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
Vvi17g0573 . . . . . . Aed10g1025 Aed6g1558 Aev01g2104 . Ahy11g1878 . Aip01g02076 . . . . . Apr1g0898 . . . . Bach2g02037 . . Bva06g01245 . . Car05g00752 Cca03g00551 Cca11g01938 . . Dod05g1720 . . . . . Gma06g01709 Gma04g01674 . Gma17g00926 Gso6g1610 Gso6g1610 . Gso6g1610 . Lal7g1401 . Lal17g1007 . . . . . . . . . Lapu9g00667 . . . . . . . . . . Lja1g5499 Lja4g2162 Mal5g4230 Mal2g4861 . . . . . . Mtr4g3912 Mtr3g0951 . . . Phco7g02275 . . . Psa5g4386 . . . . . . . . . Pvu9g1955 . . . . . Spst9g02327 Ssu1g2138 Ssu6g1282 . . . Tpr3g4388 . Trre5g01670 . Tsu03g01596 . . . . . Vimu10g01006 . . . Vivi3g06263 Vra3g1096 .
Vvi17g0574 Acco04g2709 . Accr8g00052 . Adu01g03302 . . Aed6g1559 . . Ahy11g1879 Ahy20g2524 Aip01g02077 Aip10g02959 Alju06g2676 . . Amo20g3306 Apr1g0899 Apr9g3017 Arst1g02571 . . . Bisa08g1860 . Bva06g01244 Bva05g00457 Car07g00962 . Cca03g00554 Cca11g01939 Dere03g0897 . . Dod02g2499 Enph6g0687 . Glsi02g0816 . Gma06g01710 Gma04g01673 Gma05g00276 Gma17g00927 Gso6g1611 Gso6g1611 Gso6g1611 Gso6g1611 Lal19g1482 . . . . . Lan1g1030 . . . . . . . Lasa4g03250 . Lele21g1876 Lele22g1844 Lele23g0139 Lele24g1796 . . . . Lja1g5501 . Mal5g4232 . Mepo1g01279 . Mesa29g01310 . Mibi09g0158 . Mtr4g3914 . . . Phco8g01324 . Prci4g3000 . . . Pste6g02536 . Pte3g00301 Pte2g02324 . . . . Pvu3g1979 . Rops2g03905 . Seca12g01411 . Spst3g04681 . Ssu1g2137 Ssu6g1281 Sto3g1522 . Tpr5g3022 . Trre15g04185 . Tsu04g03675 . Vian1g00759 . Vifa4g03334 . Vimu7g00777 . Viun3g04562 . Vivi1g01989 . Vra3g1095 .
Vvi17g0575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0576 . . . . . . . . Aev01g2105 . Ahy11g1880 . Aip01g02078 . . . . . . Apr9g3016 . . . . . . Bva06g01243 Bva05g00458 . . . Cca11g01940 . . . . . . . . . . Gma05g00275 . . . . . . Lal7g1400 . . Lal4g1173 . . . . . . . . . . . . . . . . . . . Lja1g5502 Lja4g2160 Mal5g4233 . . . . . . . Mtr4g3915 . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g1280 Sto3g1523 Sto12g0880 Tpr5g3023 . . . Tsu04g03676 . . . . . . . . . . . . .
Vvi17g0577 . . . . . . Aed10g1026 . . . Ahy11g1881 . Aip01g02079 . . . . . Apr1g0901 . . . . Bach2g02034 . . Bva06g01242 Bva05g00459 . Car05g00750 Cca03g00555 . . . Dod05g1722 . . . . . Gma06g01712 Gma04g01671 . . Gso6g1613 Gso6g1613 . . . . Lal14g1919 . . . . . . . . . . Lapu9g00668 . . . . . . . . . . Lja1g5503 . . Mal2g4866 . . . . . . . Mtr3g0948 . . . Phco7g02273 . . . . . . . . . . . . . Pvu9g1954 . . . . . Spst9g02329 Ssu1g2134 . Sto3g1524 . . Tpr3g4389 . Trre5g01671 . . . . . . . . . . . Vivi3g06265 Vra3g1094 .
