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
Vvi16g0869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma09g02405 . . . Gso9g2166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0870 . . . . . . . Aed7g0567 Aev05g2938 . Ahy15g3511 . Aip05g03816 . . . . . . Apr6g0720 . . Bach1g01190 . . . Bva03g01421 . . . . Cca08g00637 . . Dod02g3060 . . . . . Gma16g01594 . . . Gso16g1555 . . . Lal1g0822 . . . . . Lan13g0978 . . . . . . . . . . . . . . . . . Lja2g2592 . . . . . . . . . . Mtr6g1369 . . . . . . . . Pste9g01191 . . . . . . . Pvu4g1246 . . . . . Spst4g03175 . . . Sto10g2563 . . Tpr2g4364 . . . . . . . . . . . . Vivi2g05462 . . Vra1g1873
Vvi16g0871 . . . . . Adu09g02380 Aed1g2247 . . Aev09g2240 . Ahy19g3546 . Aip09g04006 . . . Amo19g4449 . . . Arst9g03136 . . . . Bva03g01420 . . . Cca02g02273 . . . . Dod06g0768 . . . . Gma10g02243 . . . Gso10g2112 . . . . . . . Lal12g0044 . . . . . . . . Lapu7g02056 . Lasa6g04119 . . . . . . . . . Lja5g0616 Mal1g2023 . . Mepo4g04257 . Mesa1g04670 . . Mtr1g3770 . . Phac7g01036 . Phco6g02494 . . Psa6g4564 . . Pste4g01898 . . . . . Pumo3g00926 . Pvu7g0706 . Rops6g02766 . Seca8g07405 . Spst10g00992 Ssu7g0768 . Sto10g2564 . Tpr1g0730 . . Trre1g05426 Tsu01g04446 . . Vian3g00619 . Vifa3g02944 . Vimu3g03077 . Viun7g03286 . Vivi1g04352 Vra8g2251 .
Vvi16g0872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0873 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva03g01419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0874 . . . . . . Aed1g2248 . . Aev09g2239 . Ahy19g3547 . Aip09g04007 . . . . . . . . . . . . Bva03g01418 Bva04g01136 . . Cca02g02272 . . . . . . . . . Gma10g02242 . . . Gso10g2111 . . . . . . . Lal12g0045 . . . . . . . . . . . . . . . . . . . . Lja5g0617 Mal1g2024 . . . . . . . Mtr1g3769 . . . . . . . Psa6g4563 . . . . . . . . . . . . . . . . . Ssu7g0769 . Sto10g2565 . Tpr1g0731 . . . Tsu01g04445 . . . . . . . . . . . . .
Vvi16g0875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0876 . . . . . . Aed1g2250 . Aev05g2934 Aev09g2238 Ahy15g3512 Ahy19g3548 Aip05g03817 Aip09g04008 . . . Amo19g4448 . Apr6g0719 . . . . . . Bva03g01417 Bva04g01137 . . Cca02g02271 . . . Dod02g3058 Dod06g0769 . . . . Gma10g02241 . . . Gso10g2110 . . . Lal1g0824 . . Lal24g0039 Lal12g0046 . . . . . . . . . . . . . . . . . . . Lja2g2593 . Mal1g2025 . . . . . . . Mtr1g3768 Mtr6g1377 . . . . . . Psa6g4562 . . . . . . . . . . . . . . . . . Ssu7g0770 . . . Tpr1g0732 Tpr2g4367 . . Tsu01g04443 . . . . . . . . . . . Vra8g2250 .
Vvi16g0877 . . . . . Adu09g02377 Aed1g2251 . . . . Ahy19g3549 . Aip09g04009 . . . Amo19g4447 . . . Arst9g03133 . . . . . Bva04g01138 . . Cca02g02270 . . . . Dod06g0770 . . . . Gma10g02240 . . . Gso10g2109 . . . . . . Lal24g0040 . . . . . . . . . . . Lasa6g04116 . . . . . . . . . . Mal1g2026 . . Mepo4g04254 . . . . Mtr1g3767 . . Phac7g01044 . Phco6g02492 . . Psa6g4561 . . Pste4g01903 . . Pte16g00263 . . Pumo3g00929 . Pvu7g0708 . Rops6g02759 . Seca8g07400 . Spst10g00989 Ssu7g0771 . Sto10g2567 . Tpr1g0733 . . Trre1g05422 Tsu01g04442 . . Vian3g00621 . . . Vimu3g03075 . Viun7g03282 . Vivi1g04355 Vra8g2249 .
