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
Vvi4g1204 Acco12g2116 . Accr10g00009 . . . . . . . . . . . Alju12g0036 . . . Apr3g0303 . . . Bach10g00569 . Bisa01g1827 . Bva08g00784 . . . . . Dere13g0685 . . . Enph14g0574 . Glsi09g0590 . . . Gma02g00484 . . . . . . . . . . . . . . . . . Lapu3g01718 . Lasa4g02305 . Lele53g0035 Lele54g0030 Lele55g1462 Lele56g1398 . . . . . . . . . . Mesa29g02249 . Mibi10g0030 . . Mtr8g2466 Phac3g04028 . . . Prci5g0057 . . Psa4g2233 Pste7g01545 . . . . . Pumo4g02154 . Pvu3g2645 . Rops2g03325 . Seca12g02770 . Spst3g03861 . . . . Sto11g1523 . Tpr4g4213 . . . . Vian1g01792 . Vifa4g02407 . Vimu11g00669 . Viun3g03645 . Vivi1g03058 . . .
Vvi4g1205 Acco12g2117 . Accr10g00008 . . . Aed11g1259 . . Aev08g0257 . Ahy17g2368 Aip05g00852 Aip07g02542 Alju12g0035 . . Amo17g2232 Apr3g0304 . Arst1g00143 . Bach10g00570 . Bisa01g4005 . Bva08g00785 . . . Cca06g01310 . Dere13g0686 . Dod02g0526 Dod08g2212 Enph14g0575 . Glsi09g0591 . . . Gma02g00483 Gma16g01246 . . . . Lal16g1845 . . . . . Lan6g1472 . . . . . . . Lasa4g02304 . Lele53g0034 Lele54g0029 Lele55g1463 Lele56g1399 . . . . Lja2g0497 Lja4g3195 Mal6g1090 . Mepo1g02082 . . . Mibi10g0029 . Mtr5g0822 Mtr8g2465 Phac3g04030 . Phco8g00457 . . . Psa2g3575 Psa4g2235 Pste7g01548 . Pte3g01384 Pte2g00276 . . Pumo4g02155 . Pvu3g2646 . Rops2g03324 . Seca12g02774 . Spst3g03860 . . . . Sto11g1522 Tpr2g1035 Tpr4g4214 Trre15g04101 . Tsu05g00777 Tsu04g03447 Vian1g01793 . Vifa4g02402 . Vimu7g03000 . Viun3g03643 . Vivi1g03059 . Vra11g0729 .
Vvi4g1206 . . . . . . . . . Aev08g0256 . Ahy17g2366 . Aip07g02540 . . . Amo17g2229 Apr3g0305 . . . . . . . Bva08g00786 . . . . . . . . . . . . . . . Gma02g00482 Gma16g01245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00456 . . . . . Pste7g01549 . . Pte2g01256 . . Pumo4g02156 . Pvu3g2647 . . . . . Spst3g03858 . . . . . . . . . . . Vian1g01794 . . . Vimu11g00671 . Viun3g03641 . . . . .
Vvi4g1207 . . . . . . . . . Aev08g0254 . Ahy17g2363 . Aip07g02538 . . . Amo17g2226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1208 . . . . . . . . . Aev08g0252 . Ahy17g2362 . Aip07g02537 . . . Amo17g2225 . . . . . . . . . . . . . . . . . Dod08g2216 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1209 Acco12g2118 . Accr10g00007 . . . . . . . . . . . Alju12g0032 . . . Apr3g0306 . . . . . Bisa01g1824 . Bva08g00787 . . . . . Dere13g0687 . . . Enph14g0576 . Glsi09g0592 . . . Gma02g00481 . . . . . . Lal15g1490 . . . . . . . . . . Lapu3g01720 . Lasa4g02302 . Lele53g0033 . Lele55g1464 Lele56g1400 . . . . . Lja4g3194 . Mal5g3393 Mepo1g02083 . Mesa29g02250 . Mibi10g0027 . . Mtr8g2464 Phac3g04033 . Phco8g00455 . Prci5g0056 . . Psa4g2238 Pste7g01558 . Pte14g00894 . . . . . Pvu3g2648 . . . . . Spst3g03856 . . . . Sto11g1521 . Tpr4g4215 Trre15g04102 . . . . . . . Vimu11g00673 . . . Vivi1g03060 . . .