Vvi17g0578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0579 . Acco13g0709 . Accr12g00659 . . Aed10g1027 Aed6g1561 . . . . . . . Alju13g1463 . . Apr1g0903 Apr9g3015 . . Bach10g01030 Bach2g01711 . Bisa02g1408 Bva06g01241 Bva05g00460 Car07g00958 . Cca03g00556 Cca11g01942 . Dere14g0473 . . . Enph5g0565 . Glsi13g1178 Gma06g01714 Gma04g01667 Gma05g00274 Gma17g00928 Gso6g1615 Gso6g1615 Gso6g1615 Gso6g1615 . . . Lal17g1012 . . . . . . . . . Lapu9g00669 Lasa4g03254 . . . . . Lele17g0959 Lele18g0572 Lele19g0600 Lele20g0848 Lja1g5504 . Mal5g4234 . Mepo1g01277 . . . . Mibi13g0696 Mtr4g3916 . . . Phco8g01326 Phco7g02271 . Prci9g1558 . . Pste6g02539 . Pte14g00136 . . . . . Pvu3g1977 Pvu9g1953 . . Seca4g03228 . Spst3g04683 Spst9g02630 Ssu1g2133 . Sto3g1526 Sto12g0881 Tpr5g3024 . Trre15g04187 . Tsu04g03679 . Vian1g00760 . . . Vimu7g03876 Vimu10g01008 Viun3g04564 . . . Vra3g1093 .
Vvi17g0580 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0581 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g1531 . . . . . . . . . . . . . . . . . . .
Vvi17g0582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Pte Pte14g00136 Chr14 5309150 5313427 -
Pte Pte14g00136 Chr14 5309150 5313427 -
Vvi Vvi17g0573 Chr17 6396683 6408410 +
Aed Aed10g1025 Chr10 9013176 9027264 +
Aed Aed6g1558 Chr6 19682873 19690774 +
Aev Aev01g2104 Chr01 25525773 25532508 +
Ahy Ahy11g1878 Chr11 122547937 122555404 +
Aip Aip01g02076 Chr01 112080148 112087363 +
Apr Apr1g0898 Chr1 12131037 12143982 +
Bach Bach2g02037 Chr2 27822983 27829545 -
Bva Bva06g01245 Chr06 9574976 9581571 -
Car Car05g00752 Chr05 42371965 42379276 -
Cca Cca03g00551 Chr03 9413028 9423894 +
Cca Cca11g01938 Chr11 44752095 44763855 +
Dod Dod05g1720 Chr05 42564153 42572232 +
Gma Gma06g01709 Chr06 17236371 17245992 +
Gma Gma04g01674 Chr04 45540933 45548789 -
Gma Gma17g00926 Chr17 7906070 7914850 +
Gso Gso6g1610 Chr6 16875753 16885483 +
Gso Gso6g1610 Chr6 16875753 16885483 +
Gso Gso6g1610 Chr6 16875753 16885483 +
Lal Lal7g1401 Chr7 18979351 18987557 -
Lal Lal17g1007 Chr17 8202230 8215394 +
Lapu Lapu9g00667 Chr9 7980093 7989090 +
Lja Lja1g5499 Chr1 94408899 94418782 +
Lja Lja4g2162 Chr4 23270573 23278632 -
Mal Mal5g4230 Chr5 113196990 113204732 +
Mal Mal2g4861 Chr2 109913554 109923625 -
Mtr Mtr4g3912 Chr4 52882085 52890375 +
Mtr Mtr3g0951 Chr3 14860647 14868662 -
Phco Phco7g02275 Chr7 40065469 40073092 -
Psa Psa5g4386 Chr5 375061445 375063460 +
Pvu Pvu9g1955 Chr9 28074584 28082852 -
Spst Spst9g02327 Chr9 54612358 54620207 +
Ssu Ssu1g2138 Chr1 60931923 60940093 -
Ssu Ssu6g1282 Chr6 20794265 20816404 -
