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
Vvi3g0743 . . . . Adu09g02620 . Aed1g1984 . Aev09g2493 . Ahy19g3309 . Aip09g03772 . . . Amo19g4189 . Apr8g2439 . Arst9g03485 . . . . . . Bva14g00438 Car04g01443 . Cca02g02526 . . . Dod06g0465 . . . . . . . . . . . . . . . . Lal13g0391 . Lal24g0307 . . . . . . Lapu7g02299 . Lasa6g04465 . . . . . . . . . Lja5g0416 . . Mal1g0535 Mepo4g04553 . Mesa1g04982 . . . . Mtr1g4059 . . Phco6g02789 . . . Psa6g4949 . Pste4g01125 . . Pte9g01370 . . Pumo3g00649 . Pvu7g0425 . Rops6g03110 . Seca8g07727 . Spst10g01289 . Ssu7g0482 . . Sto10g0332 . Tpr1g0458 Trre1g05803 . . Tsu01g04728 Vian3g00388 . Vifa3g03344 . Vimu3g03386 . Viun7g03630 . Vivi1g03898 . Vra8g2426 .
Vvi3g0744 . . . . . . . . . . . . . . . . . . . Apr7g0016 . . . . . . . Bva14g00439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0745 . . . . Adu09g02619 . Aed1g1985 . Aev09g2492 . Ahy19g3310 Ahy15g1337 Aip09g03773 Aip05g01403 . . Amo19g4284 Amo15g0185 Apr8g2438 . Arst9g03483 . Bach11g00316 . . . Bva13g00357 Bva14g00440 Car04g01442 . Cca02g02525 . . . Dod06g0466 . . . . . . . . . . . . . . . . Lal13g0390 . . . . . . . . . . Lasa6g04464 . . . . . . . . . Lja5g0417 . . Mal1g0538 Mepo4g04552 . Mesa1g04981 . . . . Mtr1g4058 . . Phco6g02788 . . . . . Pste4g01128 . . Pte9g01367 . . Pumo3g00650 . Pvu7g0426 . Rops6g03109 . Seca8g07726 . Spst10g01287 . Ssu7g0483 . Sto2g0522 Sto10g0334 . Tpr1g0459 Trre1g05802 . . Tsu01g04727 . . Vifa3g03340 . Vimu3g03385 . Viun7g03629 . Vivi4g05688 . Vra8g2425 .
Vvi3g0746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0747 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00358 Bva14g00441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0335 . . . . . . . . . . . . . . . . . .
Vvi3g0748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0750 . . . . . . Aed1g1987 . Aev09g2491 . Ahy19g3311 . Aip09g03774 . . . Amo19g4283 . Apr8g2437 . Arst9g03482 . . . . . . Bva14g00442 Car04g01441 . Cca02g02522 . . . Dod06g0467 . . . . . . . . . . . . . . . . . . Lal24g0306 . . . . . . Lapu7g02297 . Lasa6g04463 . . . . . . . . . Lja5g0418 . . Mal1g0542 Mepo4g04551 . Mesa1g04980 . . . . Mtr1g4055 . . Phco6g02787 . . . Psa6g4943 . Pste4g01132 . . . . . Pumo3g00651 . Pvu7g0429 . Rops6g03108 . Seca8g07725 . Spst10g01285 . Ssu7g0485 . . Sto10g0336 . Tpr1g0460 Trre1g05801 . . Tsu01g04726 Vian3g00392 . Vifa3g03335 . Vimu3g03381 . Viun7g03625 . Vivi1g03902 . . .
Vvi3g0751 . . . . . . Aed1g1988 . . . . . . . . . . . Apr8g2436 . . . . . . . . . . . Cca02g02521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g0419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0486 . . . . . . . . . . . . . . . . . . . Vra8g2423 .
