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
Vvi3g0653 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0181 . . . . . . . . . . . . . . . . . .
Vvi3g0655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0657 . . . . . Adu03g00467 . . Aev04g3338 . Ahy13g0690 . Aip03g00730 . . . Amo13g0713 . Apr5g0291 . . Arst3g00614 . . . . Bva13g00209 Bva14g00277 Car06g03763 . Cca04g00451 Cca07g00149 . . Dod03g3137 . . . . . . . Gma11g01087 Gma12g00398 . . . . . Lal2g0149 . . . . . . . . . . . Lapu11g00745 . Lasa7g02043 . . . . . . . . Lja3g0521 . Mal7g2536 . . Mepo2g02310 . Mesa13g02800 . . Mtr4g2087 . . . . Phco9g00524 . . Psa7g3251 . . Pste1g01877 . . . . . Pumo10g00694 . Pvu11g0474 . Rops3g00578 . Seca4g03528 . Spst2g02509 Ssu3g2831 . Sto2g0696 . Tpr3g2290 . . Trre7g02872 Tsu02g02378 . . Vian5g01484 . . . Vimu5g02328 . Viun11g02419 . . Vra2g0422 .
Vvi3g0658 . Acco01g2011 . Accr1g01711 . Adu03g00468 . . Aev04g3339 . Ahy13g0691 . Aip03g00731 . . Alju02g2033 Amo13g0714 . Apr5g0292 . . . . . . . Bva13g00208 Bva14g00276 . . Cca04g00450 . . . Dod03g3138 . . Enph12g0545 . . . . Gma11g01086 Gma12g00397 . . . . Lal1g0233 Lal2g0148 . . . . Lan13g0243 Lan13g0243 . . . . . Lapu11g01360 . . . . . . . . . . Lja3g0520 . Mal7g2537 . . Mepo2g02312 . . . Mibi01g1889 Mtr4g2089 . . . . Phco9g00522 . . Psa7g3252 . . Pste1g01871 . . . . . Pumo11g01795 . Pvu11g0473 . . . . . Spst2g02510 Ssu3g2832 . Sto2g0697 Sto10g0180 Tpr3g2291 . . . Tsu02g02380 . . Vian5g01485 . . . Vimu5g02329 . . . . Vra2g0421 .
Vvi3g0659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0660 . . . . . . . . . Aev05g0525 . Ahy15g0779 . Aip05g00787 . . . . . . . . . . . . Bva13g00206 Bva14g00275 . Car08g00583 . Cca07g00148 . . . . . . . . Gma04g00122 . . . Gso4g0115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3652 . . . . . . . . . . . . . . . . . . Sto2g0698 Sto10g0179 . . . . . . . . . . . . . . . . . Vra5g1761
Vvi3g0661 . Acco01g2012 . Accr1g01712 . Adu03g00469 . Aed9g0118 Aev04g3340 . Ahy13g0692 . Aip03g00732 . . Alju02g2032 Amo13g0715 . Apr5g0293 . . Arst3g00617 . . . Bisa01g3942 Bva13g00205 Bva14g00274 Car06g03765 . Cca04g00449 Cca07g00147 . Dere06g0223 Dod03g3139 . . Enph12g0548 . Glsi01g0240 Gma04g00121 Gma06g00115 Gma11g01083 Gma12g00396 Gso4g0114 Gso4g0114 Gso4g0114 Gso4g0114 Lal1g0231 Lal2g0147 Lal9g0165 . . . Lan13g0242 Lan13g0242 Lan13g0242 . . . . Lapu11g00747 Lasa5g04678 Lasa7g02048 . . . . Lele45g1256 Lele46g1348 Lele47g0154 Lele48g0157 Lja3g0519 . Mal7g2539 . Mepo3g07710 Mepo2g02314 Mesa9g05642 Mesa13g02797 . Mibi01g1888 Mtr4g2090 . . . Phco7g00165 Phco9g00519 . Prci14g0274 Psa7g3253 . . Pste1g01868 . . . . . Pumo10g00698 Pvu9g0248 Pvu11g0472 Rops10g02592 Rops3g00575 Seca4g00231 Seca4g03526 . Spst2g02511 Ssu3g2833 . Sto2g0699 Sto10g0177 Tpr3g2293 . Trre5g05856 Trre7g02870 Tsu02g02382 . . Vian5g01486 Vifa2g04681 . Vimu10g03612 Vimu5g02331 Viun9g03835 Viun11g02421 Vivi3g00850 . Vra2g0420 Vra5g1762