Tpr Tpr3g4388 Chr3 48804210 48811692 -
Trre Trre5g01670 Chr5 12060862 12068006 -
Tsu Tsu03g01596 Chr03 15734496 15742569 -
Vimu Vimu10g01006 Chr10 9237614 9245610 +
Vivi Vivi3g06263 Chr3 164301594 164309800 +
Vra Vra3g1096 Chr3 11347629 11357008 -
Vvi Vvi17g0574 Chr17 6410783 6413303 +
Acco Acco04g2709 Chr04 43903725 43905473 +
Accr Accr8g00052 Chr8 775609 784609 -
Adu Adu01g03302 Chr01 105897333 105899815 -
Aed Aed6g1559 Chr6 19691871 19693455 +
Ahy Ahy11g1879 Chr11 122566744 122569094 +
Ahy Ahy20g2524 Chr20 133037687 133043717 +
Aip Aip01g02077 Chr01 112097915 112100107 +
Aip Aip10g02959 Chr10 125339854 125345301 +
Alju Alju06g2676 Chr06 53774453 53777892 +
Amo Amo20g3306 Chr20 141049934 141053709 +
Apr Apr1g0899 Chr1 12148900 12150636 +
Apr Apr9g3017 Chr9 37018455 37020800 -
Arst Arst1g02571 Chr1 87165939 87169406 +
Bisa Bisa08g1860 Chr08 44595779 44598502 -
Bva Bva06g01244 Chr06 9570415 9572562 -
Bva Bva05g00457 Chr05 2257085 2258689 +
Car Car07g00962 Chr07 8477841 8480233 -
Cca Cca03g00554 Chr03 9467031 9470172 +
Cca Cca11g01939 Chr11 44771974 44774347 +
Dere Dere03g0897 Chr03 13782939 13784983 +
Dod Dod02g2499 Chr02 55191800 55195447 -
Enph Enph6g0687 Chr6 9990073 9991574 +
Glsi Glsi02g0816 Chr02 5268851 5270434 +
Gma Gma06g01710 Chr06 17260294 17262201 +
Gma Gma04g01673 Chr04 45533274 45535091 -
Gma Gma05g00276 Chr05 2487754 2490207 -
Gma Gma17g00927 Chr17 7918780 7921079 +
Gso Gso6g1611 Chr6 16900008 16902047 +
Gso Gso6g1611 Chr6 16900008 16902047 +
Gso Gso6g1611 Chr6 16900008 16902047 +
Gso Gso6g1611 Chr6 16900008 16902047 +
Lal Lal19g1482 Chr19 17279742 17282132 -
Lan Lan1g1030 Chr1 20615933 20618453 +
Lasa Lasa4g03250 Chr4 578487444 578488990 +
Lele Lele21g1876 Chr21 26138575 26139948 +
Lele Lele22g1844 Chr22 23426857 23431963 +
Lele Lele23g0139 Chr23 889901 891543 -
Lele Lele24g1796 Chr24 23057180 23058645 +
Lja Lja1g5501 Chr1 94434117 94436207 +
Mal Mal5g4232 Chr5 113210513 113212596 +
Mepo Mepo1g01279 Chr1 12544000 12546388 -
Mesa Mesa29g01310 Chr29 16854068 16855869 -
Mibi Mibi09g0158 Chr09 2059734 2062634 -
Mtr Mtr4g3914 Chr4 52894450 52896872 +
Phco Phco8g01324 Chr8 13808250 13810095 +
Prci Prci4g3000 Chr4 41663502 41664994 +
Pste Pste6g02536 Chr6 12612461 12615632 +
Pte Pte3g00301 Chr3 2485464 2487127 +
Pte Pte2g02324 Chr2 42912729 42914531 -
Pvu Pvu3g1979 Chr3 40387758 40389694 -
Rops Rops2g03905 Chr2 71561467 71563136 +
Seca Seca12g01411 Chr12 14138295 14156433 -
Spst Spst3g04681 Chr3 98625517 98627312 +
Ssu Ssu1g2137 Chr1 60908208 60909757 -
Ssu Ssu6g1281 Chr6 20785620 20788002 -
