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
Vvi1g1561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1563 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr7g2271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr6g1037 . . . Tsu07g02867 . . . . . . . . . . . . .
Vvi1g1565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1566 . . . . . . Aed3g0180 . . . . . . . . . . . . . . . . . . . Bva06g01687 Bva05g00092 . . Cca07g02368 . . . . . . . . . . . Gma08g02403 . . . . . Lal6g1649 . Lal18g0576 . . . Lan8g0122 . Lan8g0122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g0235 . . . . . . . . . . . . . . . . . . . Vra4g1222 .
Vvi1g1567 . . . . Adu03g02881 . Aed3g0182 . . . . . . . . . . . . . Arst3g03804 . . . . . Bva06g01686 Bva05g00093 . . Cca07g02367 . . . . . . . . . . . Gma08g02402 . . . . . Lal6g1648 . . . . . Lan8g0123 . . . . . Lapu3g03525 . . . . . . . . . . . . Lja4g0480 . Mal7g4857 . . . . . . . Mtr8g3394 Phac2g04271 . Phco4g03219 . . . . Psa7g0882 Pste3g01237 . Pte2g02490 Pte3g00128 . . . . Pvu2g2915 . . . . . Spst3g01176 . Ssu3g0236 . Sto3g2181 . . Tpr3g0711 . . . Tsu02g00533 . . . . . . . . . . Vra4g1221 .
Vvi1g1568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1569 . . . . . . Aed3g0185 . . . . . . . . . . . . . . . . . . . Bva06g01682 Bva05g00098 . . Cca07g02364 . . . . . . . . . . . Gma08g02398 . . . . . . . Lal18g0571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g0239 . . . . . . . . . . . . . . . . . . . Vra4g1218 .
Vvi1g1570 . . . . Adu03g02908 . Aed3g0186 . . . . . . . Alju09g1662 . . . . . Arst3g03837 Arst3g03837 . Bach2g02309 Bisa11g0995 . Bva06g01681 Bva05g00100 . . Cca07g02363 . Dere09g0272 . . . Enph13g1364 . Glsi05g2053 . . . Gma08g02397 . . . . . Lal6g1646 . . . . . Lan8g0125 . . . . . . Lapu9g00919 . Lasa5g03505 Lele49g0620 Lele50g0647 Lele51g0638 Lele52g0640 . . . . . Lja4g0496 . . . Mepo3g06950 . Mesa9g04496 Mibi12g1425 . . . Phac2g04246 Phac9g02685 Phco4g03204 Phco7g01888 Prci10g0988 . . Psa7g0898 Pste3g01288 Pste2g00247 . Pte3g00118 Pte3g00118 . Pumo6g00570 Pumo10g01827 Pvu2g2902 Pvu9g1670 Rops2g00661 Rops10g00864 Seca12g06390 Seca4g01785 Spst3g01190 . Ssu3g0240 . . Sto4g0180 . . . Trre5g04743 . . Vian1g03756 . Vifa2g03370 Vifa2g03370 Vimu11g04312 Vimu10g01632 Viun3g00689 Viun9g01583 Vivi5g05734 Vivi3g02248 Vra4g1217 .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g1561 Chr1 22317495 22318046 -
Vvi Vvi1g1562 Chr1 22323505 22323657 +
Vvi Vvi1g1563 Chr1 22328196 22330760 +
Bva Bva06g01688 Chr06 11849910 11851136 -
Vvi Vvi1g1564 Chr1 22336280 22338766 +
Mtr Mtr7g2271 Chr7 39104063 39109008 -
Tpr Tpr6g1037 Chr6 9700443 9703672 -
Tsu Tsu07g02867 Chr07 33818371 33820899 -
Vvi Vvi1g1565 Chr1 22356346 22356408 +
Vvi Vvi1g1566 Chr1 22356991 22364888 +
Aed Aed3g0180 Chr3 1323214 1324660 +
Bva Bva06g01687 Chr06 11833930 11841140 -
Bva Bva05g00092 Chr05 460447 468108 +
