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
Vvi2g0812 . . . . . . . . . . . . . . . . . . Apr7g1771 . . . . . . . Bva08g01133 Bva11g01305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal6g0679 . . . . . . . Mtr5g1216 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g4167 Sto11g1297 Tpr2g1467 . . . Tsu05g01233 . . . . . . . . . . . . .
Vvi2g0813 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0814 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0816 . . . . . . Aed6g0155 . . . . . . . . . . . Apr7g1774 . Arst5g00169 . . . Bisa11g2076 . . . . . Cca06g00992 . Dere09g1352 . . . Enph13g1638 . Glsi05g1059 . Gma01g00134 Gma09g01926 . . Gso1g0135 Gso1g0135 . . . . . . . . . . . . . . . . Lasa2g03745 . Lele49g0893 Lele50g0937 Lele51g0909 Lele52g0919 . . . . Lja2g0816 . Mal6g0674 . Mepo5g01359 . Mesa17g01478 . . . Mtr5g1213 . Phac2g02180 . Phco4g00531 . Prci10g1451 . Psa2g3127 . Pste1g00841 . . . . . . . Pvu2g1418 . . . . . Spst2g01216 . Ssu2g1970 . Sto6g4158 . Tpr2g1462 . Trre9g01823 . Tsu05g01229 . . . . . Vimu7g03477 . . . Vivi2g02423 . Vra11g1047 .
Vvi2g0817 Acco11g1294 . . . . . . . . . . . . . Alju09g1311 . . . . . Arst5g00170 . . . . . . . . . . . . . . . . . . . Gma01g00132 . . . Gso1g0133 . . . . . . . . . . . . . . . Lapu2g00856 . . . . . . . . . . . Lja2g0815 . . . . . . . Mibi12g1092 . . . . . Phco4g00532 . Prci10g1449 . . . . . . . . . Pumo8g01404 . Pvu2g1417 . Rops1g01265 . Seca10g01290 . Spst2g01215 . . . Sto6g4157 . . . . . . . Vian10g01080 . Vifa1g05876 . Vimu7g03476 . Viun2g01450 . Vivi2g02434 . . .
Vvi2g0818 . Acco12g0484 . Accr10g01523 Adu05g00135 . Aed6g0153 . Aev05g0162 . Ahy15g0122 . Aip05g00121 . . Alju12g1610 . . Apr7g1776 Apr3g0631 . . Bach4g00969 Bach10g00787 . . . . . . Cca06g00994 . . Dere13g0970 Dod02g0175 . . Enph14g0965 . Glsi09g0871 Gma01g00130 Gma09g01928 . . Gso1g0131 Gso1g0131 . . Lal15g0387 Lal16g0441 . . . Lal23g1128 Lan18g0781 Lan18g0781 . . . Lan18g0781 Lapu2g00859 . Lasa2g03743 Lasa4g01816 . . . . Lele53g1114 Lele54g1082 Lele55g0373 Lele56g0362 Lja2g0813 . Mal6g0667 . Mepo5g01356 Mepo1g02564 Mesa17g01474 Mesa29g02747 . Mibi10g1536 Mtr5g1211 . . . Phco4g00536 Phco8g00180 . Prci5g1934 . . Pste1g00820 . Pte14g00709 Pte12g00643 Pte14g00709 Pte12g00643 Pumo8g01409 . Pvu2g1415 Pvu3g2912 Rops1g01267 . Seca10g01288 . Spst2g01212 Spst3g03548 Ssu2g1973 . . Sto11g1294 Tpr2g1460 . Trre9g01819 Trre15g02008 Tsu05g01227 . Vian10g01076 . . . Vimu7g03473 Vimu7g03473 Viun2g01456 . Vivi2g02437 . Vra11g1044 .