Vvi3g0662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0653 Chr3 5608901 5610203 +
Vvi Vvi3g0654 Chr3 5614639 5615199 +
Sto Sto10g0181 Chr10 1473146 1474545 -
Vvi Vvi3g0655 Chr3 5617604 5618292 +
Vvi Vvi3g0656 Chr3 5622711 5623261 +
Vvi Vvi3g0657 Chr3 5652172 5655774 +
Adu Adu03g00467 Chr03 4267571 4273839 +
Aev Aev04g3338 Chr04 32241088 32252209 +
Ahy Ahy13g0690 Chr13 7215266 7221549 +
Aip Aip03g00730 Chr03 7038443 7044679 +
Amo Amo13g0713 Chr13 8768560 8774876 +
Apr Apr5g0291 Chr5 2579493 2585235 +
Arst Arst3g00614 Chr3 4273556 4279824 +
Bva Bva13g00209 Chr13 1007909 1014819 -
Bva Bva14g00277 Chr14 1429009 1435549 -
Car Car06g03763 Chr06 69252950 69260405 +
Cca Cca04g00451 Chr04 4447844 4454131 -
Cca Cca07g00149 Chr07 1859366 1867485 -
Dod Dod03g3137 Chr03 64015651 64024428 +
Gma Gma11g01087 Chr11 9159978 9166918 -
Gma Gma12g00398 Chr12 3248760 3255626 -
Lal Lal2g0149 Chr2 896770 902878 -
Lapu Lapu11g00745 Chr11 10411236 10418358 +
Lasa Lasa7g02043 Chr7 486151732 486157584 +
Lja Lja3g0521 Chr3 5215659 5223252 -
Mal Mal7g2536 Chr7 86874230 86880417 +
Mepo Mepo2g02310 Chr2 32836617 32843925 +
Mesa Mesa13g02800 Chr13 32839560 32846255 -
Mtr Mtr4g2087 Chr4 34391871 34400273 +
Phco Phco9g00524 Chr9 3793622 3799065 -
Psa Psa7g3251 Chr7 245128201 245134095 +
Pste Pste1g01877 Chr1 5788787 5793673 -
Pumo Pumo10g00694 Chr10 8945894 8951331 +
Pvu Pvu11g0474 Chr11 3960721 3967881 -
Rops Rops3g00578 Chr3 7174113 7182648 -
Seca Seca4g03528 Chr4 61258371 61266239 -
Spst Spst2g02509 Chr2 24710391 24715807 +
Ssu Ssu3g2831 Chr3 82803121 82808617 +
Sto Sto2g0696 Chr2 5917515 5923610 +
Tpr Tpr3g2290 Chr3 21587693 21595744 +
Trre Trre7g02872 Chr7 25066697 25072222 -
Tsu Tsu02g02378 Chr02 24287940 24296120 +
Vian Vian5g01484 Chr5 37397594 37403024 +
Vimu Vimu5g02328 Chr5 34185302 34196728 +
Viun Viun11g02419 Chr11 37980174 37986061 +
Vra Vra2g0422 Chr2 3273352 3279137 -
Vvi Vvi3g0658 Chr3 5657878 5662336 -
Acco Acco01g2011 Chr01 35996081 35999957 -
Accr Accr1g01711 Chr1 47111164 47114645 -
Adu Adu03g00468 Chr03 4274472 4277660 -
Aev Aev04g3339 Chr04 32253183 32255822 -
Ahy Ahy13g0691 Chr13 7222092 7225750 -
Aip Aip03g00731 Chr03 7045243 7049262 -
Alju Alju02g2033 Chr02 19666462 19669912 +
Amo Amo13g0714 Chr13 8775338 8779098 -
Apr Apr5g0292 Chr5 2587278 2590669 -
