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
Vvi4g0124 . . . . . . Aed4g1657 . Aev07g1266 Aev08g0477 Ahy16g3273 Ahy17g3145 Aip06g03517 Aip07g03417 . . . . . . . . . . . . Bva10g00542 Bva06g02252 Car05g02846 . Cca03g01717 . . . Dod08g1821 . . . . . . . Gma04g00491 . . . . . Lal21g0272 . Lal17g0159 . . . Lan3g1142 . Lan3g1142 . . . . . . . . . . . . . . . Lja1g4023 . Mal2g1049 . . . . . . . Mtr3g3782 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu1g3617 . Sto5g1008 . Tpr7g0788 . . . Tsu07g00798 . . . . . . . . . . . Vra5g1379 .
Vvi4g0125 . . . . . . . . Aev07g1070 . Ahy16g3274 . Aip06g03518 . . . . . . . . . . . . . Bva10g00541 . . . . . . . Dod08g1822 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco2g00524 . . . . . Pste8g00211 . . . . . Pumo9g00554 . Pvu1g0460 . . . Seca8g03341 . Spst8g01482 . . . Sto9g3423 . . . . . . . Vian7g00486 . . . Vimu1g02688 . Viun8g00678 . . . .
Vvi4g0126 . . . . . . Aed4g1658 . . Aev08g0478 Ahy16g3275 Ahy17g3144 Aip06g03519 Aip07g03416 . . Amo16g3991 . . . . . . . . . Bva10g00540 . . . Cca03g01716 . . . Dod08g1823 . . . . . . . Gma04g00492 Gma06g00483 . . . . Lal21g0273 Lal4g0171 . . . . Lan3g1141 Lan3g1141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g1007 Sto9g3421 . . . . . . . . . . . . . . . . Vra5g1378 .
Vvi4g0127 . . . . . . . . . Aev08g0479 . Ahy17g3142 . Aip07g03415 . . . . . . . . . . . . . Bva06g02254 Car05g02847 . . . . . . . . . . . . . . . . . . . Lal21g0274 . . . . . Lan3g1140 . . . . . . . . . . . . . . . . . Lja1g4022 . Mal2g1048 . . . . . . . Mtr3g3783 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr7g0787 . . . Tsu07g00797 . . . . . . . . . . . . .
Vvi4g0128 . . . . . . . . . Aev08g0480 Ahy16g3276 Ahy17g3141 Aip06g03520 Aip07g03414 . . Amo16g3992 Amo17g2944 . . . . . . . . Bva10g00538 Bva06g02255 Car05g02848 . . . . . Dod08g1825 . . . . . . . . . . . . . . Lal4g0172 . . . . . . . . . . . . . . . . . . . . . . Lja1g4021 . Mal2g1047 . . . . . . . Mtr3g3784 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g1005 Sto9g3420 Tpr7g0786 . . . Tsu07g00796 . . . . . . . . . . . . .
Vvi4g0129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0130 . . . . Adu08g00882 . . . . Aev08g0481 . Ahy17g3140 . Aip07g03412 . . . . . . . Arst10g02422 Bach12g00387 . . . Bva10g00537 Bva06g02256 Car05g02849 . . . . . . . . . . . . . Gma04g00497 Gma06g00486 . . . . . Lal4g0173 Lal17g0160 . . . . . . . . . . . . . . . . . . . . . Lja1g4020 . Mal2g1046 . Mepo3g07291 . . . . . Mtr3g3785 . . . . Phco2g00505 . . . . Pste2g01351 Pste8g00294 Pte3g01237 . . . Pumo10g00238 Pumo9g00532 Pvu9g0818 Pvu1g0442 Rops10g01253 Rops9g02013 Seca4g01216 . . Spst8g01850 . . Sto5g1003 . Tpr7g0785 . . . . . Vian4g02114 Vian7g00506 . Vifa3g04663 Vimu10g03126 Vimu1g02717 . . . . . .
Vvi4g0131 . . . . . . Aed4g1660 . . Aev08g0482 . Ahy17g3139 . Aip07g03410 . . . . . . . . . . . . Bva10g00536 Bva06g02257 Car05g02850 . Cca03g01714 . . . . . . . . . . . . . . . . . Lal21g0275 . . . . . Lan3g1139 . . . . . . . . . . . . . . . . . Lja1g4019 . Mal2g1045 . . . . . . . Mtr3g3786 . . . . . . . Psa5g0754 . . . . . . . . . . . . . . . . . Ssu1g3615 . Sto5g1002 . Tpr7g0784 . . . Tsu07g00795 . . . . . . . . . . . Vra5g1376 .
