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
Vvi16g0589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0590 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva07g00279 . Car06g03064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0591 . . . . . . Aed5g0057 . . . . . . . . . . . . . . . . . . . . . . . Cca04g00067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g3289 . . . . . . . . . . . . . . . . . . . . .
Vvi16g0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0593 Acco08g1599 . Accr13g01556 . Adu03g01017 . Aed5g0055 . Aev04g3730 . Ahy13g1241 . Aip03g01360 . . . Amo13g1617 . Apr5g0657 . Arst3g01310 . Bach9g01452 . Bisa02g2340 . . . . Car06g03110 Cca04g00065 . Dere07g1577 . Dod03g2510 . Enph8g0036 . Glsi04g1650 . Gma09g02118 . . . Gso9g1896 . . . Lal1g0026 . Lal9g0019 . . . Lan13g0032 . Lan13g0032 . . . Lapu11g01105 . . . Lele29g1077 Lele30g0377 Lele31g0461 . . . . . Lja3g0057 . Mal7g1169 . . . . . Mibi07g1521 . Mtr4g1057 . . . Phco9g00099 . . . . . . . . . . . Pumo11g02268 . Pvu11g0062 . Rops3g00085 . Seca6g00123 . Spst2g02962 . Ssu3g3291 . . Sto4g2497 Tpr4g1187 . . . . . Vian5g01846 . . . Vimu5g02814 . Viun11g02994 . Vivi7g05045 . Vra2g0065 .
Vvi16g0594 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0595 . . . . Adu03g01020 . Aed5g0054 . Aev04g3731 . Ahy13g1243 Ahy15g0983 Aip03g01363 Aip05g01010 . . Amo13g1618 . Apr5g0658 . Arst3g01313 . Bach9g01458 . . . . Bva07g00858 . Car06g03111 Cca04g00063 . . . Dod03g2509 . . . . . Gma09g02119 . . . Gso9g1897 . . . . . . . . . . . . . . . Lapu11g01106 . . . . . . . . . . . Lja3g0055 . Mal7g1167 . . . . . . . Mtr4g1056 . . . Phco9g00097 . . . . . . . . . . . Pumo11g02269 . Pvu11g0061 . Rops3g00081 . Seca6g00117 . Spst2g02964 . Ssu3g3292 . Sto7g2428 . Tpr4g1186 . . . Tsu06g00925 . Vian5g01847 . . . Vimu5g02816 . Viun11g02996 . Vivi7g05044 . Vra2g0064 .
Vvi16g0596 . . Accr1g02140 . Adu03g01021 . Aed5g0053 Aed11g1643 Aev04g3732 . Ahy13g1245 . Aip03g01364 . . . Amo13g1619 . Apr5g0659 . Arst3g01314 . . . Bisa02g2338 . . . . . Cca04g00062 Cca06g01715 Dere07g1580 . . . . . . . Gma09g02120 . . . Gso9g1898 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja3g0054 Lja2g0083 . . . . . . . . . . . . Phco9g00096 . . . Psa2g4070 . . . . . . . Pumo11g02270 . Pvu11g0060 . Rops3g00080 . Seca6g00116 . . . Ssu3g3293 Ssu2g2769 Sto7g2429 Sto4g2498 . . . . . . Vian5g01848 . . . Vimu5g02818 . Viun11g02999 . . . Vra2g0063 .
Vvi16g0597 . . . . . . . . . . . . . . . . . . . . . Arst9g01986 . . . . Bva03g01552 Bva07g00848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Pte18g02127 . . Pumo3g01848 . Pvu7g1192 . Rops6g01737 . . . Spst10g00183 . . Sto10g2636 Sto4g2500 . . . . . . . Vian3g01281 . . . . . Viun7g02250 . . . .
