Hierarchical alignments with the V. vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Fabaceae genomes. We used P. vulgaris as a reference, and by comparing homologous gene locus maps and Ks values between P. vulgaris and other Fabaceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created two hierarchical lists of homologous genes using P. vulgaris as a reference.
  The relevant gene ids can be obtained from the Fabaceae blast and match under the Tools module. This link is Fabaceae blast and match.
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Select Download Tree Vvi Acco_1 Acco_2 Accr_1 Accr_2 Adu_1 Adu_2 Aed_1 Aed_2 Aev_1 Aev_2 Ahy_1 Ahy_2 Aip_1 Aip_2 Alju_1 Alju_2 Amo_1 Amo_2 Apr_1 Apr_2 Arst_1 Arst_2 Bach_1 Bach_2 Bisa_1 Bisa_2 Bva_1 Bva_2 Car_1 Car_2 Cca_1 Cca_2 Dere_1 Dere_2 Dod_1 Dod_2 Enph_1 Enph_2 Glsi_1 Glsi_2 Gma_1 Gma_2 Gma_3 Gma_4 Gso_1 Gso_2 Gso_3 Gso_4 Lal_1 Lal_2 Lal_3 Lal_4 Lal_5 Lal_6 Lan_1 Lan_2 Lan_3 Lan_4 Lan_5 Lan_6 Lapu_1 Lapu_2 Lasa_1 Lasa_2 Lele_1 Lele_2 Lele_3 Lele_4 Lele_5 Lele_6 Lele_7 Lele_8 Lja_1 Lja_2 Mal_1 Mal_2 Mepo_1 Mepo_2 Mesa_1 Mesa_2 Mibi_1 Mibi_2 Mtr_1 Mtr_2 Phac_1 Phac_2 Phco_1 Phco_2 Prci_1 Prci_2 Psa_1 Psa_2 Pste_1 Pste_2 Pte_1 Pte_2 Pte_3 Pte_4 Pumo_1 Pumo_2 Pvu_1 Pvu_2 Rops_1 Rops_2 Seca_1 Seca_2 Spst_1 Spst_2 Ssu_1 Ssu_2 Sto_1 Sto_2 Tpr_1 Tpr_2 Trre_1 Trre_2 Tsu_1 Tsu_2 Vian_1 Vian_2 Vifa_1 Vifa_2 Vimu_1 Vimu_2 Viun_1 Viun_2 Vivi_1 Vivi_2 Vra_1 Vra_2
Vvi3g0083 . . . . . . . . Aev04g3435 . Ahy13g0792 . Aip03g00844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g2649 . . . . . . . Mtr4g2187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0084 . . . . . Adu03g01150 . . . . . . . . . . . . . . . Arst3g00741 . . . . . . . . . . . . . . . . . . . . . . . . . . Lal1g0184 . . . . . Lan13g0192 . . . . . . Lapu11g01382 . Lasa7g02212 . . . . . . . . . . . . . . . . . . . . . Phac11g01803 . Phco9g00431 . . . . . . . . . . . . . Pvu11g0388 . . . . . Spst2g02606 . . Sto2g0851 . . . . . . . . . . . . Vimu5g02441 . . . Vivi5g02893 . .
Vvi3g0085 . . . . . . . . . Aev05g0423 . Ahy15g0412 . Aip05g00404 . . . . . . . . . . . . . . . . . . . . . Dod02g0465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0086 . . . . . . . . . . . . . . . . . . . . Arst3g00741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa5g04807 . . . . . . . . . . . Mal7g2651 . . . . . . . Mtr4g2189 . . . Phco7g00093 . . . . . . . Pte3g01843 . . . . . Pvu9g0019 . . . . . Spst9g00083 . . . Sto2g0852 . . . . . . . . . . . . . . . . . . .