Vvi4g0132 . . . . . . . . . Aev08g0483 . Ahy17g3138 . Aip07g03409 . . . . . . . . . . . . Bva10g00535 . Car05g02851 . . . . . . . . . . . . . . . . . . . . . Lal17g0161 . . . . . . . . . . . . . . . . . . . . . Lja1g4018 . Mal2g1044 . . . . . . . Mtr3g3787 . . . . . . . Psa5g0829 . . . . . . . . . . . . . . . . . . . Sto5g1001 . Tpr7g0783 . . . Tsu07g00794 . . . . . . . . . . . . .
Vvi4g0133 . . . . Adu08g00879 . Aed4g1666 . . Aev08g0484 . Ahy17g3137 . Aip07g03408 . . . . . . Arst8g01178 . . . . . Bva10g00534 . Car05g02853 . Cca03g01709 . . . . . . . . . . . Gma04g00499 . . . . . . . Lal17g0162 . . . . . . . . . . . Lasa5g03887 . . . . . . . . . Lja1g4017 . Mal2g1043 . Mepo3g07294 . Mesa9g04842 . . . Mtr3g3788 . . . Phco7g00608 . . . Psa5g0828 . Pste2g01359 . . Pte1g02447 . . Pumo10g00235 . Pvu9g0821 . Rops10g01256 . Seca4g01212 . Spst9g00630 . Ssu1g3610 . Sto5g1000 . Tpr7g0782 . Trre5g05027 . . . . . Vifa2g03797 . Vimu10g03122 . Viun9g03269 . Vivi3g01600 . Vra5g1372 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0124 Chr4 1115013 1118921 -
Aed Aed4g1657 Chr4 21172781 21177083 -
Aev Aev07g1266 Chr07 11292514 11309455 +
Aev Aev08g0477 Chr08 2693482 2696483 -
Ahy Ahy16g3273 Chr16 149412945 149419776 -
Ahy Ahy17g3145 Chr17 133203104 133206751 +
Aip Aip06g03517 Chr06 132403974 132410728 -
Aip Aip07g03417 Chr07 123939926 123943733 +
Bva Bva10g00542 Chr10 5037951 5042462 +
Bva Bva06g02252 Chr06 14696194 14700198 -
Car Car05g02846 Chr05 73506297 73510427 -
Cca Cca03g01717 Chr03 36283781 36287703 +
Dod Dod08g1821 Chr08 42806886 42813149 -
Gma Gma04g00491 Chr04 4386347 4390370 -
Lal Lal21g0272 Chr21 1807414 1810797 -
Lal Lal17g0159 Chr17 974467 978515 -
Lan Lan3g1142 Chr3 23736121 23741108 +
Lan Lan3g1142 Chr3 23736121 23741108 +
Lja Lja1g4023 Chr1 50966716 50971564 +
Mal Mal2g1049 Chr2 12219155 12222775 +
Mtr Mtr3g3782 Chr3 51688082 51692128 -
Ssu Ssu1g3617 Chr1 91618447 91623452 +
Sto Sto5g1008 Chr5 6793724 6797104 +
Tpr Tpr7g0788 Chr7 6935342 6938522 +
Tsu Tsu07g00798 Chr07 6533431 6537058 +
Vra Vra5g1379 Chr5 20549719 20553347 +
Vvi Vvi4g0125 Chr4 1119730 1127582 +
Aev Aev07g1070 Chr07 8149960 8155637 +
Ahy Ahy16g3274 Chr16 149420878 149427248 +
Aip Aip06g03518 Chr06 132411707 132417575 +
Bva Bva10g00541 Chr10 5032290 5037528 -
Dod Dod08g1822 Chr08 42816651 42827823 +
Phco Phco2g00524 Chr2 4895470 4905631 +
Pste Pste8g00211 Chr8 1187888 1194068 -
Pumo Pumo9g00554 Chr9 9264626 9271496 +
Pvu Pvu1g0460 Chr1 4772363 4781592 +
Seca Seca8g03341 Chr8 95857830 95865223 +
Spst Spst8g01482 Chr8 14990085 14996431 +
