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
Vvi4g1414 . . . Accr5g00525 . Adu03g04232 . . . . . . . . . Alju03g0702 . . Apr3g2040 . . . . . . Bisa07g0499 . . . . . . . Dere02g2433 . . . . . Glsi11g2745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g02346 . Prci3g0484 . . . Pste3g03205 . . . . . . . Pvu2g2104 . . . . . . . . . . . . . . . . . Vian1g02943 . Vifa1g10836 . Vimu11g01354 . . . . . .
Vvi4g1415 . . . . Adu08g02632 . . . . . . . . . . Alju03g0707 . . Apr3g2039 . Arst10g02224 Arst3g05599 . . . Bisa07g0495 . . . . . . . Dere02g2434 . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g01161 . Lasa5g03295 . . . . . . . . . . . . . . Mepo2g03557 . . . . . . . . Phco7g01684 Phco4g02344 . Prci3g0485 . . Pste2g03684 Pste3g03203 . Pte1g02120 . . Pumo10g01628 Pumo6g01569 Pvu9g1521 Pvu2g2103 . . . . Spst9g01740 Spst3g00316 . . . . . . . . . . Vian4g01108 Vian1g02942 Vifa2g03133 Vifa1g10837 Vimu10g01799 . . . . . . .
Vvi4g1416 . . . Accr5g00527 . Adu03g04233 . . . . . . . . . Alju03g0722 . . Apr3g2038 . . Arst3g05600 . Bach11g00660 . Bisa07g0491 . . . . . . . Dere02g2436 . . . . . Glsi11g2751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo2g03563 . . . . . . . Phac2g03107 . . . Prci3g0487 . . . Pste3g03198 . . Pte2g00651 Pte19g00729 . . . Pvu2g2102 . . . . . . . . . . . . . . . . . Vian1g02941 . Vifa1g10838 . Vimu11g01357 . . . . . .
Vvi4g1417 . . . . . Adu05g00275 . . . . . . . . . . . . Apr3g2037 . . Arst5g00348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02096 . Lasa2g03590 . . . . . . . . . . . . . Mepo5g01160 . . . . . . . . . Phco4g00715 . . . . . . . . . . . . . Pvu2g1249 . . . . . Spst2g01051 . . . . . . . . . . . . . . . Vimu7g03254 . . . Vivi2g02681 . .
Vvi4g1418 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1420 . . . Accr5g00527 . Adu10g00577 . . . . . . . . . Alju03g0722 . . . . . . . . . Bisa07g0491 . . . . . . . Dere02g2436 . . . . . Glsi11g2751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Prci3g0487 . . . . . . . . . . . Pvu6g2176 . . . . . . . . . . . . . . . . . . . . . Vimu2g00353 . . . . . .
Vvi4g1421 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mesa5g04518 . . . . . . . Phco11g00135 . . . . . Pste2g01639 . . Pte19g00729 Pte2g00651 . Pumo2g01133 . Pvu6g2175 . . . . . . . . . . . . . . . . . Vian6g02019 . Vifa1g10838 . . . . . . . .
Vvi4g1423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Accr Accr5g00525 Chr5 26455533 26458966 +
Adu Adu03g04232 Chr03 131341621 131343392 +
Alju Alju03g0702 Chr03 30602504 30605700 -
Bisa Bisa07g0499 Chr07 12620690 12630465 -
Dere Dere02g2433 Chr02 26170729 26176598 +
Glsi Glsi11g2745 Chr11 20555528 20558819 +
Phco Phco4g02346 Chr4 44592359 44597217 -
Prci Prci3g0484 Chr3 6276412 6283849 -
Pste Pste3g03205 Chr3 24745471 24747587 -
Pvu Pvu2g2104 Chr2 36454138 36462937 -
Vian Vian1g02943 Chr1 48206297 48212223 -
Vifa Vifa1g10836 Chr1 1822548790 1822551522 +
Vimu Vimu11g01354 Chr11 15077771 15078184 +
Alju Alju03g0707 Chr03 30751350 30757415 +
Arst Arst3g05599 Chr3 130105610 130107686 +
Bisa Bisa07g0495 Chr07 12490994 12495788 -
Dere Dere02g2434 Chr02 26192317 26197268 +
Mepo Mepo2g03557 Chr2 45043737 45047928 +
Phco Phco4g02344 Chr4 44564115 44566370 -
Prci Prci3g0485 Chr3 6326108 6330843 +