Vvi3g0752 . . . . Adu09g02617 . Aed1g1990 . Aev09g2487 . Ahy19g3313 . Aip09g03777 . . . Amo19g4281 . Apr8g2434 . Arst9g03477 . Bach11g00318 . . . Bva13g00359 Bva14g00444 Car04g01438 . Cca02g02516 . . . Dod06g0469 . . . . . . . . . . . . . . . . . . Lal24g0305 . . . . . . Lapu7g02294 . Lasa6g04457 . . . . . . . . . Lja5g0420 . . Mal1g0544 Mepo4g04548 . Mesa1g04978 . . . . Mtr1g4053 . . Phco6g02784 . . . . . Pste4g01138 . . Pte9g01366 . . Pumo3g00654 . Pvu7g0432 . Rops6g03096 . Seca8g07722 . Spst10g01282 . Ssu7g0489 . Sto2g0521 . . Tpr1g0464 Trre1g05797 . . Tsu01g04722 Vian3g00394 . Vifa3g03330 . Vimu3g03378 . Viun7g03622 . Vivi1g03905 . Vra8g2420 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0743 Chr3 6552006 6559802 -
Adu Adu09g02620 Chr09 113661853 113665198 +
Aed Aed1g1984 Chr1 16816215 16820185 -
Aev Aev09g2493 Chr09 26663875 26666575 +
Ahy Ahy19g3309 Chr19 156148259 156151591 -
Aip Aip09g03772 Chr09 144517676 144521845 -
Amo Amo19g4189 Chr19 158542619 158546133 -
Apr Apr8g2439 Chr8 34505516 34509521 +
Arst Arst9g03485 Chr9 111558220 111561544 +
Bva Bva14g00438 Chr14 2132136 2135870 -
Car Car04g01443 Chr04 14687561 14691467 +
Cca Cca02g02526 Chr02 46442151 46445393 +
Dod Dod06g0465 Chr06 5764782 5771138 -
Lal Lal13g0391 Chr13 2457170 2462339 +
Lal Lal24g0307 Chr24 2185937 2189525 +
Lapu Lapu7g02299 Chr7 39269612 39275918 +
Lasa Lasa6g04465 Chr6 643973191 643977630 +
Lja Lja5g0416 Chr5 3688089 3691236 -
Mal Mal1g0535 Chr1 6176476 6179444 -
Mepo Mepo4g04553 Chr4 55239114 55242418 +
Mesa Mesa1g04982 Chr1 76739883 76742802 +
Mtr Mtr1g4059 Chr1 52144695 52148005 +
Phco Phco6g02789 Chr6 49202008 49206757 +
Psa Psa6g4949 Chr6 431156505 431160824 +
Pste Pste4g01125 Chr4 8438023 8440721 -
Pte Pte9g01370 Chr9 35033097 35038041 +
Pumo Pumo3g00649 Chr3 9749160 9754180 -
Pvu Pvu7g0425 Chr7 3340038 3344256 -
Rops Rops6g03110 Chr6 54460779 54466160 +
Seca Seca8g07727 Chr8 174538644 174542553 +
Spst Spst10g01289 Chr10 13537315 13542644 +
Ssu Ssu7g0482 Chr7 9002835 9007736 -
Sto Sto10g0332 Chr10 2653246 2660334 -
Tpr Tpr1g0458 Chr1 3857938 3861351 -
Trre Trre1g05803 Chr1 62824545 62827516 +
Tsu Tsu01g04728 Chr01 54526367 54529689 +
Vian Vian3g00388 Chr3 3687480 3693889 -
Vifa Vifa3g03344 Chr3 958778511 958783010 +
Vimu Vimu3g03386 Chr3 47111978 47114137 +
Viun Viun7g03630 Chr7 37356845 37361262 +
Vivi Vivi1g03898 Chr1 82436676 82441619 -
Vra Vra8g2426 Chr8 42350243 42355760 +
Vvi Vvi3g0744 Chr3 6566136 6568198 -
Apr Apr7g0016 Chr7 918759 920494 +
Bva Bva14g00439 Chr14 2136564 2140019 -
Vvi Vvi3g0745 Chr3 6572070 6589424 -
Adu Adu09g02619 Chr09 113653361 113658356 +
Aed Aed1g1985 Chr1 16820874 16826785 -
Aev Aev09g2492 Chr09 26657151 26662783 +
Ahy Ahy19g3310 Chr19 156152829 156160033 -
