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
Vvi4g0374 . . . . Adu10g02071 . . . . Aev08g1233 . Ahy20g2286 . Aip10g02705 . . . Amo20g3017 Apr5g1136 . Arst10g02638 . . . . . Bva10g00223 Bva06g02526 Car05g03076 . Cca03g01445 . . . . Dod09g1069 . . . . . . Gma04g00731 Gma06g00720 . . . . Lal21g0399 . Lal17g0297 . . . Lan3g1497 . Lan3g1497 . . . Lapu9g01770 . Lasa5g04244 . . . . . . . . . Lja1g3743 . Mal2g0718 . Mepo3g07572 . Mesa9g05253 . . . Mtr3g4048 . . . Phco7g00890 . . . . . Pste2g02138 . Pte3g01035 . . . Pumo10g00910 . Pvu9g1083 . Rops10g01545 . Seca4g00762 . . . Ssu1g3316 . Sto5g0704 . Tpr7g0459 . Trre5g05400 . Tsu07g00481 . Vian4g01852 . Vifa2g04180 . Vimu10g02771 . Viun9g02870 . Vivi3g00058 . Vra5g1066 .
Vvi4g0375 . . . . Adu10g02077 . . . . Aev08g1234 . Ahy20g2291 . Aip10g02714 . . . . Apr5g1137 . Arst10g02643 . . . . . Bva10g00224 . Car05g03075 . Cca03g01446 . . . . Dod09g1068 . . . . . . Gma04g00730 Gma06g00719 . . . . . . Lal17g0296 . . . . . . . . . Lapu9g01771 . Lasa5g04243 . . . . . . . . . Lja1g3745 . Mal2g0720 . Mepo3g07571 . Mesa9g05252 . . . Mtr3g4047 . . . Phco7g00889 . . . . . Pste2g02137 . . . . . Pumo10g00909 . Pvu9g1082 . Rops10g01544 . Seca4g00764 . . . Ssu1g3317 . Sto5g0705 . Tpr7g0460 . Trre5g05399 . Tsu07g00482 . Vian4g01853 . Vifa2g04179 . Vimu10g02773 . Viun9g02871 . Vivi3g00057 . Vra5g1067 .
Vvi4g0376 . . . . . . . . . . . . . . . . . . Apr5g1139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3201 . . . . . . . . . . . . . . . . . .
Vvi4g0377 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0378 Acco10g2027 Acco05g2403 . Accr3g00607 . . . Aed6g1017 . Aev08g1235 Ahy16g3001 . Aip06g03218 Aip10g02716 Alju08g0769 Alju07g2364 Amo16g3631 . Apr5g1140 Apr9g0152 . Arst6g03499 . . Bisa09g1234 Bisa05g1303 Bva10g00332 Bva06g02524 Car05g03074 . Cca03g01448 Cca05g00658 Dere04g0601 Dere05g2007 Dod08g1548 Dod09g1067 Enph1g1411 Enph7g1062 Glsi08g1550 Glsi10g0849 Gma14g01297 Gma17g01797 Gma04g00728 Gma06g00718 Gso14g1112 Gso14g1112 Gso14g1112 Gso14g1112 Lal21g0398 . Lal17g0295 . . . Lan3g1496 . Lan3g1496 . . . . . . Lasa5g04241 . Lele02g0600 . Lele04g0618 Lele25g0515 Lele26g0532 Lele27g1563 Lele28g0524 Lja1g3746 Lja5g2183 Mal2g0722 . . . . . Mibi05g0694 Mibi08g2085 Mtr3g4046 . . Phac1g01115 Phco7g00793 Phco2g00902 Prci15g0965 Prci2g0819 Psa5g0558 Psa6g0783 Pste2g01851 . Pte3g01102 . . . Pumo10g00042 . Pvu9g0989 Pvu1g0814 . . Seca8g03079 . Spst9g00824 . Ssu1g3319 Ssu5g0702 Sto5g0806 Sto9g3202 Tpr7g0461 . . . Tsu07g00483 . Vian4g01937 . . . Vimu10g02915 . Viun9g03025 . Vivi4g05055 Vivi3g02318 Vra5g1069 Vra6g1241
Vvi4g0379 . . . . . . . Aed6g1018 . . . . . . . . . . . Apr9g0057 . . . . . . . . . . . Cca05g00655 . . . . . . . . Gma14g01295 . . . Gso14g1110 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3747 . . . . . . . . . . . . . . . . . . Psa6g0780 . . . . . . . . . . . . . . . . . Ssu5g0701 . . . . . . . . . . . . . . . . . . . .