Sto Sto9g3423 Chr9 33812367 33815976 -
Vian Vian7g00486 Chr7 12111682 12118300 -
Vimu Vimu1g02688 Chr1 38806638 38820191 -
Viun Viun8g00678 Chr8 5437293 5444430 +
Vvi Vvi4g0126 Chr4 1129965 1131419 +
Aed Aed4g1658 Chr4 21181121 21182437 +
Aev Aev08g0478 Chr08 2701355 2702866 +
Ahy Ahy16g3275 Chr16 149443901 149446350 +
Ahy Ahy17g3144 Chr17 133193479 133195410 -
Aip Aip06g03519 Chr06 132431313 132433548 +
Aip Aip07g03416 Chr07 123922127 123923370 -
Amo Amo16g3991 Chr16 151926937 151929366 +
Bva Bva10g00540 Chr10 5027705 5029663 -
Cca Cca03g01716 Chr03 36266373 36268903 -
Dod Dod08g1823 Chr08 42834602 42837289 +
Gma Gma04g00492 Chr04 4396499 4398232 +
Gma Gma06g00483 Chr06 4125953 4128100 +
Lal Lal21g0273 Chr21 1815439 1816884 +
Lal Lal4g0171 Chr4 1080253 1081671 +
Lan Lan3g1141 Chr3 23729451 23731355 -
Lan Lan3g1141 Chr3 23729451 23731355 -
Sto Sto5g1007 Chr5 6782635 6784209 -
Sto Sto9g3421 Chr9 33807572 33809552 -
Vra Vra5g1378 Chr5 20545432 20547158 -
Vvi Vvi4g0127 Chr4 1133825 1141602 -
Aev Aev08g0479 Chr08 2704819 2707325 -
Ahy Ahy17g3142 Chr17 133166209 133169096 +
Aip Aip07g03415 Chr07 123909641 123912507 +
Bva Bva06g02254 Chr06 14706242 14709183 -
Car Car05g02847 Chr05 73515920 73518593 -
Lal Lal21g0274 Chr21 1818676 1821767 -
Lan Lan3g1140 Chr3 23724334 23727298 +
Lja Lja1g4022 Chr1 50961979 50964836 +
Mal Mal2g1048 Chr2 12213489 12216687 +
Mtr Mtr3g3783 Chr3 51694514 51699528 -
Tpr Tpr7g0787 Chr7 6929801 6933510 +
Tsu Tsu07g00797 Chr07 6526447 6530245 +
Vvi Vvi4g0128 Chr4 1148006 1165769 +
Aev Aev08g0480 Chr08 2710524 2716045 +
Ahy Ahy16g3276 Chr16 149466698 149474441 +
Ahy Ahy17g3141 Chr17 133136909 133143831 -
Aip Aip06g03520 Chr06 132453077 132460811 +
Aip Aip07g03414 Chr07 123874781 123880829 -
Amo Amo16g3992 Chr16 151936215 151943869 +
Amo Amo17g2944 Chr17 131718234 131722294 +
Bva Bva10g00538 Chr10 5016894 5023267 -
Bva Bva06g02255 Chr06 14713274 14719071 +
Car Car05g02848 Chr05 73522433 73531600 +
Dod Dod08g1825 Chr08 42865161 42868378 +
Lal Lal4g0172 Chr4 1085301 1093282 +
Lja Lja1g4021 Chr1 50947411 50958584 -
Mal Mal2g1047 Chr2 12200040 12208639 -
Mtr Mtr3g3784 Chr3 51709315 51717898 +
Sto Sto5g1005 Chr5 6763924 6771407 -
Sto Sto9g3420 Chr9 33797142 33804927 -
Tpr Tpr7g0786 Chr7 6919099 6928008 -
Tsu Tsu07g00796 Chr07 6501331 6513354 -
Vvi Vvi4g0129 Chr4 1167250 1170760 -
Vvi Vvi4g0130 Chr4 1179166 1182805 +
Adu Adu08g00882 Chr08 16336420 16339208 -
Aev Aev08g0481 Chr08 2720821 2723426 +
Ahy Ahy17g3140 Chr17 133123792 133128249 -
Aip Aip07g03412 Chr07 123845195 123848053 -