Cca Cca07g02368 Chr07 52311878 52320589 -
Gma Gma08g02403 Chr08 23792252 23801161 -
Lal Lal6g1649 Chr6 19258540 19269444 -
Lal Lal18g0576 Chr18 4864752 4873798 -
Lan Lan8g0122 Chr8 1966123 1976922 +
Lan Lan8g0122 Chr8 1966123 1976922 +
Ssu Ssu3g0235 Chr3 4191695 4200836 +
Vra Vra4g1222 Chr4 19171172 19179956 -
Vvi Vvi1g1567 Chr1 22388239 22389150 -
Adu Adu03g02881 Chr03 109437420 109438662 -
Aed Aed3g0182 Chr3 1333040 1335807 -
Arst Arst3g03804 Chr3 108162673 108164116 -
Bva Bva06g01686 Chr06 11830145 11831582 +
Bva Bva05g00093 Chr05 468412 471359 -
Cca Cca07g02367 Chr07 52291130 52292020 +
Gma Gma08g02402 Chr08 23773171 23774783 +
Lal Lal6g1648 Chr6 19253259 19257002 +
Lan Lan8g0123 Chr8 1981578 1982779 -
Lapu Lapu3g03525 Chr3 58652928 58653974 +
Lja Lja4g0480 Chr4 3922934 3924392 -
Mal Mal7g4857 Chr7 117111037 117111882 +
Mtr Mtr8g3394 Chr8 44470370 44472032 +
Phac Phac2g04271 Chr2 41189287 41192009 +
Phco Phco4g03219 Chr4 52883328 52884260 +
Psa Psa7g0882 Chr7 66247542 66249189 +
Pste Pste3g01237 Chr3 7841446 7842381 +
Pte Pte2g02490 Chr2 44129957 44131242 -
Pte Pte3g00128 Chr3 1321585 1322538 +
Pvu Pvu2g2915 Chr2 44692837 44694266 +
Spst Spst3g01176 Chr3 15267176 15268102 -
Ssu Ssu3g0236 Chr3 4207380 4208192 -
Sto Sto3g2181 Chr3 19247626 19281151 -
Tpr Tpr3g0711 Chr3 6834799 6836052 -
Tsu Tsu02g00533 Chr02 4503746 4505252 -
Vra Vra4g1221 Chr4 19166768 19168017 +
Vvi Vvi1g1568 Chr1 22389705 22391239 +
Vvi Vvi1g1569 Chr1 22415119 22416757 -
Aed Aed3g0185 Chr3 1365312 1369918 -
Bva Bva06g01682 Chr06 11810208 11812877 +
Bva Bva05g00098 Chr05 494021 496943 -
Cca Cca07g02364 Chr07 52253290 52256321 +
Gma Gma08g02398 Chr08 23720483 23722570 +
Lal Lal18g0571 Chr18 4796060 4798721 +
Ssu Ssu3g0239 Chr3 4257929 4259832 -
Vra Vra4g1218 Chr4 19140999 19143976 +
Vvi Vvi1g1570 Chr1 22422944 22442015 -
Adu Adu03g02908 Chr03 110411939 110417511 -
Aed Aed3g0186 Chr3 1371767 1381162 -
Alju Alju09g1662 Chr09 40437878 40440176 +
Arst Arst3g03837 Chr3 109117068 109123103 -
Arst Arst3g03837 Chr3 109117068 109123103 -
Bach Bach2g02309 Chr2 29634036 29643237 -
Bisa Bisa11g0995 Chr11 26674878 26677612 +
Bva Bva06g01681 Chr06 11800767 11809702 +
Bva Bva05g00100 Chr05 500106 506635 -
Cca Cca07g02363 Chr07 52241814 52250658 +
Dere Dere09g0272 Chr09 5480514 5483342 +
Enph Enph13g1364 Chr13 19316471 19319013 -
Glsi Glsi05g2053 Chr05 67343152 67344848 -
Gma Gma08g02397 Chr08 23707286 23717107 +
Lal Lal6g1646 Chr6 19231784 19243060 +
Lan Lan8g0125 Chr8 1997461 2006671 -
Lapu Lapu9g00919 Chr9 13908204 13915780 +
Lasa Lasa5g03505 Chr5 569139375 569146069 +
Lele Lele49g0620 Chr49 3758791 3760740 -
Lele Lele50g0647 Chr50 3972861 3974044 -
Lele Lele51g0638 Chr51 3859268 3861201 -
Lele Lele52g0640 Chr52 4056869 4058823 -
Lja Lja4g0496 Chr4 4056733 4065372 -
Mepo Mepo3g06950 Chr3 83145367 83146813 +
Mesa Mesa9g04496 Chr9 78518442 78533214 +