Vvi4g0380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0381 . . . . . . . Aed6g1019 . Aev08g1236 Ahy16g3002 Ahy20g2301 Aip06g03219 Aip10g02720 . . Amo16g3632 . Apr5g1141 Apr9g0058 . . . . . . Bva10g00226 . . . Cca03g01449 Cca05g00654 . . Dod08g1549 Dod09g1066 . . . . Gma14g01294 . . . Gso14g1109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0781 . . . . . . . . . . . . . . . . Ssu1g3322 Ssu5g0700 Sto5g0707 Sto9g3203 . . . . . . . . . . . . . . . . Vra5g1071 .
Vvi4g0382 . . . . . . . Aed6g1020 Aev07g1582 . Ahy16g3003 . Aip06g03220 . . . Amo16g3633 . . Apr9g0059 . . . . . . Bva10g00227 . . Car04g03070 . Cca05g00653 . . Dod08g1551 . . . . . Gma14g01293 . . . Gso14g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g5348 . . . . . . . Mtr1g0097 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0699 . Sto9g3204 . Tpr1g3258 . . . Tsu01g00820 . . . . . . . . . . . Vra6g1243
Vvi4g0383 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0374 Chr4 3200325 3211901 -
Adu Adu10g02071 Chr10 91970344 91977970 -
Aev Aev08g1233 Chr08 7724982 7730600 -
Ahy Ahy20g2286 Chr20 125290909 125298249 -
Aip Aip10g02705 Chr10 117449263 117457021 -
Amo Amo20g3017 Chr20 132804329 132812021 -
Apr Apr5g1136 Chr5 15938772 15947973 -
Arst Arst10g02638 Chr10 91258333 91265764 -
Bva Bva10g00223 Chr10 3418473 3424483 -
Bva Bva06g02526 Chr06 16004628 16011443 +
Car Car05g03076 Chr05 75550987 75562605 +
Cca Cca03g01445 Chr03 32864724 32874907 -
Dod Dod09g1069 Chr09 31348518 31362679 +
Gma Gma04g00731 Chr04 6819370 6827710 +
Gma Gma06g00720 Chr06 6533703 6543868 +
Lal Lal21g0399 Chr21 2756020 2762650 +
Lal Lal17g0297 Chr17 1854317 1861591 +
Lan Lan3g1497 Chr3 26491216 26497899 +
Lan Lan3g1497 Chr3 26491216 26497899 +
Lapu Lapu9g01770 Chr9 32565245 32574952 -
Lasa Lasa5g04244 Chr5 642967592 642976761 +
Lja Lja1g3743 Chr1 46972643 46980307 -
Mal Mal2g0718 Chr2 8383641 8391725 -
Mepo Mepo3g07572 Chr3 89061949 89071588 +
Mesa Mesa9g05253 Chr9 87293727 87302841 +
Mtr Mtr3g4048 Chr3 54166323 54176497 +
Phco Phco7g00890 Chr7 7112436 7121721 +
Pste Pste2g02138 Chr2 21430409 21440459 +
Pte Pte3g01035 Chr3 8820933 8826961 -
Pumo Pumo10g00910 Chr10 11871069 11878848 +
Pvu Pvu9g1083 Chr9 15908924 15918483 +
Rops Rops10g01545 Chr10 28815747 28826502 +
Seca Seca4g00762 Chr4 12790307 12803501 -
Ssu Ssu1g3316 Chr1 85946881 85959194 -
Sto Sto5g0704 Chr5 4774182 4780740 -
Tpr Tpr7g0459 Chr7 3899126 3908487 -
Trre Trre5g05400 Chr5 54711696 54720473 +
Tsu Tsu07g00481 Chr07 3749453 3755722 -