Vvi3g0087 . . . . . . . . Aev04g3438 . . . Aip03g00849 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal1g0183 . . . . . Lan13g0191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4157 . . . . . . . . . . Pvu11g1386 . . . . . . . . Sto2g0853 Sto10g0108 . . . . . . . . . . . Vimu5g01278 . . . . . .
Vvi3g0088 . . . . . . . . . . . . . . . . . . . . Arst3g00742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g02455 . Lasa5g04805 . . . . . . . . . . . . . . . Mesa9g05684 . . . . . . . Phco7g00092 . . . . . . . . . . . . . Pvu9g0018 . . . . . Spst9g00082 . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0089 . . . . . . . . Aev04g3445 . . . Aip03g00853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal1g0182 . . . . . Lan13g0189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4155 . . . . . . . . . . Pvu11g1385 . . . . . . . . Sto2g0856 . . . . . . . . . . . . Vimu5g01258 . . . . . .
Vvi3g0090 . . . . . . . . . . . . . . . . . . . . Arst3g01460 Arst3g00750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g02461 Lapu11g01387 Lasa5g04804 Lasa7g02215 . . . . . . . . . . Mal7g2665 . Mepo3g08021 Mepo2g02415 Mesa9g05686 Mesa13g02651 . . Mtr4g2195 . . Phac11g01810 Phco7g00091 Phco9g00428 . . Psa7g3235 . . Pste1g01531 . . . . . . Pvu9g0017 Pvu11g0385 . . . . Spst9g00081 Spst2g02612 . . Sto2g0858 . . . . . Tsu02g02522 . . . . . . Vimu5g02444 . . . Vivi5g02896 . .
Vvi3g0091 . . . . . Adu03g01155 . . . . . . . . . . . . . . . Arst3g00755 . . . . Bva13g01625 . . . . . . . . . . . . . . . . . . . . . Lal1g0181 . . . . . . . . . . . . . . Lasa7g02216 . . . . . . . . . . Mal7g2673 . . Mepo2g02416 . . . . Mtr4g2199 . . Phac11g01812 . Phco9g00427 . . Psa7g4153 . . . . . . . . . . Pvu11g0384 . . . . . Spst2g02614 . . Sto2g0866 . . . . . Tsu02g02531 . . . . . . Vimu5g02445 . . . Vivi5g02897 . .
Vvi3g0092 . . . . . . . . . . . . . . . . . . . . Arst3g01461 Arst3g01460 . . . . . . . . . . . . . . . . . . . . . . . . . . Lal1g0180 . . . . . . . . . . . . . Lasa5g04802 . . . . . . . . . . . . . . . . . . . . . . . . Phco9g01521 . . . . . . . . . . . . Pvu9g0016 Pvu11g1378 . . . . Spst9g00198 . . . Sto2g0867 . . . . . . . . . . . Vimu10g03689 Vimu5g01263 . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0083 Chr3 867890 868156 +
Aev Aev04g3435 Chr04 32844208 32844471 -
Ahy Ahy13g0792 Chr13 8345845 8347055 +
Aip Aip03g00844 Chr03 8136350 8136616 +
Mal Mal7g2649 Chr7 88569577 88569861 +
Mtr Mtr4g2187 Chr4 35396931 35397684 +
Vvi Vvi3g0084 Chr3 869627 869914 +
Adu Adu03g01150 Chr03 12713177 12713452 +