Vvi16g0598 . . . . . . Aed5g0051 . . . Ahy13g1248 . Aip03g01366 . . . Amo13g1622 . Apr5g0661 . . . . . . . . Bva07g00847 . Car06g02995 Cca04g00060 . . . Dod03g2504 . . . . . Gma09g02122 . . . Gso9g1900 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja3g0051 Lja2g0080 Mal7g1161 Mal6g1604 . . . . . . Mtr4g1052 Mtr5g0396 . . . . . . Psa2g4072 . . . . . . . . . . . . . . . . . Ssu3g3295 . Sto7g2432 . Tpr4g1184 Tpr2g3790 . . Tsu06g00923 Tsu05g00360 . . . . . . . . . . Vra2g0061 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lja Lja2g0080 Chr2 612602 613854 +
Mal Mal6g1604 Chr6 29880534 29882319 -
Mtr Mtr5g0396 Chr5 3589359 3593832 +
Psa Psa2g4072 Chr2 418417175 418420027 -
Tpr Tpr2g3790 Chr2 40813734 40818242 -
Tsu Tsu05g00360 Chr05 2685527 2687380 +
Aed Aed11g1643 Chr11 20339802 20340571 +
Cca Cca06g01715 Chr06 32476263 32479408 +
Lja Lja2g0083 Chr2 624589 627909 -
Psa Psa2g4070 Chr2 418356519 418360622 +
Ssu Ssu2g2769 Chr2 88429933 88436484 +
Vvi Vvi16g0589 Chr16 11935172 11935891 +
Vvi Vvi16g0590 Chr16 11946895 11947987 -
Bva Bva07g00279 Chr07 3991608 3997814 -
Car Car06g03064 Chr06 53506409 53512019 +
Vvi Vvi16g0591 Chr16 11950754 11951365 +
Aed Aed5g0057 Chr5 430363 431124 -
Cca Cca04g00067 Chr04 607207 607854 -
Ssu Ssu3g3289 Chr3 89413036 89413815 +
Vvi Vvi16g0592 Chr16 11951525 11952115 -
Vvi Vvi16g0593 Chr16 11982894 11990393 +
Acco Acco08g1599 Chr08 21708238 21712091 +
Accr Accr13g01556 Chr13 26366114 26370285 +
Adu Adu03g01017 Chr03 10508187 10511668 +
Aed Aed5g0055 Chr5 418479 422533 -
Aev Aev04g3730 Chr04 34655388 34657964 +
Ahy Ahy13g1241 Chr13 14426584 14429690 +
Aip Aip03g01360 Chr03 13929087 13932238 +
Amo Amo13g1617 Chr13 21935903 21939134 +
Apr Apr5g0657 Chr5 9046998 9050201 +
Arst Arst3g01310 Chr3 10938986 10942113 +
Bach Bach9g01452 Chr9 13148700 13151726 +
Bisa Bisa02g2340 Chr02 56320522 56325923 -
Car Car06g03110 Chr06 55995880 56000135 +
Cca Cca04g00065 Chr04 592876 596201 -
Dere Dere07g1577 Chr07 22624681 22629791 +
Dod Dod03g2510 Chr03 56635426 56639053 -
Enph Enph8g0036 Chr8 3630624 3634108 -
Glsi Glsi04g1650 Chr04 52750273 52759921 -
Gma Gma09g02118 Chr09 46741767 46744569 +
Gso Gso9g1896 Chr9 43368976 43371800 +
Lal Lal1g0026 Chr1 210008 212287 +
Lal Lal9g0019 Chr9 99777 102402 -
Lan Lan13g0032 Chr13 155503 157010 +
Lan Lan13g0032 Chr13 155503 157010 +
Lapu Lapu11g01105 Chr11 13164243 13168612 +
Lele Lele29g1077 Chr29 8339311 8341866 +
Lele Lele30g0377 Chr30 8574350 8578625 -
Lele Lele31g0461 Chr31 12493569 12496126 -
Lja Lja3g0057 Chr3 678443 681929 -
Mal Mal7g1169 Chr7 37163834 37167142 -
Mibi Mibi07g1521 Chr07 27816104 27820693 +