Mibi Mibi12g1425 Chr12 29843032 29845602 +
Phac Phac2g04246 Chr2 41043103 41061705 +
Phac Phac9g02685 Chr9 25503028 25511896 +
Phco Phco4g03204 Chr4 52758570 52761718 +
Phco Phco7g01888 Chr7 22165006 22173177 -
Prci Prci10g0988 Chr10 6756132 6758798 -
Psa Psa7g0898 Chr7 68179886 68201134 -
Pste Pste3g01288 Chr3 8105557 8126642 -
Pste Pste2g00247 Chr2 1535752 1543079 +
Pte Pte3g00118 Chr3 1158282 1164332 +
Pte Pte3g00118 Chr3 1158282 1164332 +
Pumo Pumo6g00570 Chr6 7207166 7219043 -
Pumo Pumo10g01827 Chr10 24048537 24056286 +
Pvu Pvu2g2902 Chr2 44567325 44579805 +
Pvu Pvu9g1670 Chr9 23489781 23497230 +
Rops Rops2g00661 Chr2 9401478 9412534 -
Rops Rops10g00864 Chr10 19614949 19624036 -
Seca Seca12g06390 Chr12 155897399 155910526 +
Seca Seca4g01785 Chr4 29434934 29461928 -
Spst Spst3g01190 Chr3 15408589 15410904 -
Ssu Ssu3g0240 Chr3 4266941 4274703 -
Sto Sto4g0180 Chr4 1326656 1338239 +
Trre Trre5g04743 Chr5 49290267 49296392 -
Vian Vian1g03756 Chr1 60468960 60486401 +
Vifa Vifa2g03370 Chr2 970855146 970860737 +
Vifa Vifa2g03370 Chr2 970855146 970860737 +
Vimu Vimu11g04312 Chr11 64473219 64490481 +
Vimu Vimu10g01632 Chr10 20421708 20429738 -
Viun Viun3g00689 Chr3 4247744 4275764 -
Viun Viun9g01583 Chr9 23252582 23258504 -
Vivi Vivi5g05734 Chr5 160881583 160892777 +
Vivi Vivi3g02248 Chr3 36986436 36992627 -
Vra Vra4g1217 Chr4 19128474 19139516 +
Arst Arst3g03837 Chr3 109117068 109123103 -
Bach Bach2g02309 Chr2 29634036 29643237 -
Lapu Lapu9g00919 Chr9 13908204 13915780 +
Lasa Lasa5g03505 Chr5 569139375 569146069 +
Lja Lja4g0496 Chr4 4056733 4065372 -
Mepo Mepo3g06950 Chr3 83145367 83146813 +
Mesa Mesa9g04496 Chr9 78518442 78533214 +
Phac Phac9g02685 Chr9 25503028 25511896 +
Phco Phco7g01888 Chr7 22165006 22173177 -
Psa Psa7g0898 Chr7 68179886 68201134 -
Pste Pste2g00247 Chr2 1535752 1543079 +
Pte Pte3g00118 Chr3 1158282 1164332 +
Pumo Pumo10g01827 Chr10 24048537 24056286 +
Pvu Pvu9g1670 Chr9 23489781 23497230 +
Rops Rops10g00864 Chr10 19614949 19624036 -
Seca Seca4g01785 Chr4 29434934 29461928 -
Trre Trre5g04743 Chr5 49290267 49296392 -
Vifa Vifa2g03370 Chr2 970855146 970860737 +
Vimu Vimu10g01632 Chr10 20421708 20429738 -
Viun Viun9g01583 Chr9 23252582 23258504 -
Vivi Vivi3g02248 Chr3 36986436 36992627 -
Adu Adu03g02881 Chr03 109437420 109438662 -
Arst Arst3g03804 Chr3 108162673 108164116 -
Lapu Lapu3g03525 Chr3 58652928 58653974 +
Lja Lja4g0480 Chr4 3922934 3924392 -
Mal Mal7g4857 Chr7 117111037 117111882 +
Mtr Mtr8g3394 Chr8 44470370 44472032 +
Phac Phac2g04271 Chr2 41189287 41192009 +
Phco Phco4g03219 Chr4 52883328 52884260 +
Psa Psa7g0882 Chr7 66247542 66249189 +
Pste Pste3g01237 Chr3 7841446 7842381 +
Pte Pte2g02490 Chr2 44129957 44131242 -
Pte Pte3g00128 Chr3 1321585 1322538 +
Pvu Pvu2g2915 Chr2 44692837 44694266 +
Spst Spst3g01176 Chr3 15267176 15268102 -
Tpr Tpr3g0711 Chr3 6834799 6836052 -
Tsu Tsu02g00533 Chr02 4503746 4505252 -