Vvi4g1210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1211 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lal Lal16g1845 Chr16 17505158 17512786 -
Seca Seca12g02774 Chr12 49282136 49286391 -
Vimu Vimu7g03000 Chr7 25272497 25276462 +
Vvi Vvi4g1204 Chr4 18947784 18950547 +
Acco Acco12g2116 Chr12 32662713 32665773 +
Accr Accr10g00009 Chr10 158572 161688 -
Alju Alju12g0036 Chr12 588200 591329 -
Apr Apr3g0303 Chr3 5870828 5873555 +
Bach Bach10g00569 Chr10 4047151 4049277 +
Bisa Bisa01g1827 Chr01 31755864 31759534 -
Bva Bva08g00784 Chr08 4031789 4034132 +
Dere Dere13g0685 Chr13 8670193 8674798 +
Enph Enph14g0574 Chr14 7606985 7611851 +
Glsi Glsi09g0590 Chr09 4085112 4087921 +
Gma Gma02g00484 Chr02 4901003 4903875 -
Lapu Lapu3g01718 Chr3 27042677 27046443 +
Lasa Lasa4g02305 Chr4 456690086 456694818 -
Lele Lele53g0035 Chr53 290780 295616 -
Lele Lele54g0030 Chr54 300498 304106 -
Lele Lele55g1462 Chr55 20788105 20791864 +
Lele Lele56g1398 Chr56 17055915 17059487 +
Mesa Mesa29g02249 Chr29 30822732 30827379 +
Mibi Mibi10g0030 Chr10 588092 591863 -
Mtr Mtr8g2466 Chr8 35091457 35095908 -
Phac Phac3g04028 Chr3 39803739 39807447 +
Prci Prci5g0057 Chr5 1353345 1364125 -
Psa Psa4g2233 Chr4 179880191 179886566 +
Pste Pste7g01545 Chr7 14180762 14188128 +
Pumo Pumo4g02154 Chr4 31258158 31261057 +
Pvu Pvu3g2645 Chr3 48474121 48477743 +
Rops Rops2g03325 Chr2 61043246 61047134 -
Seca Seca12g02770 Chr12 49091870 49094692 +
Spst Spst3g03861 Chr3 88669778 88672716 -
Sto Sto11g1523 Chr11 14431872 14435052 -
Tpr Tpr4g4213 Chr4 49242518 49246422 +
Vian Vian1g01792 Chr1 21110988 21115798 +
Vifa Vifa4g02407 Chr4 725860408 725868189 -
Vimu Vimu11g00669 Chr11 7158009 7161550 +
Viun Viun3g03645 Chr3 43307314 43311094 -
Vivi Vivi1g03058 Chr1 67559047 67563500 +
Vvi Vvi4g1205 Chr4 18957444 18961809 +
Acco Acco12g2117 Chr12 32667453 32672713 +
Accr Accr10g00008 Chr10 151486 156936 -
Aed Aed11g1259 Chr11 17725842 17733582 -
Aev Aev08g0257 Chr08 1456603 1463292 +
Ahy Ahy17g2368 Chr17 114165204 114169572 +
Aip Aip05g00852 Chr05 11612871 11616907 +
Aip Aip07g02542 Chr07 105958732 105963086 +
Alju Alju12g0035 Chr12 570198 575538 -
Amo Amo17g2232 Chr17 114761753 114766152 +
Apr Apr3g0304 Chr3 5875922 5880743 +
Arst Arst1g00143 Chr1 1238145 1244273 +
Bach Bach10g00570 Chr10 4052423 4057470 +
Bisa Bisa01g4005 Chr01 96408796 96415263 +
Bva Bva08g00785 Chr08 4034856 4040325 +
Cca Cca06g01310 Chr06 27876738 27880839 -
Dere Dere13g0686 Chr13 8676383 8681729 +
Dod Dod02g0526 Chr02 6860642 6866109 -
Dod Dod08g2212 Chr08 49806920 49813129 -
Enph Enph14g0575 Chr14 7616061 7621815 +
Glsi Glsi09g0591 Chr09 4089457 4093850 +
Gma Gma02g00483 Chr02 4891597 4896607 -