Vvi16g0878 . . . . . . Aed1g2252 . Aev05g2932 Aev09g2237 Ahy15g3513 Ahy19g3550 Aip05g03818 Aip09g04010 . . . Amo19g4446 . Apr6g0718 . . . . . . Bva03g01416 . . . Cca02g02269 . . . Dod02g3055 Dod06g0771 . . . . Gma10g02239 . . . Gso10g2108 . . . . . Lal9g0804 . Lal12g0047 Lal13g0035 . . . . . . . . . . . . . . . . . . Lja2g2595 Lja5g0618 Mal1g2027 . . . . . . . Mtr1g3766 . . . . . . . Psa6g4560 . . . . . . . . . . . . . . . . . Ssu7g0772 . Sto10g2568 . Tpr1g0734 . . . Tsu01g04441 . . . . . . . . . . . Vra8g2248 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Gma Gma09g02405 Chr09 49363521 49366999 -
Vvi Vvi16g0869 Chr16 16807669 16809342 +
Gma Gma09g02405 Chr09 49363521 49366999 -
Gso Gso9g2166 Chr9 45937290 45940841 -
Vvi Vvi16g0870 Chr16 16810894 16818602 +
Aed Aed7g0567 Chr7 4135622 4145618 +
Aev Aev05g2938 Chr05 30147625 30152349 -
Ahy Ahy15g3511 Chr15 157863018 157867409 +
Aip Aip05g03816 Chr05 146402846 146407111 +
Apr Apr6g0720 Chr6 11198741 11204938 -
Bach Bach1g01190 Chr1 25152827 25164537 -
Bva Bva03g01421 Chr03 13567800 13575594 -
Cca Cca08g00637 Chr08 11537564 11545837 +
Dod Dod02g3060 Chr02 64823731 64825108 -
Gma Gma16g01594 Chr16 36763507 36770459 -
Gso Gso16g1555 Chr16 36108707 36115878 -
Lal Lal1g0822 Chr1 5658020 5677251 +
Lan Lan13g0978 Chr13 14114219 14119015 +
Lja Lja2g2592 Chr2 35127691 35142054 +
Mtr Mtr6g1369 Chr6 21213149 21221501 +
Pste Pste9g01191 Chr9 9670767 9674033 -
Pvu Pvu4g1246 Chr4 38353254 38358559 -
Spst Spst4g03175 Chr4 71353834 71354192 +
Sto Sto10g2563 Chr10 35936252 35943618 +
Tpr Tpr2g4364 Chr2 47467120 47473547 +
Vivi Vivi2g05462 Chr2 179958138 179963150 -
Vra Vra1g1873 Chr1 35718379 35735302 -
Vvi Vvi16g0871 Chr16 16825838 16834775 -
Adu Adu09g02380 Chr09 111093324 111099600 +
Aed Aed1g2247 Chr1 18698573 18706876 -
Aev Aev09g2240 Chr09 25031965 25038505 +
Ahy Ahy19g3546 Chr19 158181921 158188492 -
Aip Aip09g04006 Chr09 146461642 146467911 -
Amo Amo19g4449 Chr19 161467836 161474373 +
Arst Arst9g03136 Chr9 108990471 108997042 +
Bva Bva03g01420 Chr03 13557353 13568867 +
Cca Cca02g02273 Chr02 43243078 43252778 +
Dod Dod06g0768 Chr06 9321459 9329587 -
Gma Gma10g02243 Chr10 49993379 49996899 +
Gso Gso10g2112 Chr10 48113000 48115653 +
Lal Lal12g0044 Chr12 306319 315437 -
Lapu Lapu7g02056 Chr7 36781138 36789874 +
Lasa Lasa6g04119 Chr6 618466033 618474992 +
Lja Lja5g0616 Chr5 5525387 5533961 -
Mal Mal1g2023 Chr1 26560530 26572227 -
Mepo Mepo4g04257 Chr4 52367086 52377209 +
Mesa Mesa1g04670 Chr1 72597664 72606852 +
Mtr Mtr1g3770 Chr1 49269093 49278828 +
Phac Phac7g01036 Chr7 6558094 6566922 -
Phco Phco6g02494 Chr6 46350310 46358262 +
Psa Psa6g4564 Chr6 397241892 397250612 +
Pste Pste4g01898 Chr4 14166529 14180536 -
Pumo Pumo3g00926 Chr3 14344274 14353032 -
