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
Vvi3g0233 . . . . Adu09g02862 . Aed1g1762 . Aev09g2711 . Ahy19g3057 . Aip09g03518 . . . Amo19g3921 . Apr8g2657 . Arst9g03825 . . . . . . Bva14g02369 . . Cca02g02748 . . . Dod06g0295 . . . . . . . . . . . . . . . . . Lal12g0273 . . . . . . . Lapu7g02509 . Lasa6g04793 . . . . . . . . . . . . Mal1g0205 Mepo4g04867 . Mesa1g05277 . . . . Mtr1g4324 . . Phco6g03053 . . . . . Pste4g00400 . . . . . Pumo3g00191 . Pvu7g0179 . Rops6g03424 . Seca8g08021 . Spst10g01558 . Ssu7g0213 . Sto2g1088 . . Tpr1g0188 Trre1g06181 . . Tsu01g04995 . . Vifa3g00166 . Vimu3g03676 . Viun7g03987 . . . Vra8g2647 .
Vvi3g0234 . . . . . . . . Aev09g2712 . Ahy19g3056 . Aip09g03517 . . . Amo19g3920 . . . . . . . . . . Bva14g02370 . . Cca02g02749 . . . Dod06g0296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g0204 . . . . . . . Mtr1g4325 . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0211 . . . . . . . . Tsu01g04996 . . . . . . . . . . . .
Vvi3g0235 . . . . . . . . Aev09g2714 . Ahy19g3055 . Aip09g03516 . . . Amo19g3919 . . . . . . . . . . Bva14g02372 . . . . . . Dod06g0298 . . . . . . . . . . . . . . . . Lal13g0247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g1094 . . . . . . . . . . . . . . . . . . .
Vvi3g0236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0239 . . . . . . . Aed9g0015 Aev04g3575 . Ahy13g1002 . Aip03g01102 . . . Amo13g1296 . . . . . . . . . . . . . . Cca07g00019 . . Dod03g3366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra5g1882
Vvi3g0240 . . . . . . . . . . Ahy20g0110 . Aip10g00097 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa5g03441 . . . . . . . . . . . . . . . . . . . . . . . Phco7g00025 . . . . . . . . . . . . . Pvu9g1196 . . . . . Spst9g00014 . . . . . . . . . . . . . . . . . . . Vivi3g01113 . . .
Vvi3g0241 Acco02g3643 . Accr2g00253 . Adu09g02869 . Aed1g1759 . . . . . . . Alju01g3642 . . . Apr8g2658 . Arst9g03829 . . . Bisa03g3675 . . Bva14g02374 . . Cca02g02751 . Dere01g0217 . . . Enph2g2603 . . . . . . . . . . . . . . . Lal12g0274 Lal24g0202 . . . . . . Lapu7g02510 . Lasa6g04794 . Lele05g2697 . Lele07g2721 . . . . . . . . Mal1g0201 Mepo4g04871 . Mesa1g05285 . Mibi02g3336 . . Mtr1g4327 . . Phco6g03056 . Prci1g0207 . . . Pste4g00397 . Pte18g00505 Pte9g01592 . . Pumo3g00188 . Pvu7g0177 . Rops6g03426 . Seca8g08024 . Spst10g01561 . Ssu7g0209 . . Sto10g0043 . Tpr1g0187 Trre1g06185 . . Tsu01g04998 Vian3g00173 . . . Vimu3g03679 . Viun7g03988 . . . Vra8g2648 .