Vian Vian4g01852 Chr4 34893315 34902540 -
Vifa Vifa2g04180 Chr2 1225725116 1225734254 +
Vimu Vimu10g02771 Chr10 39059875 39068849 -
Viun Viun9g02870 Chr9 37097954 37106007 -
Vivi Vivi3g00058 Chr3 849665 858908 +
Vra Vra5g1066 Chr5 17059703 17069823 -
Vvi Vvi4g0375 Chr4 3216246 3227825 +
Adu Adu10g02077 Chr10 92175842 92179089 +
Aev Aev08g1234 Chr08 7733113 7735019 +
Ahy Ahy20g2291 Chr20 125553035 125556912 +
Aip Aip10g02714 Chr10 117695534 117697098 +
Apr Apr5g1137 Chr5 15949421 15953430 +
Arst Arst10g02643 Chr10 91463820 91467057 +
Bva Bva10g00224 Chr10 3425489 3428494 +
Car Car05g03075 Chr05 75547867 75550907 -
Cca Cca03g01446 Chr03 32879666 32883582 +
Dod Dod09g1068 Chr09 31341625 31344996 -
Gma Gma04g00730 Chr04 6812788 6816641 -
Gma Gma06g00719 Chr06 6521451 6530613 -
Lal Lal17g0296 Chr17 1849563 1852265 -
Lapu Lapu9g01771 Chr9 32576741 32580703 +
Lasa Lasa5g04243 Chr5 642951494 642953865 -
Lja Lja1g3745 Chr1 46989231 46992519 +
Mal Mal2g0720 Chr2 8405507 8407515 +
Mepo Mepo3g07571 Chr3 89056254 89059279 -
Mesa Mesa9g05252 Chr9 87286659 87289372 -
Mtr Mtr3g4047 Chr3 54160730 54163943 -
Phco Phco7g00889 Chr7 7110026 7112389 -
Pste Pste2g02137 Chr2 21417261 21420863 -
Pumo Pumo10g00909 Chr10 11860110 11864411 -
Pvu Pvu9g1082 Chr9 15903859 15907587 -
Rops Rops10g01544 Chr10 28804168 28806490 -
Seca Seca4g00764 Chr4 12811964 12815686 +
Ssu Ssu1g3317 Chr1 85972664 85976673 +
Sto Sto5g0705 Chr5 4781447 4784176 +
Tpr Tpr7g0460 Chr7 3911718 3914666 +
Trre Trre5g05399 Chr5 54676906 54679812 -
Tsu Tsu07g00482 Chr07 3760690 3763940 +
Vian Vian4g01853 Chr4 34908803 34911620 +
Vifa Vifa2g04179 Chr2 1225351992 1225354254 -
Vimu Vimu10g02773 Chr10 39071760 39074500 +
Viun Viun9g02871 Chr9 37110223 37113894 +
Vivi Vivi3g00057 Chr3 841885 844381 -
Vra Vra5g1067 Chr5 17072215 17075451 +
Vvi Vvi4g0376 Chr4 3229212 3231208 -
Apr Apr5g1139 Chr5 15961014 15962519 -
Sto Sto9g3201 Chr9 32401350 32402927 -
Vvi Vvi4g0377 Chr4 3241702 3245692 +
Vvi Vvi4g0378 Chr4 3247689 3250173 -
Acco Acco10g2027 Chr10 32778014 32780436 +
Acco Acco05g2403 Chr05 39800002 39802556 +
Accr Accr3g00607 Chr3 6831151 6833701 -
Aed Aed6g1017 Chr6 14138207 14143675 +
Aev Aev08g1235 Chr08 7745501 7748306 -
Ahy Ahy16g3001 Chr16 145008410 145014826 -
Aip Aip06g03218 Chr06 128153965 128159321 -
Aip Aip10g02716 Chr10 117856248 117860387 -
Alju Alju08g0769 Chr08 5795520 5797817 -
Alju Alju07g2364 Chr07 49435822 49438417 +
Amo Amo16g3631 Chr16 146959281 146966067 -
Apr Apr5g1140 Chr5 15973815 15977270 -