Gma Gma16g01246 Chr16 30550379 30555413 -
Lal Lal16g1845 Chr16 17505158 17512786 -
Lan Lan6g1472 Chr6 21570595 21577015 +
Lasa Lasa4g02304 Chr4 456679082 456682471 -
Lele Lele53g0034 Chr53 284539 289478 -
Lele Lele54g0029 Chr54 286509 299157 -
Lele Lele55g1463 Chr55 20793138 20798812 +
Lele Lele56g1399 Chr56 17060799 17068452 +
Lja Lja2g0497 Chr2 4524352 4528866 +
Lja Lja4g3195 Chr4 60404441 60422719 -
Mal Mal6g1090 Chr6 16541743 16545406 -
Mepo Mepo1g02082 Chr1 21432790 21437157 +
Mibi Mibi10g0029 Chr10 585853 587048 -
Mtr Mtr5g0822 Chr5 8088987 8094040 +
Mtr Mtr8g2465 Chr8 35084005 35089597 -
Phac Phac3g04030 Chr3 39809381 39814124 +
Phco Phco8g00457 Chr8 4279035 4284097 -
Psa Psa2g3575 Chr2 389171438 389176015 -
Psa Psa4g2235 Chr4 179897303 179901502 +
Pste Pste7g01548 Chr7 14201666 14205971 +
Pte Pte3g01384 Chr3 12024662 12026787 -
Pte Pte2g00276 Chr2 2219424 2222752 -
Pumo Pumo4g02155 Chr4 31269164 31274370 +
Pvu Pvu3g2646 Chr3 48479752 48484017 +
Rops Rops2g03324 Chr2 61034066 61040701 -
Seca Seca12g02774 Chr12 49282136 49286391 -
Spst Spst3g03860 Chr3 88664369 88668021 -
Sto Sto11g1522 Chr11 14424968 14429250 -
Tpr Tpr2g1035 Chr2 12204074 12209257 +
Tpr Tpr4g4214 Chr4 49247985 49252724 +
Trre Trre15g04101 Chr15 51551669 51555618 +
Tsu Tsu05g00777 Chr05 6561372 6565593 +
Tsu Tsu04g03447 Chr04 43675221 43679952 +
Vian Vian1g01793 Chr1 21124685 21128775 +
Vifa Vifa4g02402 Chr4 725711911 725715106 -
Vimu Vimu7g03000 Chr7 25272497 25276462 +
Viun Viun3g03643 Chr3 43299379 43303670 -
Vivi Vivi1g03059 Chr1 67568880 67573169 +
Vra Vra11g0729 Chr11 5870085 5874324 +
Vvi Vvi4g1206 Chr4 18963085 18965679 -
Aev Aev08g0256 Chr08 1448538 1451246 +
Ahy Ahy17g2366 Chr17 113936712 113940726 +
Aip Aip07g02540 Chr07 105747025 105750620 +
Amo Amo17g2229 Chr17 114522616 114526086 +
Apr Apr3g0305 Chr3 5882667 5886197 -
Bva Bva08g00786 Chr08 4040561 4043265 -
Gma Gma02g00482 Chr02 4886776 4890124 +
Gma Gma16g01245 Chr16 30545710 30549903 +
Phco Phco8g00456 Chr8 4274004 4277264 +
Pste Pste7g01549 Chr7 14209067 14213786 -
Pte Pte2g01256 Chr2 14164841 14168222 -
Pumo Pumo4g02156 Chr4 31276877 31281121 -
Pvu Pvu3g2647 Chr3 48487019 48491229 -
Spst Spst3g03858 Chr3 88658426 88661467 +
Vian Vian1g01794 Chr1 21129726 21132620 -
Vimu Vimu11g00671 Chr11 7174879 7176991 -
Viun Viun3g03641 Chr3 43293924 43297513 +
Vvi Vvi4g1207 Chr4 18973846 18976834 +
Aev Aev08g0254 Chr08 1427721 1429332 -
Ahy Ahy17g2363 Chr17 113601422 113604409 -
Aip Aip07g02538 Chr07 105424505 105427329 -
Amo Amo17g2226 Chr17 113735841 113738855 -
Vvi Vvi4g1208 Chr4 18984081 18984554 +
Aev Aev08g0252 Chr08 1419580 1420083 -
Ahy Ahy17g2362 Chr17 113565674 113567128 -