Vvi3g0242 . . . . Adu09g02873 . . . Aev09g2720 . Ahy19g3051 . Aip09g03511 . . . Amo19g3914 . Apr8g2660 . Arst9g03833 . . . . . . . . . Cca02g02753 . . . Dod06g0302 . . . . . Gma04g00016 Gma06g00012 . . Gso4g0012 Gso4g0012 . . . . . Lal13g0249 . . . . . . . . Lapu7g02512 . Lasa6g04796 . . . . . . . . . . . . Mal1g0198 Mepo4g04873 . Mesa1g05286 . . . . Mtr1g4329 . . Phco6g03058 . . . Psa6g5333 . Pste4g00393 . . . . . Pumo3g00186 . Pvu7g0175 . Rops6g03428 . Seca8g08027 . . . Ssu7g0207 . Sto2g1101 . . Tpr1g0185 Trre1g06189 . . Tsu01g05000 . . Vifa3g00164 . Vimu3g03684 . Viun7g03991 . . . Vra8g2650 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0233 Chr3 2022219 2024081 -
Adu Adu09g02862 Chr09 116307459 116308903 -
Aed Aed1g1762 Chr1 15152142 15153602 +
Aev Aev09g2711 Chr09 27952713 27954301 -
Ahy Ahy19g3057 Chr19 153358772 153361240 +
Aip Aip09g03518 Chr09 141880335 141881779 +
Amo Amo19g3921 Chr19 154951439 154952964 +
Apr Apr8g2657 Chr8 36348804 36351168 -
Arst Arst9g03825 Chr9 114203744 114205451 -
Bva Bva14g02369 Chr14 20402594 20404550 -
Cca Cca02g02748 Chr02 48977236 48978907 -
Dod Dod06g0295 Chr06 3986166 3988355 -
Lal Lal12g0273 Chr12 1950292 1951974 -
Lapu Lapu7g02509 Chr7 41489268 41490765 -
Lasa Lasa6g04793 Chr6 669672130 669673667 -
Mal Mal1g0205 Chr1 2300123 2301844 +
Mepo Mepo4g04867 Chr4 58000851 58002634 -
Mesa Mesa1g05277 Chr1 80008735 80010331 -
Mtr Mtr1g4324 Chr1 54932307 54934174 -
Phco Phco6g03053 Chr6 51561255 51563684 -
Pste Pste4g00400 Chr4 3078990 3084970 +
Pumo Pumo3g00191 Chr3 2402251 2404049 +
Pvu Pvu7g0179 Chr7 1176924 1179412 +
Rops Rops6g03424 Chr6 58891159 58892907 -
Seca Seca8g08021 Chr8 177785178 177787453 -
Spst Spst10g01558 Chr10 16250767 16252451 -
Ssu Ssu7g0213 Chr7 3506839 3508352 +
Sto Sto2g1088 Chr2 9537686 9541463 +
Tpr Tpr1g0188 Chr1 1509892 1512208 +
Trre Trre1g06181 Chr1 65584941 65586662 -
Tsu Tsu01g04995 Chr01 56736239 56738274 -
Vifa Vifa3g00166 Chr3 12880898 12882832 -
Vimu Vimu3g03676 Chr3 49384373 49385962 -
Viun Viun7g03987 Chr7 39459285 39461512 -
Vra Vra8g2647 Chr8 44389468 44391800 -
Vvi Vvi3g0234 Chr3 2025302 2027513 -
Aev Aev09g2712 Chr09 27954989 27956389 -
Ahy Ahy19g3056 Chr19 153354126 153356154 +
Aip Aip09g03517 Chr09 141876384 141877793 +
Amo Amo19g3920 Chr19 154947052 154948932 +
Bva Bva14g02370 Chr14 20406134 20407528 -
Cca Cca02g02749 Chr02 48982550 48983248 -
Dod Dod06g0296 Chr06 3989717 3991621 -
Mal Mal1g0204 Chr1 2297398 2298792 +
Mtr Mtr1g4325 Chr1 54934661 54936218 -
Ssu Ssu7g0211 Chr7 3504611 3505126 +
Tsu Tsu01g04996 Chr01 56741211 56742065 -
