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
Vvi17g0303 . . . . Adu05g02679 . Aed7g0233 . Aev05g3459 . Ahy15g2734 . Aip05g03053 . . . Amo15g1794 . Apr6g1039 Apr2g1759 Arst5g03391 . Bach1g01492 . Bisa01g0427 . Bva04g00835 Bva03g00689 Car08g01670 . Cca08g00257 . Dere06g1733 . Dod02g3677 . . . Glsi01g1943 . . . . Gma09g01681 . . . . . . . . Lal10g0971 . . . . . . . Lapu4g00212 . Lasa1g03975 . . . . . . . . . Lja2g2123 . . Mal8g3811 Mepo7g00954 . Mesa22g02698 . . . . Mtr6g2141 Phac4g02042 . . . . . Psa1g0811 . Pste9g01477 . . . . . Pumo6g03006 . Pvu4g1633 . Rops5g00279 . Seca10g04863 . . . . . . Sto8g2186 . Tpr5g0285 Trre11g01647 . . Tsu03g03114 Vian8g01450 . Vifa1g07138 . Vimu8g01572 . Viun4g00326 . Vivi4g00274 . Vra1g0635 .
Vvi17g0304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0305 . . . . . . . . Aev05g3454 . . . Aip05g03064 . . . . . . . . . . . . . . Bva03g00679 . . . . . . Dod02g3674 . . . . . . . . . . . . . . . . Lal8g0440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr6g2145 . . . . . . Psa1g0828 . . . . . . . . . . . . . . . . . . . . Sto8g2184 . Tpr5g0278 . . . . . . . . . . . . . . . .
Vvi17g0306 . . . . . . . . . . Ahy15g2748 . Aip05g03066 . . . Amo15g1772 . . Apr2g1469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr6g2149 . . . . . . Psa1g0829 . . . . . . . . . . . . . . . . . . . . . . Tpr5g0272 . . . . . . . . . . . . . . . .
Vvi17g0307 . . . . . . . . . . . . . . . . . . Apr6g1042 Apr2g1760 . . . . . . . . Car08g01671 . Cca08g00253 . . . . . . . . . Gma07g00860 . . Gma09g01683 Gso7g0814 . . Gso7g0814 . . . Lal8g0439 . Lal25g0463 . . . . . . . . . . . . . . . . . . Lja2g2118 . . Mal8g3836 . . . . . . . Mtr6g2152 . . . . . . Psa1g0833 . . . . . . . . . . . . . . . . . . . . Sto8g2182 . . . . . Tsu03g03136 . . . . . . . . . . Vra1g0633 .
Vvi17g0308 . . . . Adu05g02670 . Aed7g0229 . . . . . . . . . . . . . . . . . . . Bva04g00832 . Car08g01675 . Cca08g00251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g2117 . . . . . . . . . . . . . . . . . Psa1g0835 . . . . . . . . . Pvu4g1637 . . . . . . . . . . . . . . . . . . . Vifa1g07101 . . . . . . . . .
Vvi17g0309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0310 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g00673 . . . . . . . . . . . . . . Gma05g02301 Gma09g01687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g0300 . . . . . . . Mtr8g3764 Mtr6g2158 . . . . . . . Psa7g0265 . . . . . . . . . . . . . . . . . . . . Tpr3g0345 . . . Tsu02g00152 . . . . . . . . . . . . .
Vvi17g0311 . . . . Adu05g02661 . . . . . . . . . . . . . . . Arst5g03358 . Bach1g01501 . . . . . Car08g01677 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu4g00204 . Lasa1g04023 . . . . . . . . . Lja2g2113 . . Mal8g3852 . . Mesa22g03129 . . . . Mtr6g2159 . . . . . . . Psa7g0264 Pste9g01482 . . . . . Pumo6g03022 . Pvu4g1650 . Rops5g00253 . Seca12g06861 . Spst4g02760 . . . . . . Tpr5g0263 . . . Tsu03g03152 Vian8g01463 . . . Vimu8g01538 . Viun4g00306 . . . . .