Sto Sto3g1522 Chr3 11252936 11255028 +
Tpr Tpr5g3022 Chr5 53169904 53172850 +
Trre Trre15g04185 Chr15 52460842 52463378 +
Tsu Tsu04g03675 Chr04 45815916 45818527 +
Vian Vian1g00759 Chr1 7933903 7935563 +
Vifa Vifa4g03334 Chr4 1043589446 1043591057 +
Vimu Vimu7g00777 Chr7 7756493 7758175 +
Viun Viun3g04562 Chr3 53258393 53260357 +
Vivi Vivi1g01989 Chr1 42058014 42059927 -
Vra Vra3g1095 Chr3 11340868 11342446 -
Vvi Vvi17g0575 Chr17 6419940 6423613 -
Vvi Vvi17g0576 Chr17 6427858 6430258 -
Aev Aev01g2105 Chr01 25532932 25535109 -
Ahy Ahy11g1880 Chr11 122796581 122804564 -
Aip Aip01g02078 Chr01 112328576 112341081 -
Apr Apr9g3016 Chr9 37014129 37017819 +
Bva Bva06g01243 Chr06 9566634 9569058 +
Bva Bva05g00458 Chr05 2259026 2261625 -
Cca Cca11g01940 Chr11 44774576 44778729 -
Gma Gma05g00275 Chr05 2482937 2487228 +
Lal Lal7g1400 Chr7 18970247 18976801 +
Lal Lal4g1173 Chr4 15317880 15324901 +
Lja Lja1g5502 Chr1 94489408 94493756 -
Lja Lja4g2160 Chr4 23201069 23204246 +
Mal Mal5g4233 Chr5 113214993 113218586 -
Mtr Mtr4g3915 Chr4 52898941 52902868 -
Ssu Ssu6g1280 Chr6 20780022 20785128 +
Sto Sto3g1523 Chr3 11257400 11261629 -
Sto Sto12g0880 Chr12 5510661 5512827 -
Tpr Tpr5g3023 Chr5 53174789 53177164 -
Tsu Tsu04g03676 Chr04 45820206 45824075 -
Vvi Vvi17g0577 Chr17 6455684 6456541 -
Aed Aed10g1026 Chr10 9028782 9030646 -
Ahy Ahy11g1881 Chr11 122859519 122861470 -
Aip Aip01g02079 Chr01 112378678 112380022 -
Apr Apr1g0901 Chr1 12215097 12216332 +
Bach Bach2g02034 Chr2 27810006 27810831 +
Bva Bva06g01242 Chr06 9564405 9565147 +
Bva Bva05g00459 Chr05 2264609 2264994 -
Car Car05g00750 Chr05 42331293 42334258 +
Cca Cca03g00555 Chr03 9481936 9484357 -
Dod Dod05g1722 Chr05 42582134 42584894 -
Gma Gma06g01712 Chr06 17282371 17284398 -
Gma Gma04g01671 Chr04 45393776 45395428 +
Gso Gso6g1613 Chr6 16923221 16925484 -
Gso Gso6g1613 Chr6 16923221 16925484 -
Lal Lal14g1919 Chr14 18474373 18475557 +
Lapu Lapu9g00668 Chr9 8012157 8013147 -
Lja Lja1g5503 Chr1 94519021 94520673 -
Mal Mal2g4866 Chr2 110108572 110110040 -
Mtr Mtr3g0948 Chr3 14824982 14826514 -
Phco Phco7g02273 Chr7 40050493 40051497 +
Pvu Pvu9g1954 Chr9 28056083 28057570 -
Spst Spst9g02329 Chr9 54645004 54646078 -
Ssu Ssu1g2134 Chr1 60841252 60842318 +
Sto Sto3g1524 Chr3 11264336 11266149 -
Tpr Tpr3g4389 Chr3 48815000 48817066 -
Trre Trre5g01671 Chr5 12074302 12075646 -
Vivi Vivi3g06265 Chr3 164680013 164681646 +
Vra Vra3g1094 Chr3 11335996 11337600 +
Vvi Vvi17g0578 Chr17 6459559 6464007 +
Vvi Vvi17g0579 Chr17 6467984 6469315 +
Acco Acco13g0709 Chr13 5226655 5229078 +