Bva Bva13g00208 Chr13 1004461 1007085 +
Bva Bva14g00276 Chr14 1425046 1427903 +
Cca Cca04g00450 Chr04 4442908 4446818 +
Dod Dod03g3138 Chr03 64026103 64030068 -
Enph Enph12g0545 Chr12 11981361 11983418 +
Gma Gma11g01086 Chr11 9155494 9158393 +
Gma Gma12g00397 Chr12 3243979 3247574 +
Lal Lal1g0233 Chr1 1378489 1381735 +
Lal Lal2g0148 Chr2 890634 895856 +
Lan Lan13g0243 Chr13 1507162 1510435 +
Lan Lan13g0243 Chr13 1507162 1510435 +
Lapu Lapu11g01360 Chr11 15900597 15903881 -
Lja Lja3g0520 Chr3 5211157 5214351 +
Mal Mal7g2537 Chr7 86889128 86892216 -
Mepo Mepo2g02312 Chr2 32848193 32853373 -
Mibi Mibi01g1889 Chr01 27722307 27725820 +
Mtr Mtr4g2089 Chr4 34406203 34409803 -
Phco Phco9g00522 Chr9 3787413 3790444 +
Psa Psa7g3252 Chr7 245139834 245144980 -
Pste Pste1g01871 Chr1 5779693 5783481 +
Pumo Pumo11g01795 Chr11 49755797 49758860 -
Pvu Pvu11g0473 Chr11 3956171 3959645 +
Spst Spst2g02510 Chr2 24718092 24721752 -
Ssu Ssu3g2832 Chr3 82812095 82815239 -
Sto Sto2g0697 Chr2 5926865 5928205 -
Sto Sto10g0180 Chr10 1466912 1469304 +
Tpr Tpr3g2291 Chr3 21601344 21606645 -
Tsu Tsu02g02380 Chr02 24307352 24311045 -
Vian Vian5g01485 Chr5 37405398 37408330 -
Vimu Vimu5g02329 Chr5 34193577 34196515 -
Vra Vra2g0421 Chr2 3268476 3271624 +
Vvi Vvi3g0659 Chr3 5664142 5664525 -
Vvi Vvi3g0660 Chr3 5671204 5673391 +
Aev Aev05g0525 Chr05 3641307 3644818 -
Ahy Ahy15g0779 Chr15 10625218 10628956 +
Aip Aip05g00787 Chr05 10237036 10240172 +
Bva Bva13g00206 Chr13 999019 1002471 -
Bva Bva14g00275 Chr14 1420877 1424320 -
Car Car08g00583 Chr08 4950584 4955373 +
Cca Cca07g00148 Chr07 1854858 1858142 -
Gma Gma04g00122 Chr04 1034135 1037155 -
Gso Gso4g0115 Chr4 1016975 1020400 -
Psa Psa2g3652 Chr2 393169218 393174193 -
Sto Sto2g0698 Chr2 5932640 5943841 +
Sto Sto10g0179 Chr10 1461400 1464806 -
Vra Vra5g1761 Chr5 23759532 23761662 +
Vvi Vvi3g0661 Chr3 5675594 5685586 +
Acco Acco01g2012 Chr01 36004159 36011472 +
Accr Accr1g01712 Chr1 47123626 47130813 +
Adu Adu03g00469 Chr03 4280437 4287901 +
Aed Aed9g0118 Chr9 830186 837229 -
Aev Aev04g3340 Chr04 32258670 32264574 +
Ahy Ahy13g0692 Chr13 7229684 7237157 +
Aip Aip03g00732 Chr03 7052276 7059770 +
Alju Alju02g2032 Chr02 19628426 19635766 -
Amo Amo13g0715 Chr13 8783162 8801192 +
Apr Apr5g0293 Chr5 2610880 2617654 +
Arst Arst3g00617 Chr3 4286442 4293850 +
Bisa Bisa01g3942 Chr01 95011803 95018801 +
Bva Bva13g00205 Chr13 991573 997890 -
Bva Bva14g00274 Chr14 1412797 1419601 -
Car Car06g03765 Chr06 69304823 69312101 +
Cca Cca04g00449 Chr04 4428584 4436732 -
Cca Cca07g00147 Chr07 1845698 1852627 -
Dere Dere06g0223 Chr06 3113731 3120897 -