Arst Arst3g00741 Chr3 5339844 5343261 +
Lal Lal1g0184 Chr1 1117067 1117315 -
Lan Lan13g0192 Chr13 1202902 1203536 -
Lapu Lapu11g01382 Chr11 16197676 16197952 -
Lasa Lasa7g02212 Chr7 505032724 505032999 -
Phac Phac11g01803 Chr11 24045056 24047052 -
Phco Phco9g00431 Chr9 3111857 3112902 -
Pvu Pvu11g0388 Chr11 3270439 3271018 +
Spst Spst2g02606 Chr2 25795250 25795528 +
Sto Sto2g0851 Chr2 7422029 7424058 -
Vimu Vimu5g02441 Chr5 35007174 35008002 -
Vivi Vivi5g02893 Chr5 116822128 116825593 -
Vvi Vvi3g0085 Chr3 876808 877695 +
Aev Aev05g0423 Chr05 2912231 2916744 -
Ahy Ahy15g0412 Chr15 4793099 4798401 -
Aip Aip05g00404 Chr05 4504020 4509183 -
Dod Dod02g0465 Chr02 6125723 6130949 -
Vvi Vvi3g0086 Chr3 880950 881237 -
Arst Arst3g00741 Chr3 5339844 5343261 +
Lasa Lasa5g04807 Chr5 697071125 697071406 -
Mal Mal7g2651 Chr7 88575153 88575434 +
Mtr Mtr4g2189 Chr4 35402226 35403055 +
Phco Phco7g00093 Chr7 590018 590323 +
Pte Pte3g01843 Chr3 29322896 29323667 +
Pvu Pvu9g0019 Chr9 393231 393758 +
Spst Spst9g00083 Chr9 645734 649957 +
Sto Sto2g0852 Chr2 7426543 7431065 -
Vvi Vvi3g0087 Chr3 883689 883976 -
Aev Aev04g3438 Chr04 32850120 32850383 -
Aip Aip03g00849 Chr03 8148150 8148416 +
Lal Lal1g0183 Chr1 1113971 1114240 -
Lan Lan13g0191 Chr13 1200596 1201291 -
Psa Psa7g4157 Chr7 338954741 338955225 +
Pvu Pvu11g1386 Chr11 30599281 30599920 +
Sto Sto2g0853 Chr2 7436474 7436728 -
Sto Sto10g0108 Chr10 838702 839867 +
Vimu Vimu5g01278 Chr5 22749812 22750744 +
Vvi Vvi3g0088 Chr3 885397 885684 -
Arst Arst3g00742 Chr3 5343818 5344423 -
Lapu Lapu9g02455 Chr9 38941420 38941902 -
Lasa Lasa5g04805 Chr5 696963705 696963977 -
Mesa Mesa9g05684 Chr9 92554090 92554353 +
Phco Phco7g00092 Chr7 587629 587925 +
Pvu Pvu9g0018 Chr9 390801 391331 +
Spst Spst9g00082 Chr9 643339 643647 +
Vvi Vvi3g0089 Chr3 888666 888953 +
Aev Aev04g3445 Chr04 32869028 32869282 -
Aip Aip03g00853 Chr03 8176632 8177153 +
Lal Lal1g0182 Chr1 1111792 1112070 -
Lan Lan13g0189 Chr13 1169490 1170021 -
Psa Psa7g4155 Chr7 338780079 338781272 +
Pvu Pvu11g1385 Chr11 30597678 30598178 +
Sto Sto2g0856 Chr2 7448153 7448407 -
Vimu Vimu5g01258 Chr5 22615767 22617310 +
Vvi Vvi3g0090 Chr3 892027 892314 +
Arst Arst3g01460 Chr3 13138786 13139255 -
Arst Arst3g00750 Chr3 5378593 5379361 -
Lapu Lapu9g02461 Chr9 38982565 38983100 -
Lapu Lapu11g01387 Chr11 16217956 16218218 +
Lasa Lasa5g04804 Chr5 696961718 696961999 -
Lasa Lasa7g02215 Chr7 505103488 505103763 -
Mal Mal7g2665 Chr7 88680777 88681034 +
Mepo Mepo3g08021 Chr3 93072075 93072461 -
Mepo Mepo2g02415 Chr2 33944510 33945016 +