Vvi17g0312 . . . . . . Aed7g0223 . . . Ahy15g2761 . Aip05g03078 . . . . . Apr6g1048 Apr2g1468 . . . . . . Bva04g00830 . . Car06g00251 Cca08g00244 . . . Dod02g3661 . . . . . Gma07g00853 Gma08g00429 . . Gso7g0806 Gso7g0806 . . . Lal16g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr6g2160 . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g3376 . . Sto8g2174 . . . . . . . . . . . . . . . . Vra1g0618 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Sto Sto8g2184 Chr8 14384832 14389658 -
Sto Sto8g2182 Chr8 14371932 14377624 -
Vvi Vvi17g0303 Chr17 3175959 3178995 -
Adu Adu05g02679 Chr05 93887017 93890654 +
Aed Aed7g0233 Chr7 1661775 1668023 +
Aev Aev05g3459 Chr05 33966589 33969836 +
Ahy Ahy15g2734 Chr15 144335443 144339166 -
Aip Aip05g03053 Chr05 133370402 133372944 -
Amo Amo15g1794 Chr15 119138946 119142690 +
Apr Apr6g1039 Chr6 15102485 15106824 -
Apr Apr2g1759 Chr2 23235896 23243372 -
Arst Arst5g03391 Chr5 92545113 92548712 +
Bach Bach1g01492 Chr1 28375257 28379707 -
Bisa Bisa01g0427 Chr01 5995825 5998512 -
Bva Bva04g00835 Chr04 5498667 5502451 +
Bva Bva03g00689 Chr03 4122871 4127683 +
Car Car08g01670 Chr08 26529968 26542229 -
Cca Cca08g00257 Chr08 3634359 3640546 +
Dere Dere06g1733 Chr06 32140605 32143168 +
Dod Dod02g3677 Chr02 75437407 75442416 +
Glsi Glsi01g1943 Chr01 82839234 82841591 +
Gma Gma09g01681 Chr09 42363150 42368916 -
Lal Lal10g0971 Chr10 16992967 16999301 +
Lapu Lapu4g00212 Chr4 2123807 2128317 +
Lasa Lasa1g03975 Chr1 691397556 691399766 -
Lja Lja2g2123 Chr2 23630369 23636415 +
Mal Mal8g3811 Chr8 110617477 110621136 -
Mepo Mepo7g00954 Chr7 14777002 14786445 -
Mesa Mesa22g02698 Chr22 71710161 71712550 +
Mtr Mtr6g2141 Chr6 38263496 38268784 -
Phac Phac4g02042 Chr4 46935733 46940320 -
Psa Psa1g0811 Chr1 52158532 52161888 -
Pste Pste9g01477 Chr9 14392162 14397129 -
Pumo Pumo6g03006 Chr6 71862714 71866481 -
Pvu Pvu4g1633 Chr4 43604661 43608504 -
Rops Rops5g00279 Chr5 4331333 4343056 +
Seca Seca10g04863 Chr10 111997473 112003020 -
Sto Sto8g2186 Chr8 14401250 14404880 +
Tpr Tpr5g0285 Chr5 4214831 4219245 +
Trre Trre11g01647 Chr11 16224566 16231314 +
Tsu Tsu03g03114 Chr03 42917111 42920871 -
Vian Vian8g01450 Chr8 33851260 33854136 -
Vifa Vifa1g07138 Chr1 1101683138 1101685422 +
Vimu Vimu8g01572 Chr8 21498024 21501852 +
Viun Viun4g00326 Chr4 1978037 1982064 +
Vivi Vivi4g00274 Chr4 6144522 6147828 +
Vra Vra1g0635 Chr1 7372733 7376845 +
Vvi Vvi17g0304 Chr17 3189919 3194062 +
Vvi Vvi17g0305 Chr17 3203819 3213765 +
Aev Aev05g3454 Chr05 33934285 33944454 -
Aip Aip05g03064 Chr05 133604995 133613805 +
Bva Bva03g00679 Chr03 4073903 4079940 +
Dod Dod02g3674 Chr02 75315012 75316013 -
Lal Lal8g0440 Chr8 2954634 2956829 -
Mtr Mtr6g2145 Chr6 38342473 38349123 +
Psa Psa1g0828 Chr1 54537837 54546882 +
Sto Sto8g2184 Chr8 14384832 14389658 -
Tpr Tpr5g0278 Chr5 4046707 4050814 +
Vvi Vvi17g0306 Chr17 3212628 3219814 +
Ahy Ahy15g2748 Chr15 144648098 144651125 -
Aip Aip05g03066 Chr05 133676937 133707179 -
Amo Amo15g1772 Chr15 118468255 118471047 +
Apr Apr2g1469 Chr2 20722641 20730763 +
Mtr Mtr6g2149 Chr6 38378364 38382426 +
Psa Psa1g0829 Chr1 54598092 54615207 -
Tpr Tpr5g0272 Chr5 3939550 3940851 +
Vvi Vvi17g0307 Chr17 3220947 3228185 -