Vvi2g0819 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0820 . . . . . . Aed6g0152 . . . . . . . . . . . Apr7g1777 . . . . . . . . . . . Cca06g00995 . . . . . . . . . Gma01g00129 Gma09g01929 . . Gso1g0130 Gso1g0130 . . . . . . . . . . . . . . Lapu2g00860 . Lasa2g03740 . . . . . . . . . Lja2g0811 . Mal6g0665 . Mepo5g01351 . Mesa17g01471 . . . Mtr5g1210 . . . Phco4g00537 . . . Psa2g3140 . Pste1g00797 . . . . . Pumo8g00224 . Pvu2g1413 . Rops1g01268 . Seca10g01287 . Spst2g01210 . Ssu2g1974 . . . Tpr2g1456 . Trre9g01818 . Tsu05g01225 . Vian10g01075 . Vifa1g05893 . Vimu7g03468 . Viun2g01459 . Vivi2g02440 . Vra11g1043 .
Vvi2g0821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0812 Chr2 8336412 8337034 -
Apr Apr7g1771 Chr7 25031543 25032412 -
Bva Bva08g01133 Chr08 5816308 5817221 +
Bva Bva11g01305 Chr11 13390084 13391539 -
Mal Mal6g0679 Chr6 9663418 9663913 +
Mtr Mtr5g1216 Chr5 12485427 12486272 +
Sto Sto6g4167 Chr6 44989378 44989917 +
Sto Sto11g1297 Chr11 12654875 12655477 +
Tpr Tpr2g1467 Chr2 17307084 17307890 +
Tsu Tsu05g01233 Chr05 11106674 11108468 +
Vvi Vvi2g0813 Chr2 8337942 8347461 -
Vvi Vvi2g0814 Chr2 8366199 8376699 +
Vvi Vvi2g0815 Chr2 8403683 8408718 -
Vvi Vvi2g0816 Chr2 8417622 8434527 +
Aed Aed6g0155 Chr6 1403239 1412115 -
Apr Apr7g1774 Chr7 25042547 25058766 +
Arst Arst5g00169 Chr5 1523043 1528638 -
Bisa Bisa11g2076 Chr11 43803350 43808408 +
Cca Cca06g00992 Chr06 23635350 23638988 +
Dere Dere09g1352 Chr09 17563797 17569466 +
Enph Enph13g1638 Chr13 22142437 22153859 +
Glsi Glsi05g1059 Chr05 60430765 60439845 -
Gma Gma01g00134 Chr01 1525976 1528997 -
Gma Gma09g01926 Chr09 44847405 44850709 +
Gso Gso1g0135 Chr1 1539600 1544746 -
Gso Gso1g0135 Chr1 1539600 1544746 -
Lasa Lasa2g03745 Chr2 552812809 552814890 -
Lele Lele49g0893 Chr49 5536298 5540519 +
Lele Lele50g0937 Chr50 5907010 5911456 +
Lele Lele51g0909 Chr51 5611657 5616313 +
Lele Lele52g0919 Chr52 5949518 5953951 +
Lja Lja2g0816 Chr2 7614464 7617143 -
Mal Mal6g0674 Chr6 9559088 9561726 -
Mepo Mepo5g01359 Chr5 14096680 14099059 -
Mesa Mesa17g01478 Chr17 20138649 20141311 -
Mtr Mtr5g1213 Chr5 12463064 12465371 -
Phac Phac2g02180 Chr2 23560879 23568229 -
Phco Phco4g00531 Chr4 3822685 3826707 +
Prci Prci10g1451 Chr10 9744508 9753465 +
Psa Psa2g3127 Chr2 358150248 358152157 +
Pste Pste1g00841 Chr1 2593627 2597582 -
Pvu Pvu2g1418 Chr2 27070255 27079288 -
Spst Spst2g01216 Chr2 10771906 10783412 -
Ssu Ssu2g1970 Chr2 72365163 72368887 +
Sto Sto6g4158 Chr6 44922807 44927573 +
Tpr Tpr2g1462 Chr2 17263885 17269748 -
Trre Trre9g01823 Chr9 17308371 17311303 -
Tsu Tsu05g01229 Chr05 11082498 11085781 -
Vimu Vimu7g03477 Chr7 29432833 29436659 -