Ahy Ahy15g1337 Chr15 22053364 22064370 +
Aip Aip09g03773 Chr09 144523088 144530268 -
Aip Aip05g01403 Chr05 21223910 21235040 +
Amo Amo19g4284 Chr19 159535543 159541964 +
Amo Amo15g0185 Chr15 6982264 6994214 +
Apr Apr8g2438 Chr8 34495038 34503948 +
Arst Arst9g03483 Chr9 111548724 111555251 +
Bach Bach11g00316 Chr11 2143946 2147941 -
Bva Bva13g00357 Chr13 1664386 1670290 -
Bva Bva14g00440 Chr14 2140391 2147137 -
Car Car04g01442 Chr04 14672378 14680596 +
Cca Cca02g02525 Chr02 46429414 46439445 +
Dod Dod06g0466 Chr06 5776021 5780863 -
Lal Lal13g0390 Chr13 2450148 2456487 +
Lasa Lasa6g04464 Chr6 643954366 643960814 +
Lja Lja5g0417 Chr5 3692651 3700735 -
Mal Mal1g0538 Chr1 6185618 6191239 -
Mepo Mepo4g04552 Chr4 55229589 55237033 +
Mesa Mesa1g04981 Chr1 76712633 76718345 +
Mtr Mtr1g4058 Chr1 52135669 52142544 +
Phco Phco6g02788 Chr6 49187571 49199437 +
Pste Pste4g01128 Chr4 8449368 8460203 -
Pte Pte9g01367 Chr9 35016759 35025140 +
Pumo Pumo3g00650 Chr3 9756577 9764099 -
Pvu Pvu7g0426 Chr7 3345492 3354004 -
Rops Rops6g03109 Chr6 54450435 54459180 +
Seca Seca8g07726 Chr8 174526138 174534115 +
Spst Spst10g01287 Chr10 13526435 13533682 +
Ssu Ssu7g0483 Chr7 9011854 9024846 -
Sto Sto2g0522 Chr2 4498817 4503672 +
Sto Sto10g0334 Chr10 2667362 2668327 -
Tpr Tpr1g0459 Chr1 3863498 3871595 -
Trre Trre1g05802 Chr1 62815423 62821419 +
Tsu Tsu01g04727 Chr01 54516141 54524105 +
Vifa Vifa3g03340 Chr3 957740052 957746609 +
Vimu Vimu3g03385 Chr3 47102615 47109719 +
Viun Viun7g03629 Chr7 37348200 37354794 +
Vivi Vivi4g05688 Chr4 193207335 193209194 +
Vra Vra8g2425 Chr8 42342123 42349916 +
Vvi Vvi3g0746 Chr3 6623124 6623261 +
Vvi Vvi3g0747 Chr3 6633819 6635797 +
Bva Bva13g00358 Chr13 1675753 1678114 +
Bva Bva14g00441 Chr14 2151915 2154144 +
Sto Sto10g0335 Chr10 2680532 2682553 +
Vvi Vvi3g0748 Chr3 6642410 6651021 -
Vvi Vvi3g0749 Chr3 6664651 6666079 -
Vvi Vvi3g0750 Chr3 6668268 6688415 +
Aed Aed1g1987 Chr1 16829153 16832116 +
Aev Aev09g2491 Chr09 26651669 26654214 -
Ahy Ahy19g3311 Chr19 156166167 156169426 +
Aip Aip09g03774 Chr09 144536088 144539380 +
Amo Amo19g4283 Chr19 159526039 159529360 -
Apr Apr8g2437 Chr8 34488756 34492505 -
Arst Arst9g03482 Chr9 111543610 111546756 -
Bva Bva14g00442 Chr14 2156482 2159973 +
Car Car04g01441 Chr04 14665606 14668978 -
Cca Cca02g02522 Chr02 46381720 46384805 -
Dod Dod06g0467 Chr06 5783566 5787621 +
Lal Lal24g0306 Chr24 2182132 2185817 -
Lapu Lapu7g02297 Chr7 39239021 39243203 -
Lasa Lasa6g04463 Chr6 643938174 643942303 -
Lja Lja5g0418 Chr5 3701931 3704957 +
Mal Mal1g0542 Chr1 6227063 6230551 +
Mepo Mepo4g04551 Chr4 55215621 55218861 -
Mesa Mesa1g04980 Chr1 76696796 76700538 -
Mtr Mtr1g4055 Chr1 52118402 52122734 -