Apr Apr6g1042 Chr6 15124999 15131815 +
Apr Apr2g1760 Chr2 23248432 23253255 +
Car Car08g01671 Chr08 26547669 26551053 -
Cca Cca08g00253 Chr08 3590416 3592990 +
Gma Gma07g00860 Chr07 9271657 9279165 -
Gma Gma09g01683 Chr09 42392352 42402668 +
Gso Gso7g0814 Chr7 9027460 9029993 -
Gso Gso7g0814 Chr7 9027460 9029993 -
Lal Lal8g0439 Chr8 2946994 2953237 -
Lal Lal25g0463 Chr25 3176514 3180411 -
Lja Lja2g2118 Chr2 23477605 23490828 -
Mal Mal8g3836 Chr8 111602569 111604841 -
Mtr Mtr6g2152 Chr6 38406847 38416713 +
Psa Psa1g0833 Chr1 55701112 55703437 +
Sto Sto8g2182 Chr8 14371932 14377624 -
Tsu Tsu03g03136 Chr03 43305683 43308252 -
Vra Vra1g0633 Chr1 7353723 7357462 +
Vvi Vvi17g0308 Chr17 3231773 3232558 -
Adu Adu05g02670 Chr05 93749523 93760445 +
Aed Aed7g0229 Chr7 1645991 1646893 -
Bva Bva04g00832 Chr04 5483312 5488099 -
Car Car08g01675 Chr08 26576011 26587309 +
Cca Cca08g00251 Chr08 3567881 3569150 -
Lja Lja2g2117 Chr2 23467746 23475146 +
Psa Psa1g0835 Chr1 56022560 56024924 +
Pvu Pvu4g1637 Chr4 43652304 43662279 +
Vifa Vifa1g07101 Chr1 1096817014 1096818009 -
Vvi Vvi17g0309 Chr17 3235698 3236363 -
Vvi Vvi17g0310 Chr17 3248960 3251712 -
Bva Bva03g00673 Chr03 4040634 4044416 +
Gma Gma05g02301 Chr05 44026185 44030068 -
Gma Gma09g01687 Chr09 42488341 42493696 -
Mal Mal5g0300 Chr5 4916792 4920377 -
Mtr Mtr8g3764 Chr8 48148636 48151726 -
Mtr Mtr6g2158 Chr6 38635940 38641569 -
Psa Psa7g0265 Chr7 18040621 18042719 -
Tpr Tpr3g0345 Chr3 3736324 3739364 +
Tsu Tsu02g00152 Chr02 1136345 1139228 +
Vvi Vvi17g0311 Chr17 3257049 3260182 -
Adu Adu05g02661 Chr05 93497714 93502360 +
Arst Arst5g03358 Chr5 92156233 92160874 +
Bach Bach1g01501 Chr1 28654619 28657949 -
Car Car08g01677 Chr08 26597219 26602350 -
Lapu Lapu4g00204 Chr4 2026710 2030907 +
Lasa Lasa1g04023 Chr1 697623278 697625513 +
Lja Lja2g2113 Chr2 23426905 23431233 +
Mal Mal8g3852 Chr8 112182406 112187646 -
Mesa Mesa22g03129 Chr22 82350660 82356424 -
Mtr Mtr6g2159 Chr6 38645214 38650946 -
Psa Psa7g0264 Chr7 17936084 17938192 +
Pste Pste9g01482 Chr9 14500983 14506558 -
Pumo Pumo6g03022 Chr6 72252649 72258240 -
Pvu Pvu4g1650 Chr4 43791913 43796358 -
Rops Rops5g00253 Chr5 3945996 3950193 +
Seca Seca12g06861 Chr12 160600114 160603345 +
Spst Spst4g02760 Chr4 67413693 67418117 +
Tpr Tpr5g0263 Chr5 3804696 3810082 +
Tsu Tsu03g03152 Chr03 43543368 43548891 -
Vian Vian8g01463 Chr8 34082788 34086821 -
Vimu Vimu8g01538 Chr8 21271632 21275434 +
Viun Viun4g00306 Chr4 1853199 1857366 +
Vvi Vvi17g0312 Chr17 3262036 3265505 -
Aed Aed7g0223 Chr7 1592471 1598140 +
Ahy Ahy15g2761 Chr15 144955988 144961045 -
Aip Aip05g03078 Chr05 133970569 133975532 -
Apr Apr6g1048 Chr6 15165733 15169881 -
Apr Apr2g1468 Chr2 20717172 20721736 +
Bva Bva04g00830 Chr04 5474099 5476765 +
Car Car06g00251 Chr06 2589621 2592480 +
Cca Cca08g00244 Chr08 3418370 3423873 +
Dod Dod02g3661 Chr02 74918259 74923778 +
Gma Gma07g00853 Chr07 9074301 9078704 +
Gma Gma08g00429 Chr08 3587431 3591700 -
Gso Gso7g0806 Chr7 8875595 8882224 +
Gso Gso7g0806 Chr7 8875595 8882224 +
Lal Lal16g1002 Chr16 6649750 6653878 -
Mtr Mtr6g2160 Chr6 38659936 38665618 -
Ssu Ssu5g3376 Chr5 83809291 83813115 +
Sto Sto8g2174 Chr8 14335258 14339116 +
Vra Vra1g0618 Chr1 7155336 7159433 +