Pvu Pvu7g0706 Chr7 6241888 6250847 -
Rops Rops6g02766 Chr6 49660068 49677014 +
Seca Seca8g07405 Chr8 170989005 170992411 +
Spst Spst10g00992 Chr10 10583559 10591392 +
Ssu Ssu7g0768 Chr7 15498812 15506942 -
Sto Sto10g2564 Chr10 35945734 35955799 -
Tpr Tpr1g0730 Chr1 6181344 6190802 -
Trre Trre1g05426 Chr1 59855577 59866118 +
Tsu Tsu01g04446 Chr01 52142746 52153054 +
Vian Vian3g00619 Chr3 6251351 6259662 -
Vifa Vifa3g02944 Chr3 827611273 827619853 +
Vimu Vimu3g03077 Chr3 44578626 44587609 +
Viun Viun7g03286 Chr7 34956652 34965496 +
Vivi Vivi1g04352 Chr1 92851848 92861150 -
Vra Vra8g2251 Chr8 40763479 40772894 +
Vvi Vvi16g0872 Chr16 16851591 16852046 +
Vvi Vvi16g0873 Chr16 16867341 16874495 +
Bva Bva03g01419 Chr03 13550951 13552168 -
Vvi Vvi16g0874 Chr16 16882428 16894806 +
Aed Aed1g2248 Chr1 18710636 18714810 +
Aev Aev09g2239 Chr09 25029808 25031880 -
Ahy Ahy19g3547 Chr19 158188651 158191111 +
Aip Aip09g04007 Chr09 146468130 146470555 +
Bva Bva03g01418 Chr03 13542535 13546620 -
Bva Bva04g01136 Chr04 7638636 7642628 +
Cca Cca02g02272 Chr02 43236172 43239715 -
Gma Gma10g02242 Chr10 49989500 49992996 -
Gso Gso10g2111 Chr10 48109382 48113136 -
Lal Lal12g0045 Chr12 317264 319518 +
Lja Lja5g0617 Chr5 5537418 5541547 +
Mal Mal1g2024 Chr1 26576895 26583161 +
Mtr Mtr1g3769 Chr1 49258581 49263378 -
Psa Psa6g4563 Chr6 397234480 397239730 -
Ssu Ssu7g0769 Chr7 15516813 15520801 +
Sto Sto10g2565 Chr10 35960129 35963667 +
Tpr Tpr1g0731 Chr1 6193261 6197943 +
Tsu Tsu01g04445 Chr01 52135311 52139601 -
Vvi Vvi16g0875 Chr16 16896149 16897678 -
Vvi Vvi16g0876 Chr16 16907193 16908873 +
Aed Aed1g2250 Chr1 18718690 18721019 +
Aev Aev05g2934 Chr05 30127294 30128235 -
Aev Aev09g2238 Chr09 25023136 25025179 -
Ahy Ahy15g3512 Chr15 157878280 157882706 +
Ahy Ahy19g3548 Chr19 158194883 158196550 +
Aip Aip05g03817 Chr05 146415924 146421094 +
Aip Aip09g04008 Chr09 146474285 146475925 +
Amo Amo19g4448 Chr19 161459809 161461137 -
Apr Apr6g0719 Chr6 11180710 11183413 -
Bva Bva03g01417 Chr03 13532248 13533993 -
Bva Bva04g01137 Chr04 7649515 7651412 +
Cca Cca02g02271 Chr02 43227435 43229964 -
Dod Dod02g3058 Chr02 64790661 64793273 -
Dod Dod06g0769 Chr06 9347901 9350842 +
Gma Gma10g02241 Chr10 49982265 49984891 -
Gso Gso10g2110 Chr10 48102073 48104830 -
Lal Lal1g0824 Chr1 5685515 5689419 +
Lal Lal24g0039 Chr24 274463 278235 +
Lal Lal12g0046 Chr12 322712 325575 +
Lja Lja2g2593 Chr2 35148236 35151746 +
Mal Mal1g2025 Chr1 26597354 26599583 +
Mtr Mtr1g3768 Chr1 49249423 49251874 -
Mtr Mtr6g1377 Chr6 21470968 21474595 +
Psa Psa6g4562 Chr6 397181669 397183821 -
Ssu Ssu7g0770 Chr7 15542433 15545101 +
Tpr Tpr1g0732 Chr1 6202640 6205117 +
Tpr Tpr2g4367 Chr2 47493521 47498375 +
Tsu Tsu01g04443 Chr01 52125249 52127057 -