Arst Arst10g02422 Chr10 85356343 85359843 +
Bach Bach12g00387 Chr12 2588789 2591209 +
Bva Bva10g00537 Chr10 5011054 5015874 -
Bva Bva06g02256 Chr06 14719958 14723712 +
Car Car05g02849 Chr05 73536901 73540874 +
Gma Gma04g00497 Chr04 4430156 4450047 -
Gma Gma06g00486 Chr06 4151173 4155360 -
Lal Lal4g0173 Chr4 1096431 1100293 +
Lal Lal17g0160 Chr17 980292 983869 +
Lja Lja1g4020 Chr1 50937458 50941862 -
Mal Mal2g1046 Chr2 12194122 12196795 -
Mepo Mepo3g07291 Chr3 86487078 86491250 +
Mtr Mtr3g3785 Chr3 51722791 51727098 +
Phco Phco2g00505 Chr2 4641865 4646308 +
Pste Pste2g01351 Chr2 14830331 14835680 -
Pste Pste8g00294 Chr8 1609277 1614387 -
Pte Pte3g01237 Chr3 10555391 10559351 +
Pumo Pumo10g00238 Chr10 3251368 3257166 +
Pumo Pumo9g00532 Chr9 8499219 8508035 +
Pvu Pvu9g0818 Chr9 12874523 12879443 -
Pvu Pvu1g0442 Chr1 4495045 4500430 +
Rops Rops10g01253 Chr10 25113110 25116717 +
Rops Rops9g02013 Chr9 37158277 37163325 -
Seca Seca4g01216 Chr4 19317431 19322582 -
Spst Spst8g01850 Chr8 22545973 22550396 -
Sto Sto5g1003 Chr5 6758576 6761102 -
Tpr Tpr7g0785 Chr7 6913345 6917521 -
Vian Vian4g02114 Chr4 37996935 38000207 +
Vian Vian7g00506 Chr7 12436677 12440727 -
Vifa Vifa3g04663 Chr3 1338720751 1338722939 -
Vimu Vimu10g03126 Chr10 41978836 41980262 +
Vimu Vimu1g02717 Chr1 39200352 39203567 -
Vvi Vvi4g0131 Chr4 1184535 1191818 -
Aed Aed4g1660 Chr4 21187138 21194467 +
Aev Aev08g0482 Chr08 2730023 2735634 -
Ahy Ahy17g3139 Chr17 133116327 133122034 +
Aip Aip07g03410 Chr07 123837999 123843326 +
Bva Bva10g00536 Chr10 5003473 5010347 +
Bva Bva06g02257 Chr06 14724160 14727998 -
Car Car05g02850 Chr05 73542040 73547966 -
Cca Cca03g01714 Chr03 36249663 36256768 -
Lal Lal21g0275 Chr21 1823167 1830559 -
Lan Lan3g1139 Chr3 23714374 23722093 +
Lja Lja1g4019 Chr1 50926846 50935111 +
Mal Mal2g1045 Chr2 12183962 12190272 +
Mtr Mtr3g3786 Chr3 51728542 51734922 -
Psa Psa5g0754 Chr5 61662735 61663641 -
Ssu Ssu1g3615 Chr1 91568209 91575046 -
Sto Sto5g1002 Chr5 6748237 6755430 +
Tpr Tpr7g0784 Chr7 6905417 6911862 +
Tsu Tsu07g00795 Chr07 6493414 6499709 +
Vra Vra5g1376 Chr5 20531298 20538573 -
Vvi Vvi4g0132 Chr4 1195253 1195831 +
Aev Aev08g0483 Chr08 2736341 2736825 +
Ahy Ahy17g3138 Chr17 133085115 133086547 -
Aip Aip07g03409 Chr07 123814412 123815790 -
Bva Bva10g00535 Chr10 5001183 5001721 -
Car Car05g02851 Chr05 73549929 73550794 +
Lal Lal17g0161 Chr17 984315 986019 +
Lja Lja1g4018 Chr1 50924311 50925344 -
Mal Mal2g1044 Chr2 12179114 12179529 -
Mtr Mtr3g3787 Chr3 51736543 51737314 +
Psa Psa5g0829 Chr5 65811803 65812802 -
Sto Sto5g1001 Chr5 6744662 6745435 -