Vivi Vivi2g02423 Chr2 111250691 111253453 -
Vra Vra11g1047 Chr11 9649477 9657506 -
Vvi Vvi2g0817 Chr2 8468744 8483070 +
Acco Acco11g1294 Chr11 27145043 27149836 -
Alju Alju09g1311 Chr09 36808057 36811955 +
Arst Arst5g00170 Chr5 1523043 1528638 -
Gma Gma01g00132 Chr01 1511648 1514940 -
Gso Gso1g0133 Chr1 1524149 1530346 -
Lapu Lapu2g00856 Chr2 7800224 7815977 +
Lja Lja2g0815 Chr2 7565878 7570554 -
Mibi Mibi12g1092 Chr12 26135768 26140414 -
Phco Phco4g00532 Chr4 3833196 3836913 +
Prci Prci10g1449 Chr10 9744508 9753465 +
Pumo Pumo8g01404 Chr8 46675630 46679053 +
Pvu Pvu2g1417 Chr2 27061018 27067741 -
Rops Rops1g01265 Chr1 28930916 28933530 +
Seca Seca10g01290 Chr10 12941742 12946482 -
Spst Spst2g01215 Chr2 10763629 10768712 -
Sto Sto6g4157 Chr6 44910558 44918338 +
Vian Vian10g01080 Chr10 12384214 12387987 -
Vifa Vifa1g05876 Chr1 920584037 920584773 +
Vimu Vimu7g03476 Chr7 29419920 29423477 -
Viun Viun2g01450 Chr2 24909555 24915106 +
Vivi Vivi2g02434 Chr2 111740338 111743100 +
Vvi Vvi2g0818 Chr2 8528257 8532317 -
Acco Acco12g0484 Chr12 4276238 4280190 +
Accr Accr10g01523 Chr10 38988762 38992790 -
Adu Adu05g00135 Chr05 1473540 1478552 +
Aed Aed6g0153 Chr6 1380856 1386256 +
Aev Aev05g0162 Chr05 1269796 1275267 +
Ahy Ahy15g0122 Chr15 1463472 1468920 +
Aip Aip05g00121 Chr05 1392079 1397369 +
Alju Alju12g1610 Chr12 37390195 37394175 -
Apr Apr7g1776 Chr7 25081488 25086621 -
Apr Apr3g0631 Chr3 15857907 15862969 -
Bach Bach4g00969 Chr4 6521659 6525632 -
Bach Bach10g00787 Chr10 5556271 5560687 -
Cca Cca06g00994 Chr06 23663141 23668280 -
Dere Dere13g0970 Chr13 12439658 12443769 +
Dod Dod02g0175 Chr02 2487495 2493004 +
Enph Enph14g0965 Chr14 11337915 11343512 +
Glsi Glsi09g0871 Chr09 5967899 5971927 -
Gma Gma01g00130 Chr01 1486171 1491375 +
Gma Gma09g01928 Chr09 44870529 44875889 -
Gso Gso1g0131 Chr1 1499021 1504239 +
Gso Gso1g0131 Chr1 1499021 1504239 +
Lal Lal15g0387 Chr15 2610301 2615684 -
Lal Lal16g0441 Chr16 2690792 2696173 -
Lal Lal23g1128 Chr23 12806920 12811704 +
Lan Lan18g0781 Chr18 13266037 13271493 +
Lan Lan18g0781 Chr18 13266037 13271493 +
Lan Lan18g0781 Chr18 13266037 13271493 +
Lapu Lapu2g00859 Chr2 7858618 7864238 -
Lasa Lasa2g03743 Chr2 552406822 552411679 +
Lasa Lasa4g01816 Chr4 365091846 365095385 -
Lele Lele53g1114 Chr53 20221034 20225506 -
Lele Lele54g1082 Chr54 16760473 16764410 -
Lele Lele55g0373 Chr55 2324401 2328317 +
Lele Lele56g0362 Chr56 2742732 2746663 +
Lja Lja2g0813 Chr2 7510072 7515199 +
Mal Mal6g0667 Chr6 9425307 9430340 +
Mepo Mepo5g01356 Chr5 14034508 14040544 +
Mepo Mepo1g02564 Chr1 26997279 27003460 +
Mesa Mesa17g01474 Chr17 19984961 19990162 +