Mtr Mtr4g1057 Chr4 13704297 13708232 -
Phco Phco9g00099 Chr9 654192 657547 -
Pumo Pumo11g02268 Chr11 55246766 55249398 +
Pvu Pvu11g0062 Chr11 458133 461838 -
Rops Rops3g00085 Chr3 1065875 1068199 -
Seca Seca6g00123 Chr6 3351073 3355179 -
Spst Spst2g02962 Chr2 29373258 29376731 +
Ssu Ssu3g3291 Chr3 89440388 89443600 +
Sto Sto4g2497 Chr4 26360981 26363178 +
Tpr Tpr4g1187 Chr4 11375457 11379207 -
Vian Vian5g01846 Chr5 40611966 40614959 +
Vimu Vimu5g02814 Chr5 37525962 37529162 +
Viun Viun11g02994 Chr11 41264303 41267716 +
Vivi Vivi7g05045 Chr7 135911695 135914728 -
Vra Vra2g0065 Chr2 544232 547878 -
Vvi Vvi16g0594 Chr16 11999043 12003193 +
Vvi Vvi16g0595 Chr16 12003368 12005651 +
Adu Adu03g01020 Chr03 10557259 10559151 +
Aed Aed5g0054 Chr5 409608 416254 -
Aev Aev04g3731 Chr04 34670545 34673000 +
Ahy Ahy13g1243 Chr13 14486137 14492174 +
Ahy Ahy15g0983 Chr15 14981811 14986676 +
Aip Aip03g01363 Chr03 13993631 13996040 +
Aip Aip05g01010 Chr05 14467115 14469264 +
Amo Amo13g1618 Chr13 21999741 22003864 +
Apr Apr5g0658 Chr5 9068345 9076024 +
Arst Arst3g01313 Chr3 10984132 10990059 +
Bach Bach9g01458 Chr9 13258016 13260781 +
Bva Bva07g00858 Chr07 10558558 10564154 -
Car Car06g03111 Chr06 56027716 56033344 +
Cca Cca04g00063 Chr04 575681 581181 -
Dod Dod03g2509 Chr03 56614628 56621374 -
Gma Gma09g02119 Chr09 46756410 46758744 +
Gso Gso9g1897 Chr9 43380364 43386291 +
Lapu Lapu11g01106 Chr11 13173493 13179724 +
Lja Lja3g0055 Chr3 651957 657906 -
Mal Mal7g1167 Chr7 37003094 37006207 -
Mtr Mtr4g1056 Chr4 13685798 13692010 -
Phco Phco9g00097 Chr9 644451 646775 -
Pumo Pumo11g02269 Chr11 55258926 55264629 +
Pvu Pvu11g0061 Chr11 448579 454461 -
Rops Rops3g00081 Chr3 1017393 1023489 -
Seca Seca6g00117 Chr6 3264970 3269486 -
Spst Spst2g02964 Chr2 29384452 29386710 +
Ssu Ssu3g3292 Chr3 89480390 89482743 +
Sto Sto7g2428 Chr7 29762108 29764627 +
Tpr Tpr4g1186 Chr4 11357918 11363676 -
Tsu Tsu06g00925 Chr06 8327451 8331127 -
Vian Vian5g01847 Chr5 40622577 40624859 +
Vimu Vimu5g02816 Chr5 37536089 37538345 +
Viun Viun11g02996 Chr11 41273689 41279469 +
Vivi Vivi7g05044 Chr7 135668866 135671890 -
Vra Vra2g0064 Chr2 534493 540402 -
Vvi Vvi16g0596 Chr16 12051811 12053766 +
Accr Accr1g02140 Chr1 55697493 55703888 -
Adu Adu03g01021 Chr03 10564371 10571992 +
Aed Aed5g0053 Chr5 403586 407527 -
Aed Aed11g1643 Chr11 20339802 20340571 +
Aev Aev04g3732 Chr04 34675797 34681005 +
Ahy Ahy13g1245 Chr13 14502712 14510874 +
Aip Aip03g01364 Chr03 14007556 14016552 +
Amo Amo13g1619 Chr13 22014812 22022719 +
Apr Apr5g0659 Chr5 9085450 9094573 +
Arst Arst3g01314 Chr3 10994628 11002237 +
Bisa Bisa02g2338 Chr02 56287429 56303847 -