Apr Apr9g0152 Chr9 1864658 1867183 -
Arst Arst6g03499 Chr6 102730172 102737138 -
Bisa Bisa09g1234 Chr09 17813254 17815530 +
Bisa Bisa05g1303 Chr05 22859269 22862470 -
Bva Bva10g00332 Chr10 4023756 4025923 -
Bva Bva06g02524 Chr06 15988981 15992346 +
Car Car05g03074 Chr05 75522601 75526830 +
Cca Cca03g01448 Chr03 32912062 32916427 -
Cca Cca05g00658 Chr05 16202663 16208108 -
Dere Dere04g0601 Chr04 6002542 6004622 +
Dere Dere05g2007 Chr05 30030876 30033628 -
Dod Dod08g1548 Chr08 35096708 35101415 -
Dod Dod09g1067 Chr09 31290231 31294400 +
Enph Enph1g1411 Chr1 39582385 39585170 +
Enph Enph7g1062 Chr7 16291742 16294310 +
Glsi Glsi08g1550 Chr08 11178021 11180086 -
Glsi Glsi10g0849 Chr10 5445010 5447793 +
Gma Gma14g01297 Chr14 24314362 24320166 -
Gma Gma17g01797 Chr17 27171672 27177243 -
Gma Gma04g00728 Chr04 6786878 6790643 +
Gma Gma06g00718 Chr06 6504742 6507843 +
Gso Gso14g1112 Chr14 22846518 22853080 -
Gso Gso14g1112 Chr14 22846518 22853080 -
Gso Gso14g1112 Chr14 22846518 22853080 -
Gso Gso14g1112 Chr14 22846518 22853080 -
Lal Lal21g0398 Chr21 2742522 2747265 +
Lal Lal17g0295 Chr17 1841638 1846033 +
Lan Lan3g1496 Chr3 26462746 26467417 +
Lan Lan3g1496 Chr3 26462746 26467417 +
Lasa Lasa5g04241 Chr5 642674641 642678243 +
Lele Lele02g0600 Chr02 3604683 3606951 -
Lele Lele04g0618 Chr04 3747195 3749215 -
Lele Lele25g0515 Chr25 3247371 3249979 -
Lele Lele26g0532 Chr26 3377438 3379947 -
Lele Lele27g1563 Chr27 21458478 21461053 +
Lele Lele28g0524 Chr28 3334405 3336905 -
Lja Lja1g3746 Chr1 47013495 47018339 -
Lja Lja5g2183 Chr5 35219501 35223880 +
Mal Mal2g0722 Chr2 8422806 8425970 -
Mibi Mibi05g0694 Chr05 6598523 6600685 -
Mibi Mibi08g2085 Chr08 38280382 38282954 +
Mtr Mtr3g4046 Chr3 54143818 54147724 +
Phac Phac1g01115 Chr1 10834678 10840501 +
Phco Phco7g00793 Chr7 6171024 6173474 +
Phco Phco2g00902 Chr2 11011300 11016104 +
Prci Prci15g0965 Chr15 6100616 6103383 -
Prci Prci2g0819 Chr2 6211205 6214792 -
Psa Psa5g0558 Chr5 45063511 45068520 -
Psa Psa6g0783 Chr6 27407093 27411261 +
Pste Pste2g01851 Chr2 18861320 18863746 +
Pte Pte3g01102 Chr3 9400219 9402463 -
Pumo Pumo10g00042 Chr10 1010853 1013802 -
Pvu Pvu9g0989 Chr9 14828182 14830788 +
Pvu Pvu1g0814 Chr1 11870824 11876387 +
Seca Seca8g03079 Chr8 87053774 87056582 -
Spst Spst9g00824 Chr9 7166450 7168603 +
Ssu Ssu1g3319 Chr1 86018939 86021787 -
Ssu Ssu5g0702 Chr5 17141711 17147117 -
Sto Sto5g0806 Chr5 5478483 5480487 -
Sto Sto9g3202 Chr9 32410806 32413403 -
Tpr Tpr7g0461 Chr7 3941901 3946829 -
Tsu Tsu07g00483 Chr07 3774284 3779188 -