Vra Vra8g2250 Chr8 40755699 40758277 -
Vvi Vvi16g0877 Chr16 16909806 16910663 -
Adu Adu09g02377 Chr09 111082026 111084055 +
Aed Aed1g2251 Chr1 18721734 18723317 -
Ahy Ahy19g3549 Chr19 158197010 158199341 -
Aip Aip09g04009 Chr09 146476704 146478597 -
Amo Amo19g4447 Chr19 161457243 161459445 +
Arst Arst9g03133 Chr9 108979169 108981572 +
Bva Bva04g01138 Chr04 7651948 7653510 -
Cca Cca02g02270 Chr02 43223485 43225047 +
Dod Dod06g0770 Chr06 9350549 9352188 -
Gma Gma10g02240 Chr10 49979353 49981174 +
Gso Gso10g2109 Chr10 48099083 48101155 +
Lal Lal24g0040 Chr24 274834 278335 -
Lasa Lasa6g04116 Chr6 618114739 618115821 +
Mal Mal1g2026 Chr1 26599940 26602023 -
Mepo Mepo4g04254 Chr4 52348939 52350796 +
Mtr Mtr1g3767 Chr1 49247085 49249304 +
Phac Phac7g01044 Chr7 6580610 6582756 -
Phco Phco6g02492 Chr6 46336448 46337863 +
Psa Psa6g4561 Chr6 397174957 397176359 +
Pste Pste4g01903 Chr4 14230128 14231596 -
Pte Pte16g00263 Chr16 3579826 3580712 +
Pumo Pumo3g00929 Chr3 14370288 14372150 -
Pvu Pvu7g0708 Chr7 6263431 6265344 -
Rops Rops6g02759 Chr6 49577350 49579901 +
Seca Seca8g07400 Chr8 170945584 170946307 +
Spst Spst10g00989 Chr10 10573175 10574544 +
Ssu Ssu7g0771 Chr7 15546961 15548410 -
Sto Sto10g2567 Chr10 35980098 35983597 -
Tpr Tpr1g0733 Chr1 6205885 6207471 -
Trre Trre1g05422 Chr1 59829421 59831838 +
Tsu Tsu01g04442 Chr01 52122333 52124138 +
Vian Vian3g00621 Chr3 6273081 6274477 -
Vimu Vimu3g03075 Chr3 44568042 44569432 +
Viun Viun7g03282 Chr7 34945082 34946999 +
Vivi Vivi1g04355 Chr1 92890943 92893290 -
Vra Vra8g2249 Chr8 40753445 40755272 +
Vvi Vvi16g0878 Chr16 16918859 16920865 +
Aed Aed1g2252 Chr1 18724912 18726620 +
Aev Aev05g2932 Chr05 30115274 30117887 -
Aev Aev09g2237 Chr09 25014978 25016885 -
Ahy Ahy15g3513 Chr15 157883975 157885646 +
Ahy Ahy19g3550 Chr19 158200079 158201994 +
Aip Aip05g03818 Chr05 146422379 146423796 +
Aip Aip09g04010 Chr09 146479458 146480940 +
Amo Amo19g4446 Chr19 161454352 161456182 -
Apr Apr6g0718 Chr6 11169534 11172360 -
Bva Bva03g01416 Chr03 13526068 13529452 -
Cca Cca02g02269 Chr02 43218586 43220950 -
Dod Dod02g3055 Chr02 64764597 64766703 -
Dod Dod06g0771 Chr06 9362969 9365389 +
Gma Gma10g02239 Chr10 49975008 49977473 -
Gso Gso10g2108 Chr10 48094282 48096906 -
Lal Lal9g0804 Chr9 5811348 5814205 +
Lal Lal12g0047 Chr12 327927 329620 +
Lal Lal13g0035 Chr13 244955 246101 +
Lja Lja2g2595 Chr2 35191272 35194950 +
Lja Lja5g0618 Chr5 5545746 5557175 +
Mal Mal1g2027 Chr1 26608807 26611205 +
Mtr Mtr1g3766 Chr1 49238808 49241272 -
Psa Psa6g4560 Chr6 397148257 397149884 -
Ssu Ssu7g0772 Chr7 15556284 15558148 +
Sto Sto10g2568 Chr10 35988638 35991263 +
Tpr Tpr1g0734 Chr1 6213036 6215399 +
Tsu Tsu01g04441 Chr01 52115601 52117632 -
Vra Vra8g2248 Chr8 40749423 40752421 -