Tpr Tpr7g0783 Chr7 6899707 6902935 -
Tsu Tsu07g00794 Chr07 6487469 6488029 -
Vvi Vvi4g0133 Chr4 1197521 1200756 -
Adu Adu08g00879 Chr08 16311938 16314831 +
Aed Aed4g1666 Chr4 21228074 21230140 -
Aev Aev08g0484 Chr08 2738274 2740795 -
Ahy Ahy17g3137 Chr17 133082126 133085062 +
Aip Aip07g03408 Chr07 123811421 123814425 +
Arst Arst8g01178 Chr8 16280504 16283402 +
Bva Bva10g00534 Chr10 4997001 5000162 +
Car Car05g02853 Chr05 73557385 73562819 -
Cca Cca03g01709 Chr03 36163769 36166260 -
Gma Gma04g00499 Chr04 4458956 4462447 -
Lal Lal17g0162 Chr17 986253 989194 -
Lasa Lasa5g03887 Chr5 606748774 606750949 -
Lja Lja1g4017 Chr1 50921564 50923858 +
Mal Mal2g1043 Chr2 12172575 12177723 +
Mepo Mepo3g07294 Chr3 86507670 86510720 -
Mesa Mesa9g04842 Chr9 82730474 82732901 -
Mtr Mtr3g3788 Chr3 51738077 51740640 -
Phco Phco7g00608 Chr7 4591961 4594342 -
Psa Psa5g0828 Chr5 65807533 65810545 +
Pste Pste2g01359 Chr2 14908833 14912201 -
Pte Pte1g02447 Chr1 45034999 45038132 +
Pumo Pumo10g00235 Chr10 3199622 3227708 +
Pvu Pvu9g0821 Chr9 12904444 12907152 -
Rops Rops10g01256 Chr10 25133910 25136569 -
Seca Seca4g01212 Chr4 19286654 19288558 +
Spst Spst9g00630 Chr9 5506503 5509156 -
Ssu Ssu1g3610 Chr1 91499504 91502266 -
Sto Sto5g1000 Chr5 6739949 6743398 +
Tpr Tpr7g0782 Chr7 6894724 6899048 +
Trre Trre5g05027 Chr5 51807135 51809491 -
Vifa Vifa2g03797 Chr2 1112184180 1112195261 -
Vimu Vimu10g03122 Chr10 41941864 41944638 +
Viun Viun9g03269 Chr9 39582791 39585805 +
Vivi Vivi3g01600 Chr3 26172433 26174822 +
Vra Vra5g1372 Chr5 20491382 20494517 +
Arst Arst10g02422 Chr10 85356343 85359843 +
Adu Adu08g00882 Chr08 16336420 16339208 -
Bach Bach12g00387 Chr12 2588789 2591209 +
Mepo Mepo3g07291 Chr3 86487078 86491250 +
Pste Pste2g01351 Chr2 14830331 14835680 -
Pte Pte3g01237 Chr3 10555391 10559351 +
Pumo Pumo10g00238 Chr10 3251368 3257166 +
Pvu Pvu9g0818 Chr9 12874523 12879443 -
Rops Rops10g01253 Chr10 25113110 25116717 +
Seca Seca4g01216 Chr4 19317431 19322582 -
Vian Vian4g02114 Chr4 37996935 38000207 +
Vimu Vimu10g03126 Chr10 41978836 41980262 +
Arst Arst10g02422 Chr10 85356343 85359843 +
Phco Phco2g00505 Chr2 4641865 4646308 +
Pste Pste8g00294 Chr8 1609277 1614387 -
Pumo Pumo9g00532 Chr9 8499219 8508035 +
Pvu Pvu1g0442 Chr1 4495045 4500430 +
Rops Rops9g02013 Chr9 37158277 37163325 -
Spst Spst8g01850 Chr8 22545973 22550396 -
Vian Vian7g00506 Chr7 12436677 12440727 -
Vifa Vifa3g04663 Chr3 1338720751 1338722939 -
Vimu Vimu1g02717 Chr1 39200352 39203567 -
Lal Lal4g0172 Chr4 1085301 1093282 +
Pste Pste8g00294 Chr8 1609277 1614387 -