01 Soca4g03452 3452
6 47072471 47079167 + TbA06G051340.1 Tamo6g02693 2693
       
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