Vvi Vvi3g0235 Chr3 2034767 2037175 -
Aev Aev09g2714 Chr09 27959111 27961471 -
Ahy Ahy19g3055 Chr19 153348602 153351357 +
Aip Aip09g03516 Chr09 141869571 141871958 +
Amo Amo19g3919 Chr19 154941528 154944201 +
Bva Bva14g02372 Chr14 20410205 20413215 -
Dod Dod06g0298 Chr06 3996161 3998752 -
Lal Lal13g0247 Chr13 1568515 1570869 -
Sto Sto2g1094 Chr2 9593872 9596304 -
Vvi Vvi3g0236 Chr3 2039911 2040282 -
Vvi Vvi3g0237 Chr3 2042274 2047495 -
Vvi Vvi3g0238 Chr3 2047567 2047914 -
Vvi Vvi3g0239 Chr3 2049121 2050248 -
Aed Aed9g0015 Chr9 99379 105280 -
Aev Aev04g3575 Chr04 33678109 33679506 -
Ahy Ahy13g1002 Chr13 11055185 11057385 -
Aip Aip03g01102 Chr03 10706909 10709407 -
Amo Amo13g1296 Chr13 16882230 16884886 +
Cca Cca07g00019 Chr07 308001 314433 -
Dod Dod03g3366 Chr03 66326879 66328172 -
Vra Vra5g1882 Chr5 24570171 24575962 +
Vvi Vvi3g0240 Chr3 2054751 2055821 -
Ahy Ahy20g0110 Chr20 889681 893265 +
Aip Aip10g00097 Chr10 889393 893648 +
Lasa Lasa5g03441 Chr5 562392984 562394386 +
Phco Phco7g00025 Chr7 179028 180032 +
Pvu Pvu9g1196 Chr9 17433306 17433667 +
Spst Spst9g00014 Chr9 160348 161349 +
Vivi Vivi3g01113 Chr3 18593544 18594573 -
Vvi Vvi3g0241 Chr3 2060881 2065849 +
Acco Acco02g3643 Chr02 51419018 51427076 -
Accr Accr2g00253 Chr2 6615280 6623534 +
Adu Adu09g02869 Chr09 116353155 116360662 +
Aed Aed1g1759 Chr1 15136293 15141441 -
Alju Alju01g3642 Chr01 65681571 65688458 -
Apr Apr8g2658 Chr8 36362392 36368544 +
Arst Arst9g03829 Chr9 114237588 114245206 +
Bisa Bisa03g3675 Chr03 77028040 77034971 -
Bva Bva14g02374 Chr14 20418801 20425157 +
Cca Cca02g02751 Chr02 49003382 49009623 +
Dere Dere01g0217 Chr01 6026854 6037625 +
Enph Enph2g2603 Chr2 42509646 42515753 -
Lal Lal12g0274 Chr12 1955634 1961778 +
Lal Lal24g0202 Chr24 1472536 1474562 -
Lapu Lapu7g02510 Chr7 41501411 41507919 +
Lasa Lasa6g04794 Chr6 669925893 669931865 +
Lele Lele05g2697 Chr05 42838777 42847998 -
Lele Lele07g2721 Chr07 32711312 32716603 -
Mal Mal1g0201 Chr1 2257849 2266760 -
Mepo Mepo4g04871 Chr4 58022871 58030998 +
Mesa Mesa1g05285 Chr1 80067768 80074329 +
Mibi Mibi02g3336 Chr02 59096640 59103906 -
Mtr Mtr1g4327 Chr1 54961440 54967667 +
Phco Phco6g03056 Chr6 51571710 51577111 +
Prci Prci1g0207 Chr1 1922504 1929137 +
Pste Pste4g00397 Chr4 3049278 3055712 -
Pte Pte18g00505 Chr18 10790106 10792326 +
Pte Pte9g01592 Chr9 36956968 36966765 +
Pumo Pumo3g00188 Chr3 2377344 2384257 -
Pvu Pvu7g0177 Chr7 1160351 1167579 -
Rops Rops6g03426 Chr6 58913017 58924860 +
Seca Seca8g08024 Chr8 177799251 177807531 +
Spst Spst10g01561 Chr10 16288738 16294067 +
Ssu Ssu7g0209 Chr7 3464898 3472468 -