Phco Phco6g02787 Chr6 49181828 49185073 -
Psa Psa6g4943 Chr6 430831443 430836084 +
Pste Pste4g01132 Chr4 8477221 8481312 +
Pumo Pumo3g00651 Chr3 9784739 9788214 +
Pvu Pvu7g0429 Chr7 3364751 3368673 +
Rops Rops6g03108 Chr6 54441350 54445252 -
Seca Seca8g07725 Chr8 174519097 174522788 -
Spst Spst10g01285 Chr10 13511147 13514652 -
Ssu Ssu7g0485 Chr7 9094178 9097670 +
Sto Sto10g0336 Chr10 2697585 2700905 +
Tpr Tpr1g0460 Chr1 3872287 3875473 +
Trre Trre1g05801 Chr1 62809150 62812073 -
Tsu Tsu01g04726 Chr01 54510320 54513897 -
Vian Vian3g00392 Chr3 3717760 3720999 -
Vifa Vifa3g03335 Chr3 957677422 957680923 -
Vimu Vimu3g03381 Chr3 47080391 47083701 +
Viun Viun7g03625 Chr7 37326849 37330599 +
Vivi Vivi1g03902 Chr1 82486312 82490777 +
Vvi Vvi3g0751 Chr3 6691119 6693011 +
Aed Aed1g1988 Chr1 16832460 16834358 +
Apr Apr8g2436 Chr8 34486428 34488315 -
Cca Cca02g02521 Chr02 46378117 46381611 -
Lja Lja5g0419 Chr5 3713053 3714942 +
Ssu Ssu7g0486 Chr7 9099154 9101144 +
Vra Vra8g2423 Chr8 42329817 42333879 +
Vvi Vvi3g0752 Chr3 6699574 6705581 -
Adu Adu09g02617 Chr09 113639197 113640448 +
Aed Aed1g1990 Chr1 16840903 16842199 -
Aev Aev09g2487 Chr09 26641318 26641791 +
Ahy Ahy19g3313 Chr19 156182412 156184711 -
Aip Aip09g03777 Chr09 144549295 144550543 -
Amo Amo19g4281 Chr19 159510764 159513175 +
Apr Apr8g2434 Chr8 34476831 34478709 +
Arst Arst9g03477 Chr9 111535307 111536980 +
Bach Bach11g00318 Chr11 2166752 2169619 -
Bva Bva13g00359 Chr13 1682857 1684836 -
Bva Bva14g00444 Chr14 2164153 2166092 -
Car Car04g01438 Chr04 14648848 14650793 +
Cca Cca02g02516 Chr02 46360177 46362356 +
Dod Dod06g0469 Chr06 5797464 5799430 -
Lal Lal24g0305 Chr24 2179552 2184463 +
Lapu Lapu7g02294 Chr7 39226429 39228137 +
Lasa Lasa6g04457 Chr6 643532139 643533455 +
Lja Lja5g0420 Chr5 3715528 3717290 -
Mal Mal1g0544 Chr1 6240069 6241212 -
Mepo Mepo4g04548 Chr4 55198014 55199589 +
Mesa Mesa1g04978 Chr1 76683811 76685066 +
Mtr Mtr1g4053 Chr1 52100701 52102343 +
Phco Phco6g02784 Chr6 49169463 49170801 +
Pste Pste4g01138 Chr4 8511971 8513459 -
Pte Pte9g01366 Chr9 35010761 35011652 +
Pumo Pumo3g00654 Chr3 9833990 9836080 -
Pvu Pvu7g0432 Chr7 3379426 3381245 -
Rops Rops6g03096 Chr6 54150930 54152717 +
Seca Seca8g07722 Chr8 174492531 174495006 +
Spst Spst10g01282 Chr10 13501400 13502458 +
Ssu Ssu7g0489 Chr7 9130545 9131804 -
Sto Sto2g0521 Chr2 4494680 4496388 +
Tpr Tpr1g0464 Chr1 3895688 3897493 -
Trre Trre1g05797 Chr1 62793034 62794387 +
Tsu Tsu01g04722 Chr01 54498649 54499852 +
Vian Vian3g00394 Chr3 3730627 3732121 -
Vifa Vifa3g03330 Chr3 956335679 956337473 -
Vimu Vimu3g03378 Chr3 47071411 47072738 +
Viun Viun7g03622 Chr7 37316733 37318498 +
Vivi Vivi1g03905 Chr1 82519974 82521386 +
Vra Vra8g2420 Chr8 42313780 42315557 +