Pste Pste3g03203 Chr3 24718708 24722078 +
Pumo Pumo6g01569 Chr6 22872939 22875395 -
Pvu Pvu2g2103 Chr2 36443430 36445904 +
Spst Spst3g00316 Chr3 5607412 5609613 -
Vian Vian1g02942 Chr1 48187325 48192084 +
Vifa Vifa1g10837 Chr1 1823154368 1823156352 +
Accr Accr5g00527 Chr5 26529410 26535610 +
Adu Adu03g04233 Chr03 131347590 131349218 +
Alju Alju03g0722 Chr03 31330051 31333445 +
Arst Arst3g05600 Chr3 130111464 130113445 +
Bach Bach11g00660 Chr11 5023276 5032126 -
Bisa Bisa07g0491 Chr07 12322929 12327013 -
Dere Dere02g2436 Chr02 26279775 26283482 +
Glsi Glsi11g2751 Chr11 20669275 20688018 +
Mepo Mepo2g03563 Chr2 45066214 45070150 +
Phac Phac2g03107 Chr2 32738238 32740388 -
Prci Prci3g0487 Chr3 6326109 6330843 +
Pste Pste3g03198 Chr3 24663028 24665516 -
Pte Pte2g00651 Chr2 5043450 5045439 -
Pte Pte19g00729 Chr19 5825320 5830253 -
Pvu Pvu2g2102 Chr2 36429157 36431813 -
Vian Vian1g02941 Chr1 48120093 48126477 -
Vifa Vifa1g10838 Chr1 1823487681 1823489994 +
Vimu Vimu11g01357 Chr11 15184283 15191918 +
Adu Adu05g00275 Chr05 2935895 2939767 +
Arst Arst5g00348 Chr5 2955239 2959008 +
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lasa Lasa2g03590 Chr2 542825052 542827968 -
Mepo Mepo5g01160 Chr5 11752352 11758889 +
Phco Phco4g00715 Chr4 5473402 5478022 +
Pvu Pvu2g1249 Chr2 24464953 24470016 -
Spst Spst2g01051 Chr2 9209359 9213367 -
Vimu Vimu7g03254 Chr7 27514148 27524512 -
Vivi Vivi2g02681 Chr2 120256375 120261223 +
Vvi Vvi4g1414 Chr4 21075195 21076024 +
Accr Accr5g00525 Chr5 26455533 26458966 +
Adu Adu03g04232 Chr03 131341621 131343392 +
Alju Alju03g0702 Chr03 30602504 30605700 -
Apr Apr3g2040 Chr3 36389957 36393608 +
Bisa Bisa07g0499 Chr07 12620690 12630465 -
Dere Dere02g2433 Chr02 26170729 26176598 +
Glsi Glsi11g2745 Chr11 20555528 20558819 +
Phco Phco4g02346 Chr4 44592359 44597217 -
Prci Prci3g0484 Chr3 6276412 6283849 -
Pste Pste3g03205 Chr3 24745471 24747587 -
Pvu Pvu2g2104 Chr2 36454138 36462937 -
Vian Vian1g02943 Chr1 48206297 48212223 -
Vifa Vifa1g10836 Chr1 1822548790 1822551522 +
Vimu Vimu11g01354 Chr11 15077771 15078184 +
Vvi Vvi4g1415 Chr4 21087493 21089823 +
Adu Adu08g02632 Chr08 42426754 42429408 -
Alju Alju03g0707 Chr03 30751350 30757415 +
Apr Apr3g2039 Chr3 36385759 36390381 +
Arst Arst10g02224 Chr10 78673048 78685478 +
Arst Arst3g05599 Chr3 130105610 130107686 +
Bisa Bisa07g0495 Chr07 12490994 12495788 -
Dere Dere02g2434 Chr02 26192317 26197268 +
Lapu Lapu9g01161 Chr9 25140213 25144051 -
Lasa Lasa5g03295 Chr5 551329901 551332310 +
Mepo Mepo2g03557 Chr2 45043737 45047928 +
Phco Phco7g01684 Chr7 16657352 16661064 +
Phco Phco4g02344 Chr4 44564115 44566370 -
Prci Prci3g0485 Chr3 6326108 6330843 +
Pste Pste2g03684 Chr2 40271270 40276220 +
Pste Pste3g03203 Chr3 24718708 24722078 +
Pte Pte1g02120 Chr1 42376377 42384669 -
Pumo Pumo10g01628 Chr10 21395754 21400354 +
Pumo Pumo6g01569 Chr6 22872939 22875395 -
Pvu Pvu9g1521 Chr9 21539043 21543141 +
Pvu Pvu2g2103 Chr2 36443430 36445904 +
Spst Spst9g01740 Chr9 19282617 19285918 +
Spst Spst3g00316 Chr3 5607412 5609613 -
Vian Vian4g01108 Chr4 17883932 17887401 -
Vian Vian1g02942 Chr1 48187325 48192084 +
Vifa Vifa2g03133 Chr2 900859987 900864152 +
Vifa Vifa1g10837 Chr1 1823154368 1823156352 +
Vimu Vimu10g01799 Chr10 25396451 25399845 -
Vvi Vvi4g1416 Chr4 21096449 21098263 +