Sto Sto10g0043 Chr10 366385 371063 -
Tpr Tpr1g0187 Chr1 1493538 1500305 -
Trre Trre1g06185 Chr1 65612877 65618524 +
Tsu Tsu01g04998 Chr01 56752870 56759429 +
Vian Vian3g00173 Chr3 1410026 1415223 -
Vimu Vimu3g03679 Chr3 49395586 49400509 +
Viun Viun7g03988 Chr7 39470781 39476245 +
Vra Vra8g2648 Chr8 44401231 44406383 +
Vvi Vvi3g0242 Chr3 2066890 2081243 -
Adu Adu09g02873 Chr09 116367372 116370926 -
Aev Aev09g2720 Chr09 27982875 27986663 -
Ahy Ahy19g3051 Chr19 153300861 153304763 +
Aip Aip09g03511 Chr09 141823823 141827609 +
Amo Amo19g3914 Chr19 154901290 154905230 +
Apr Apr8g2660 Chr8 36372613 36377681 -
Arst Arst9g03833 Chr9 114251845 114255510 -
Cca Cca02g02753 Chr02 49014638 49020918 -
Dod Dod06g0302 Chr06 4027509 4032402 -
Gma Gma04g00016 Chr04 144074 145223 -
Gma Gma06g00012 Chr06 127698 129036 -
Gso Gso4g0012 Chr4 142965 144194 -
Gso Gso4g0012 Chr4 142965 144194 -
Lal Lal13g0249 Chr13 1574471 1583117 -
Lapu Lapu7g02512 Chr7 41512978 41518738 -
Lasa Lasa6g04796 Chr6 670010793 670013522 -
Mal Mal1g0198 Chr1 2240541 2245629 +
Mepo Mepo4g04873 Chr4 58034298 58038185 -
Mesa Mesa1g05286 Chr1 80076533 80083332 -
Mtr Mtr1g4329 Chr1 54973721 54978589 -
Phco Phco6g03058 Chr6 51582033 51588087 -
Psa Psa6g5333 Chr6 467074965 467077298 +
Pste Pste4g00393 Chr4 3021365 3028125 +
Pumo Pumo3g00186 Chr3 2366960 2371624 +
Pvu Pvu7g0175 Chr7 1149693 1155724 +
Rops Rops6g03428 Chr6 58931143 58937603 -
Seca Seca8g08027 Chr8 177815259 177817747 -
Ssu Ssu7g0207 Chr7 3447173 3454336 +
Sto Sto2g1101 Chr2 9699976 9704489 -
Tpr Tpr1g0185 Chr1 1485107 1489402 +
Trre Trre1g06189 Chr1 65623773 65627343 -
Tsu Tsu01g05000 Chr01 56763332 56768390 -
Vifa Vifa3g00164 Chr3 12403289 12405847 +
Vimu Vimu3g03684 Chr3 49405784 49411490 -
Viun Viun7g03991 Chr7 39480748 39486303 -
Vra Vra8g2650 Chr8 44410327 44416427 -
Acco Acco02g3643 Chr02 51419018 51427076 -
Accr Accr2g00253 Chr2 6615280 6623534 +
Aed Aed1g1759 Chr1 15136293 15141441 -
Alju Alju01g3642 Chr01 65681571 65688458 -
Apr Apr8g2658 Chr8 36362392 36368544 +
Bisa Bisa03g3675 Chr03 77028040 77034971 -
Cca Cca02g02751 Chr02 49003382 49009623 +
Dere Dere01g0217 Chr01 6026854 6037625 +
Enph Enph2g2603 Chr2 42509646 42515753 -
Lele Lele05g2697 Chr05 42838777 42847998 -
Lele Lele07g2721 Chr07 32711312 32716603 -
Mal Mal1g0201 Chr1 2257849 2266760 -
Mibi Mibi02g3336 Chr02 59096640 59103906 -
Mtr Mtr1g4327 Chr1 54961440 54967667 +
Prci Prci1g0207 Chr1 1922504 1929137 +
Ssu Ssu7g0209 Chr7 3464898 3472468 -
Tpr Tpr1g0187 Chr1 1493538 1500305 -
Tsu Tsu01g04998 Chr01 56752870 56759429 +
Vra Vra8g2648 Chr8 44401231 44406383 +