Aip Aip07g02537 Chr07 105396849 105398333 -
Amo Amo17g2225 Chr17 113698471 113700064 -
Dod Dod08g2216 Chr08 49888382 49890276 +
Vvi Vvi4g1209 Chr4 18987819 19005635 +
Acco Acco12g2118 Chr12 32674461 32678569 +
Accr Accr10g00007 Chr10 145483 149946 -
Alju Alju12g0032 Chr12 540466 544683 -
Apr Apr3g0306 Chr3 5899950 5903459 +
Bisa Bisa01g1824 Chr01 31727633 31734966 -
Bva Bva08g00787 Chr08 4045301 4049704 +
Dere Dere13g0687 Chr13 8682919 8686029 +
Enph Enph14g0576 Chr14 7622964 7628817 +
Glsi Glsi09g0592 Chr09 4094982 4098463 +
Gma Gma02g00481 Chr02 4872034 4875655 -
Lal Lal15g1490 Chr15 17062737 17067913 -
Lapu Lapu3g01720 Chr3 27089052 27093358 +
Lasa Lasa4g02302 Chr4 456670061 456672905 -
Lele Lele53g0033 Chr53 279429 283086 -
Lele Lele55g1464 Chr55 20799435 20803083 +
Lele Lele56g1400 Chr56 17068489 17073093 +
Lja Lja4g3194 Chr4 60397391 60401563 -
Mal Mal5g3393 Chr5 98343157 98346115 -
Mepo Mepo1g02083 Chr1 21442093 21446327 +
Mesa Mesa29g02250 Chr29 30853819 30864283 +
Mibi Mibi10g0027 Chr10 577217 580948 -
Mtr Mtr8g2464 Chr8 35078220 35082417 -
Phac Phac3g04033 Chr3 39833644 39838111 +
Phco Phco8g00455 Chr8 4257669 4261721 -
Prci Prci5g0056 Chr5 1336126 1340100 -
Psa Psa4g2238 Chr4 179988772 179992184 +
Pste Pste7g01558 Chr7 14255604 14258939 +
Pte Pte14g00894 Chr14 30654947 30658487 +
Pvu Pvu3g2648 Chr3 48502713 48506805 +
Spst Spst3g03856 Chr3 88595956 88596535 -
Sto Sto11g1521 Chr11 14419364 14422541 -
Tpr Tpr4g4215 Chr4 49255395 49259356 +
Trre Trre15g04102 Chr15 51556617 51560476 +
Vimu Vimu11g00673 Chr11 7193101 7193952 +
Vivi Vivi1g03060 Chr1 67575156 67578731 +
Vvi Vvi4g1210 Chr4 19007346 19009846 -
Vvi Vvi4g1211 Chr4 19011949 19023037 -
Vvi Vvi4g1212 Chr4 19029240 19031873 +
Vvi Vvi4g1213 Chr4 19034642 19035118 +
Aev Aev08g0257 Chr08 1456603 1463292 +
Ahy Ahy17g2368 Chr17 114165204 114169572 +
Aip Aip07g02542 Chr07 105958732 105963086 +
Amo Amo17g2232 Chr17 114761753 114766152 +
Dod Dod08g2212 Chr08 49806920 49813129 -
Dod Dod08g2212 Chr08 49806920 49813129 -
Gma Gma16g01246 Chr16 30550379 30555413 -
Aev Aev08g0256 Chr08 1448538 1451246 +
Ahy Ahy17g2366 Chr17 113936712 113940726 +
Aip Aip07g02540 Chr07 105747025 105750620 +
Amo Amo17g2229 Chr17 114522616 114526086 +
Gma Gma16g01245 Chr16 30545710 30549903 +
Aev Aev08g0254 Chr08 1427721 1429332 -
Ahy Ahy17g2363 Chr17 113601422 113604409 -
Aip Aip07g02538 Chr07 105424505 105427329 -
Amo Amo17g2226 Chr17 113735841 113738855 -
Aev Aev08g0252 Chr08 1419580 1420083 -
Ahy Ahy17g2362 Chr17 113565674 113567128 -
Aip Aip07g02537 Chr07 105396849 105398333 -
Amo Amo17g2225 Chr17 113698471 113700064 -
Dod Dod08g2216 Chr08 49888382 49890276 +
Dod Dod08g2216 Chr08 49888382 49890276 +