Accr Accr12g00659 Chr12 6191064 6192398 +
Aed Aed10g1027 Chr10 9056468 9057793 +
Aed Aed6g1561 Chr6 19702491 19703711 +
Alju Alju13g1463 Chr13 33188589 33191026 -
Apr Apr1g0903 Chr1 12318472 12321507 +
Apr Apr9g3015 Chr9 36997479 37009621 -
Bach Bach10g01030 Chr10 7591687 7593363 +
Bach Bach2g01711 Chr2 25582686 25586194 +
Bisa Bisa02g1408 Chr02 24200310 24201635 +
Bva Bva06g01241 Chr06 9548080 9552292 -
Bva Bva05g00460 Chr05 2272188 2275680 +
Car Car07g00958 Chr07 8447969 8449054 -
Cca Cca03g00556 Chr03 9535976 9540718 +
Cca Cca11g01942 Chr11 44807258 44809369 +
Dere Dere14g0473 Chr14 4893170 4896380 -
Enph Enph5g0565 Chr5 4569405 4579286 +
Glsi Glsi13g1178 Chr13 29350914 29353354 -
Gma Gma06g01714 Chr06 17361137 17363760 +
Gma Gma04g01667 Chr04 45278823 45281715 -
Gma Gma05g00274 Chr05 2471333 2472556 -
Gma Gma17g00928 Chr17 7929213 7930439 +
Gso Gso6g1615 Chr6 16991022 16994289 +
Gso Gso6g1615 Chr6 16991022 16994289 +
Gso Gso6g1615 Chr6 16991022 16994289 +
Gso Gso6g1615 Chr6 16991022 16994289 +
Lal Lal17g1012 Chr17 8319310 8321867 +
Lapu Lapu9g00669 Chr9 8073790 8076695 +
Lasa Lasa4g03254 Chr4 578632606 578633739 +
Lele Lele17g0959 Chr17 20555240 20561798 -
Lele Lele18g0572 Chr18 3387521 3390770 +
Lele Lele19g0600 Chr19 3454974 3457553 +
Lele Lele20g0848 Chr20 15114423 15117767 -
Lja Lja1g5504 Chr1 94701606 94704660 +
Mal Mal5g4234 Chr5 113223915 113225057 +
Mepo Mepo1g01277 Chr1 12522242 12524485 -
Mibi Mibi13g0696 Chr13 9055657 9059547 +
Mtr Mtr4g3916 Chr4 52906801 52908952 +
Phco Phco8g01326 Chr8 13825549 13826856 +
Phco Phco7g02271 Chr7 39989139 39991838 -
Prci Prci9g1558 Chr9 28308868 28311492 -
Pste Pste6g02539 Chr6 12647631 12649945 +
Pte Pte14g00136 Chr14 5309150 5313427 -
Pvu Pvu3g1977 Chr3 40366712 40369284 -
Pvu Pvu9g1953 Chr9 28018750 28021394 -
Seca Seca4g03228 Chr4 55462193 55463518 +
Spst Spst3g04683 Chr3 98638577 98639884 +
Spst Spst9g02630 Chr9 60358008 60362671 +
Ssu Ssu1g2133 Chr1 60760422 60761747 -
Sto Sto3g1526 Chr3 11286502 11288278 +
Sto Sto12g0881 Chr12 5522810 5524135 +
Tpr Tpr5g3024 Chr5 53181215 53182348 +
Trre Trre15g04187 Chr15 52507233 52508375 +
Tsu Tsu04g03679 Chr04 45848739 45852692 +
Vian Vian1g00760 Chr1 7955008 7956312 +
Vimu Vimu7g03876 Chr7 35788994 35796809 +
Vimu Vimu10g01008 Chr10 9289152 9290651 +
Viun Viun3g04564 Chr3 53277636 53280618 +
Vra Vra3g1093 Chr3 11290276 11293066 -
Vvi Vvi17g0580 Chr17 6469391 6469931 +
Vvi Vvi17g0581 Chr17 6471884 6479159 +
Bva Bva05g00461 Chr05 2277504 2281889 +
Sto Sto3g1531 Chr3 11330955 11335370 +
Vvi Vvi17g0582 Chr17 6493136 6493937 +