Accr Accr5g00527 Chr5 26529410 26535610 +
Adu Adu03g04233 Chr03 131347590 131349218 +
Alju Alju03g0722 Chr03 31330051 31333445 +
Apr Apr3g2038 Chr3 36377508 36381715 +
Arst Arst3g05600 Chr3 130111464 130113445 +
Bach Bach11g00660 Chr11 5023276 5032126 -
Bisa Bisa07g0491 Chr07 12322929 12327013 -
Dere Dere02g2436 Chr02 26279775 26283482 +
Glsi Glsi11g2751 Chr11 20669275 20688018 +
Mepo Mepo2g03563 Chr2 45066214 45070150 +
Phac Phac2g03107 Chr2 32738238 32740388 -
Prci Prci3g0487 Chr3 6326109 6330843 +
Pste Pste3g03198 Chr3 24663028 24665516 -
Pte Pte2g00651 Chr2 5043450 5045439 -
Pte Pte19g00729 Chr19 5825320 5830253 -
Pvu Pvu2g2102 Chr2 36429157 36431813 -
Vian Vian1g02941 Chr1 48120093 48126477 -
Vifa Vifa1g10838 Chr1 1823487681 1823489994 +
Vimu Vimu11g01357 Chr11 15184283 15191918 +
Vvi Vvi4g1417 Chr4 21120062 21127168 +
Adu Adu05g00275 Chr05 2935895 2939767 +
Apr Apr3g2037 Chr3 36368712 36371690 -
Arst Arst5g00348 Chr5 2955239 2959008 +
Lapu Lapu3g02096 Chr3 40603728 40617153 -
Lasa Lasa2g03590 Chr2 542825052 542827968 -
Mepo Mepo5g01160 Chr5 11752352 11758889 +
Phco Phco4g00715 Chr4 5473402 5478022 +
Pvu Pvu2g1249 Chr2 24464953 24470016 -
Spst Spst2g01051 Chr2 9209359 9213367 -
Vimu Vimu7g03254 Chr7 27514148 27524512 -
Vivi Vivi2g02681 Chr2 120256375 120261223 +
Vvi Vvi4g1418 Chr4 21129709 21141708 +
Vvi Vvi4g1419 Chr4 21142199 21144527 +
Vvi Vvi4g1420 Chr4 21152798 21154837 +
Accr Accr5g00527 Chr5 26529410 26535610 +
Adu Adu10g00577 Chr10 6563470 6564948 +
Alju Alju03g0722 Chr03 31330051 31333445 +
Bisa Bisa07g0491 Chr07 12322929 12327013 -
Dere Dere02g2436 Chr02 26279775 26283482 +
Glsi Glsi11g2751 Chr11 20669275 20688018 +
Prci Prci3g0487 Chr3 6326109 6330843 +
Pvu Pvu6g2176 Chr6 31200871 31203250 +
Vimu Vimu2g00353 Chr2 1986406 1988311 -
Vvi Vvi4g1421 Chr4 21163845 21172634 +
Vvi Vvi4g1422 Chr4 21178903 21179991 +
Mesa Mesa5g04518 Chr5 74586248 74589256 +
Phco Phco11g00135 Chr11 860920 862879 -
Pste Pste2g01639 Chr2 17149961 17151679 -
Pte Pte19g00729 Chr19 5825320 5830253 -
Pte Pte2g00651 Chr2 5043450 5045439 -
Pumo Pumo2g01133 Chr2 16577398 16582917 +
Pvu Pvu6g2175 Chr6 31187626 31189850 +
Vian Vian6g02019 Chr6 37292449 37294446 +
Vifa Vifa1g10838 Chr1 1823487681 1823489994 +
Vvi Vvi4g1423 Chr4 21203338 21206019 +
Alju Alju03g0707 Chr03 30751350 30757415 +
Bisa Bisa07g0495 Chr07 12490994 12495788 -
Dere Dere02g2434 Chr02 26192317 26197268 +
Prci Prci3g0485 Chr3 6326108 6330843 +
Vifa Vifa1g10837 Chr1 1823154368 1823156352 +
Accr Accr5g00525 Chr5 26455533 26458966 +
Alju Alju03g0702 Chr03 30602504 30605700 -
Bisa Bisa07g0499 Chr07 12620690 12630465 -
Dere Dere02g2433 Chr02 26170729 26176598 +
Glsi Glsi11g2745 Chr11 20555528 20558819 +
Prci Prci3g0484 Chr3 6276412 6283849 -
Adu Adu08g02632 Chr08 42426754 42429408 -
Arst Arst10g02224 Chr10 78673048 78685478 +
Lapu Lapu9g01161 Chr9 25140213 25144051 -
Lasa Lasa5g03295 Chr5 551329901 551332310 +
Phco Phco7g01684 Chr7 16657352 16661064 +
Pste Pste2g03684 Chr2 40271270 40276220 +
Pte Pte1g02120 Chr1 42376377 42384669 -
Pumo Pumo10g01628 Chr10 21395754 21400354 +
Pvu Pvu9g1521 Chr9 21539043 21543141 +
Spst Spst9g01740 Chr9 19282617 19285918 +
Vian Vian4g01108 Chr4 17883932 17887401 -
Vifa Vifa2g03133 Chr2 900859987 900864152 +
Vimu Vimu10g01799 Chr10 25396451 25399845 -