Vian Vian4g01937 Chr4 35983181 35985261 -
Vimu Vimu10g02915 Chr10 40231194 40233659 -
Viun Viun9g03025 Chr9 38041245 38043642 -
Vivi Vivi4g05055 Chr4 181442893 181445155 -
Vivi Vivi3g02318 Chr3 38901750 38903087 +
Vra Vra5g1069 Chr5 17097676 17101207 -
Vra Vra6g1241 Chr6 22339334 22343602 -
Vvi Vvi4g0379 Chr4 3274729 3275969 +
Aed Aed6g1018 Chr6 14189689 14194084 -
Apr Apr9g0057 Chr9 748638 751764 +
Cca Cca05g00655 Chr05 16004070 16006713 +
Gma Gma14g01295 Chr14 24097659 24100770 +
Gso Gso14g1110 Chr14 22644604 22647737 +
Lja Lja1g3747 Chr1 47053163 47056031 +
Psa Psa6g0780 Chr6 27290603 27292863 -
Ssu Ssu5g0701 Chr5 17026888 17029218 +
Vvi Vvi4g0380 Chr4 3279849 3281352 +
Vvi Vvi4g0381 Chr4 3287257 3288898 +
Aed Aed6g1019 Chr6 14248229 14252041 +
Aev Aev08g1236 Chr08 7770571 7774607 +
Ahy Ahy16g3002 Chr16 145050383 145052706 +
Ahy Ahy20g2301 Chr20 126153663 126158757 -
Aip Aip06g03219 Chr06 128201562 128203808 +
Aip Aip10g02720 Chr10 118050561 118054483 +
Amo Amo16g3632 Chr16 147021239 147024273 +
Apr Apr5g1141 Chr5 15996462 15999481 +
Apr Apr9g0058 Chr9 761693 764165 +
Bva Bva10g00226 Chr10 3452324 3456494 +
Cca Cca03g01449 Chr03 32958461 32963445 +
Cca Cca05g00654 Chr05 15979768 15983542 -
Dod Dod08g1549 Chr08 35391007 35393901 +
Dod Dod09g1066 Chr09 31197551 31202146 -
Gma Gma14g01294 Chr14 24076078 24078712 -
Gso Gso14g1109 Chr14 22624206 22627164 -
Psa Psa6g0781 Chr6 27313750 27315788 -
Ssu Ssu1g3322 Chr1 86157274 86157882 +
Ssu Ssu5g0700 Chr5 16957231 16959871 -
Sto Sto5g0707 Chr5 4820770 4822612 +
Sto Sto9g3203 Chr9 32433296 32437302 +
Vra Vra5g1071 Chr5 17169920 17172582 +
Vvi Vvi4g0382 Chr4 3298715 3326185 -
Aed Aed6g1020 Chr6 14251990 14279047 -
Aev Aev07g1582 Chr07 16018280 16020241 -
Ahy Ahy16g3003 Chr16 145053063 145071844 -
Aip Aip06g03220 Chr06 128204243 128224936 -
Amo Amo16g3633 Chr16 147023860 147041976 -
Apr Apr9g0059 Chr9 764977 787528 -
Bva Bva10g00227 Chr10 3457348 3471119 -
Car Car04g03070 Chr04 58711163 58731715 -
Cca Cca05g00653 Chr05 15956434 15979673 +
Dod Dod08g1551 Chr08 35404966 35438020 -
Gma Gma14g01293 Chr14 24044667 24075296 +
Gso Gso14g1108 Chr14 22595528 22624049 +
Mal Mal1g5348 Chr1 127145570 127160717 -
Mtr Mtr1g0097 Chr1 1012192 1027631 -
Ssu Ssu5g0699 Chr5 16923519 16956381 +
Sto Sto9g3204 Chr9 32438264 32451963 -
Tpr Tpr1g3258 Chr1 36990383 37005012 -
Tsu Tsu01g00820 Chr01 7377967 7393277 +
Vra Vra6g1243 Chr6 22445781 22473677 +
Vvi Vvi4g0383 Chr4 3333437 3333701 +
Apr Apr5g1140 Chr5 15973815 15977270 -