Dod Dod03g3139 Chr03 64033687 64039738 +
Enph Enph12g0548 Chr12 12025247 12035447 +
Glsi Glsi01g0240 Chr01 1913291 1920980 -
Gma Gma04g00121 Chr04 1024672 1031436 -
Gma Gma06g00115 Chr06 985295 997631 -
Gma Gma11g01083 Chr11 9139181 9147463 -
Gma Gma12g00396 Chr12 3232570 3240585 -
Gso Gso4g0114 Chr4 1007493 1014729 -
Gso Gso4g0114 Chr4 1007493 1014729 -
Gso Gso4g0114 Chr4 1007493 1014729 -
Gso Gso4g0114 Chr4 1007493 1014729 -
Lal Lal1g0231 Chr1 1369915 1376250 -
Lal Lal2g0147 Chr2 884535 890753 -
Lal Lal9g0165 Chr9 1025288 1031316 -
Lan Lan13g0242 Chr13 1498102 1504429 -
Lan Lan13g0242 Chr13 1498102 1504429 -
Lan Lan13g0242 Chr13 1498102 1504429 -
Lapu Lapu11g00747 Chr11 10427485 10435835 +
Lasa Lasa5g04678 Chr5 686536644 686545690 +
Lasa Lasa7g02048 Chr7 486473595 486480802 +
Lele Lele45g1256 Chr45 22526641 22534023 +
Lele Lele46g1348 Chr46 20545556 20552946 +
Lele Lele47g0154 Chr47 1101970 1109373 -
Lele Lele48g0157 Chr48 1811833 1818940 -
Lja Lja3g0519 Chr3 5202591 5209964 -
Mal Mal7g2539 Chr7 86964060 86971077 +
Mepo Mepo3g07710 Chr3 90414717 90423930 -
Mepo Mepo2g02314 Chr2 32862025 32869752 +
Mesa Mesa9g05642 Chr9 92072940 92081758 +
Mesa Mesa13g02797 Chr13 32805916 32812614 -
Mibi Mibi01g1888 Chr01 27690275 27697443 -
Mtr Mtr4g2090 Chr4 34430977 34438508 +
Phco Phco7g00165 Chr7 1066700 1072944 -
Phco Phco9g00519 Chr9 3775195 3782645 -
Prci Prci14g0274 Chr14 2095301 2103572 -
Psa Psa7g3253 Chr7 245295878 245303314 +
Pste Pste1g01868 Chr1 5766289 5773994 -
Pumo Pumo10g00698 Chr10 8961424 8968158 +
Pvu Pvu9g0248 Chr9 5618283 5625095 -
Pvu Pvu11g0472 Chr11 3943360 3951111 -
Rops Rops10g02592 Chr10 44979308 44986479 +
Rops Rops3g00575 Chr3 7160878 7168202 -
Seca Seca4g00231 Chr4 3642570 3650082 -
Seca Seca4g03526 Chr4 61220135 61231852 -
Spst Spst2g02511 Chr2 24729557 24738823 +
Ssu Ssu3g2833 Chr3 82825933 82834024 +
Sto Sto2g0699 Chr2 5946533 5954902 +
Sto Sto10g0177 Chr10 1452175 1458641 -
Tpr Tpr3g2293 Chr3 21627499 21633873 +
Trre Trre5g05856 Chr5 58225988 58239275 +
Trre Trre7g02870 Chr7 25038780 25045531 -
Tsu Tsu02g02382 Chr02 24329416 24335943 +
Vian Vian5g01486 Chr5 37414392 37423338 +
Vifa Vifa2g04681 Chr2 1381256679 1381265736 +
Vimu Vimu10g03612 Chr10 45487747 45493878 +
Vimu Vimu5g02331 Chr5 34209942 34216707 +
Viun Viun9g03835 Chr9 42913484 42920226 +
Viun Viun11g02421 Chr11 37996251 38004382 +
Vivi Vivi3g00850 Chr3 14020166 14029774 +
Vra Vra2g0420 Chr2 3255188 3263279 -
Vra Vra5g1762 Chr5 23764160 23770931 +
Vvi Vvi3g0662 Chr3 5686174 5687004 -
Psa Psa2g3652 Chr2 393169218 393174193 -
Cca Cca07g00148 Chr07 1854858 1858142 -
Vra Vra5g1761 Chr5 23759532 23761662 +