Cca Cca04g00062 Chr04 565760 570206 -
Cca Cca06g01715 Chr06 32476263 32479408 +
Dere Dere07g1580 Chr07 22663210 22666398 +
Gma Gma09g02120 Chr09 46760928 46765697 +
Gso Gso9g1898 Chr9 43387899 43392841 +
Lja Lja3g0054 Chr3 638969 646017 -
Lja Lja2g0083 Chr2 624589 627909 -
Phco Phco9g00096 Chr9 637283 640247 -
Psa Psa2g4070 Chr2 418356519 418360622 +
Pumo Pumo11g02270 Chr11 55271497 55276998 +
Pvu Pvu11g0060 Chr11 439550 444057 -
Rops Rops3g00080 Chr3 1002691 1003041 -
Seca Seca6g00116 Chr6 3144329 3150521 -
Ssu Ssu3g3293 Chr3 89492033 89498981 +
Ssu Ssu2g2769 Chr2 88429933 88436484 +
Sto Sto7g2429 Chr7 29773552 29780375 +
Sto Sto4g2498 Chr4 26366261 26378335 +
Vian Vian5g01848 Chr5 40628133 40631125 +
Vimu Vimu5g02818 Chr5 37542054 37545047 +
Viun Viun11g02999 Chr11 41282713 41288507 +
Vra Vra2g0063 Chr2 527880 530929 -
Vvi Vvi16g0597 Chr16 12077244 12082295 +
Arst Arst9g01986 Chr9 55168007 55179182 -
Bva Bva03g01552 Chr03 14499290 14512363 +
Bva Bva07g00848 Chr07 10480743 10485115 -
Pte Pte18g02127 Chr18 31270257 31281620 -
Pumo Pumo3g01848 Chr3 29521663 29538924 +
Pvu Pvu7g1192 Chr7 18114008 18138469 -
Rops Rops6g01737 Chr6 34968702 34984445 +
Spst Spst10g00183 Chr10 1726656 1752416 -
Sto Sto10g2636 Chr10 36654325 36655927 +
Sto Sto4g2500 Chr4 26387356 26392235 +
Vian Vian3g01281 Chr3 14164287 14192405 +
Viun Viun7g02250 Chr7 26874177 26903079 -
Vvi Vvi16g0598 Chr16 12087409 12089494 -
Aed Aed5g0051 Chr5 394889 395500 +
Ahy Ahy13g1248 Chr13 14522346 14523230 -
Aip Aip03g01366 Chr03 14027288 14031825 -
Amo Amo13g1622 Chr13 22041745 22042949 -
Apr Apr5g0661 Chr5 9113473 9117197 -
Bva Bva07g00847 Chr07 10467533 10470461 +
Car Car06g02995 Chr06 51185514 51189786 +
Cca Cca04g00060 Chr04 544952 549121 +
Dod Dod03g2504 Chr03 56572346 56572904 +
Gma Gma09g02122 Chr09 46778870 46780679 -
Gso Gso9g1900 Chr9 43404054 43408920 -
Lja Lja3g0051 Chr3 595233 598178 +
Lja Lja2g0080 Chr2 612602 613854 +
Mal Mal7g1161 Chr7 36834626 36837459 +
Mal Mal6g1604 Chr6 29880534 29882319 -
Mtr Mtr4g1052 Chr4 13618358 13622997 +
Mtr Mtr5g0396 Chr5 3589359 3593832 +
Psa Psa2g4072 Chr2 418417175 418420027 -
Ssu Ssu3g3295 Chr3 89533643 89534971 -
Sto Sto7g2432 Chr7 29807132 29827277 -
Tpr Tpr4g1184 Chr4 11335360 11341286 +
Tpr Tpr2g3790 Chr2 40813734 40818242 -
Tsu Tsu06g00923 Chr06 8307870 8310980 +
Tsu Tsu05g00360 Chr05 2685527 2687380 +
Vra Vra2g0061 Chr2 511076 515095 +
Car Car06g02995 Chr06 51185514 51189786 +
Ahy Ahy13g1248 Chr13 14522346 14523230 -
Aip Aip03g01366 Chr03 14027288 14031825 -
Amo Amo13g1622 Chr13 22041745 22042949 -
Dod Dod03g2504 Chr03 56572346 56572904 +