Mesa Mesa9g05686 Chr9 92559446 92559727 +
Mesa Mesa13g02651 Chr13 31056762 31057043 -
Mtr Mtr4g2195 Chr4 35421426 35422081 -
Phac Phac11g01810 Chr11 24089525 24089966 +
Phco Phco7g00091 Chr7 583396 583698 +
Phco Phco9g00428 Chr9 3087141 3090570 +
Psa Psa7g3235 Chr7 242732488 242733423 -
Pste Pste1g01531 Chr1 4781403 4781651 +
Pvu Pvu9g0017 Chr9 377439 377741 +
Pvu Pvu11g0385 Chr11 3257292 3257910 +
Spst Spst9g00081 Chr9 640055 641118 +
Spst Spst2g02612 Chr2 25806330 25806599 +
Sto Sto2g0858 Chr2 7460507 7469455 -
Tsu Tsu02g02522 Chr02 26126498 26126770 -
Vimu Vimu5g02444 Chr5 35018500 35019378 +
Vivi Vivi5g02896 Chr5 116828686 116831795 -
Vvi Vvi3g0091 Chr3 894854 895141 -
Adu Adu03g01155 Chr03 12730057 12730589 +
Arst Arst3g00755 Chr3 5383120 5383665 -
Bva Bva13g01625 Chr13 9747407 9748189 +
Lal Lal1g0181 Chr1 1110018 1113071 +
Lasa Lasa7g02216 Chr7 505298088 505298369 +
Mal Mal7g2673 Chr7 88816101 88816379 -
Mepo Mepo2g02416 Chr2 33946006 33946427 -
Mtr Mtr4g2199 Chr4 35452314 35452786 -
Phac Phac11g01812 Chr11 24091703 24092465 -
Phco Phco9g00427 Chr9 3075812 3078199 +
Psa Psa7g4153 Chr7 338777864 338778521 +
Pvu Pvu11g0384 Chr11 3255528 3256095 +
Spst Spst2g02614 Chr2 25820455 25820733 -
Sto Sto2g0866 Chr2 7502560 7503309 -
Tsu Tsu02g02531 Chr02 26159614 26160039 -
Vimu Vimu5g02445 Chr5 35022438 35023587 +
Vivi Vivi5g02897 Chr5 116829934 116833154 +
Vvi Vvi3g0092 Chr3 897891 898178 +
Arst Arst3g01461 Chr3 13139086 13143139 +
Arst Arst3g01460 Chr3 13138786 13139255 -
Lal Lal1g0180 Chr1 1108902 1109171 -
Lasa Lasa5g04802 Chr5 696890869 696891150 -
Phco Phco9g01521 Chr9 35575475 35576369 -
Pvu Pvu9g0016 Chr9 371980 372530 +
Pvu Pvu11g1378 Chr11 30090122 30090629 +
Spst Spst9g00198 Chr9 1751021 1752760 +
Sto Sto2g0867 Chr2 7512047 7537453 -
Vimu Vimu10g03689 Chr10 45935673 45940762 -
Vimu Vimu5g01263 Chr5 22666614 22668221 -
Arst Arst3g01461 Chr3 13139086 13143139 +
Vimu Vimu5g01263 Chr5 22666614 22668221 -
Vimu Vimu5g01258 Chr5 22615767 22617310 +
Aev Aev05g0423 Chr05 2912231 2916744 -
Ahy Ahy15g0412 Chr15 4793099 4798401 -
Aip Aip05g00404 Chr05 4504020 4509183 -
Dod Dod02g0465 Chr02 6125723 6130949 -
Adu Adu03g01150 Chr03 12713177 12713452 +
Arst Arst3g00741 Chr3 5339844 5343261 +
Lapu Lapu11g01382 Chr11 16197676 16197952 -
Lasa Lasa7g02212 Chr7 505032724 505032999 -
Phac Phac11g01803 Chr11 24045056 24047052 -
Phco Phco9g00431 Chr9 3111857 3112902 -
Pvu Pvu11g0388 Chr11 3270439 3271018 +
Spst Spst2g02606 Chr2 25795250 25795528 +
Vimu Vimu5g02441 Chr5 35007174 35008002 -
Vivi Vivi5g02893 Chr5 116822128 116825593 -