Mesa Mesa29g02747 Chr29 38055234 38061106 +
Mibi Mibi10g1536 Chr10 36408623 36412776 -
Mtr Mtr5g1211 Chr5 12391169 12397064 +
Phco Phco4g00536 Chr4 3859488 3863801 -
Phco Phco8g00180 Chr8 1593428 1598002 +
Prci Prci5g1934 Chr5 37325673 37330282 -
Pste Pste1g00820 Chr1 2544274 2549424 +
Pte Pte14g00709 Chr14 28129850 28134883 +
Pte Pte12g00643 Chr12 6277847 6282600 -
Pte Pte14g00709 Chr14 28129850 28134883 +
Pte Pte12g00643 Chr12 6277847 6282600 -
Pumo Pumo8g01409 Chr8 46721762 46726933 -
Pvu Pvu2g1415 Chr2 27029191 27034429 +
Pvu Pvu3g2912 Chr3 50915374 50921578 -
Rops Rops1g01267 Chr1 28972985 28977961 -
Seca Seca10g01288 Chr10 12918643 12923657 +
Spst Spst2g01212 Chr2 10729287 10733575 +
Spst Spst3g03548 Chr3 85485726 85490189 +
Ssu Ssu2g1973 Chr2 72403773 72407982 -
Sto Sto11g1294 Chr11 12628262 12632529 +
Tpr Tpr2g1460 Chr2 17217857 17224336 +
Trre Trre9g01819 Chr9 17225416 17230901 +
Trre Trre15g02008 Chr15 16257047 16263979 +
Tsu Tsu05g01227 Chr05 11004733 11011326 +
Vian Vian10g01076 Chr10 12340964 12345379 +
Vimu Vimu7g03473 Chr7 29393045 29397458 +
Vimu Vimu7g03473 Chr7 29393045 29397458 +
Viun Viun2g01456 Chr2 24945329 24950343 -
Vivi Vivi2g02437 Chr2 111937674 111943466 +
Vra Vra11g1044 Chr11 9612064 9617329 +
Vvi Vvi2g0819 Chr2 8572997 8573383 -
Vvi Vvi2g0820 Chr2 8574199 8584549 -
Aed Aed6g0152 Chr6 1361686 1368770 +
Apr Apr7g1777 Chr7 25109895 25115351 -
Cca Cca06g00995 Chr06 23701141 23707267 -
Gma Gma01g00129 Chr01 1453467 1460032 +
Gma Gma09g01929 Chr09 44898910 44905700 -
Gso Gso1g0130 Chr1 1466979 1473486 +
Gso Gso1g0130 Chr1 1466979 1473486 +
Lapu Lapu2g00860 Chr2 7888425 7895073 -
Lasa Lasa2g03740 Chr2 552203619 552209747 +
Lja Lja2g0811 Chr2 7467879 7473973 +
Mal Mal6g0665 Chr6 9288555 9294161 +
Mepo Mepo5g01351 Chr5 13945045 13952068 +
Mesa Mesa17g01471 Chr17 19914128 19919421 +
Mtr Mtr5g1210 Chr5 12348324 12355414 +
Phco Phco4g00537 Chr4 3889018 3894493 -
Psa Psa2g3140 Chr2 361396513 361404721 +
Pste Pste1g00797 Chr1 2483184 2487177 +
Pumo Pumo8g00224 Chr8 6581154 6583763 -
Pvu Pvu2g1413 Chr2 26967868 26974411 +
Rops Rops1g01268 Chr1 29004508 29011191 -
Seca Seca10g01287 Chr10 12868159 12874749 +
Spst Spst2g01210 Chr2 10700773 10710862 +
Ssu Ssu2g1974 Chr2 72458137 72463845 -
Tpr Tpr2g1456 Chr2 17161291 17169175 +
Trre Trre9g01818 Chr9 17181236 17187578 +
Tsu Tsu05g01225 Chr05 10956456 10963624 +
Vian Vian10g01075 Chr10 12286418 12291799 +
Vifa Vifa1g05893 Chr1 923048588 923054673 -
Vimu Vimu7g03468 Chr7 29341161 29342302 +
Viun Viun2g01459 Chr2 24983288 24989626 -
Vivi Vivi2g02440 Chr2 112407888 112414879 -
Vra Vra11g1043 Chr11 9525518 9531952 +
Vvi Vvi2g0821 Chr2 8613300 8613605 -