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
Vvi19g0340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto4g2909 . . . . . . . . . . . . . . . . . .
Vvi19g0342 . . . . . . Aed1g0655 Aed5g1100 Aev10g2390 . Ahy18g1252 . Aip08g01334 . . . Amo18g1449 . Apr2g0352 Apr5g0074 . . . . . . Bva09g00809 Bva07g01799 Car01g02090 Car07g02152 Cca10g01054 Cca04g01373 . . Dod10g1045 . . . . . Gma06g02324 Gma12g01356 Gma12g02067 Gma13g02491 Gso6g2113 Gso6g2113 Gso6g2113 Gso6g2113 Lal9g0493 . . Lal20g0302 . Lal11g1396 Lan8g1411 . . Lan8g1411 . Lan8g1411 . . . . . . . . . . . . . . Mal4g1035 Mal5g2390 . . . . . . Mtr2g2691 Mtr8g1692 . . . . . . Psa5g5664 . . . . . . . . . . . . . . . . . Ssu8g1096 Ssu3g1864 . Sto4g2910 Tpr7g3596 . . . Tsu02g04472 Tsu08g02043 . . . . . . . . . . . Vra2g1308
Vvi19g0343 . . . . Adu10g00332 . Aed1g0656 . Aev10g2388 . Ahy18g1251 . Aip08g01333 . . . Amo18g1448 . Apr2g0351 . Arst10g00438 . Bach7g00697 . . . Bva09g00808 Bva07g01800 Car01g02091 . Cca10g01053 . . . Dod10g1046 . . . . . . . Gma12g02066 Gma13g02492 . . . . . Lal1g1654 . Lal20g0301 . . . . . . . . . . Lasa1g05069 . . . . . . . . . . Lja3g4490 Mal4g1034 . . . . . . . Mtr2g2692 . Phac6g02738 . Phco11g00347 . . . Psa5g5665 . . . . . . . Pumo2g00902 . Pvu6g1982 . Rops11g00489 . Seca6g04962 . Spst6g00707 . Ssu8g1095 . Sto7g0313 Sto4g2911 . . . . Tsu02g04473 . . . Vifa1g10559 . Vimu2g00583 . Viun6g02863 . . . . .
Vvi19g0344 . . . . . . . Aed5g1099 . . . . . . . . . . . Apr5g0073 . . . . . . . Bva07g01801 . Car07g02151 . Cca04g01372 . . . . . . . . Gma06g02325 . . . Gso6g2115 . . . . . . . Lal1g0558 . . . . . . . . . . . . . . . . . . . . . . Mal5g2391 . . . . . . . Mtr8g1693 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g1866 . Sto4g2912 . . . . . Tsu08g02042 . . . . . . . . . . . Vra2g1307
Vvi19g0345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0346 Acco06g2259 . Accr5g00862 . Adu10g00340 . . . . . . . . . Alju03g1138 . . . . . Arst10g00445 . Bach7g00700 . Bisa07g0799 . . . . . . . Dere02g2571 . . . Enph4g0639 . Glsi11g2479 . . . . . . . . . . . . . . . . . . . . . Lapu6g01199 . Lasa1g00355 . Lele13g0689 Lele14g0588 Lele15g1794 Lele16g1825 . . . . . . . . Mepo6g00355 . Mesa5g04306 . Mibi06g0897 . . . Phac6g02744 . Phco11g00343 . Prci3g0888 . . . Pste2g01897 . . . . . Pumo2g00906 . Pvu6g1987 . Rops11g00482 . Seca6g04968 . Spst6g00703 . . . . . . . Trre3g00385 . . . Vian6g01830 . Vifa1g10564 . Vimu2g00580 . Viun6g02868 . . . . .
Vvi19g0347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0349 . . . . . . Aed1g0658 Aed5g1097 Aev10g2386 . Ahy18g1246 Ahy13g1805 Aip08g01323 Aip03g01995 . . . Amo13g2271 Apr2g0349 Apr5g0071 . . . . . . Bva09g00805 Bva07g01802 Car01g02095 Car07g02147 Cca10g01050 Cca04g01371 . . Dod10g1048 Dod03g1896 . . . . Gma06g02327 Gma12g01353 Gma12g02063 Gma13g02495 Gso6g2120 Gso6g2120 Gso6g2120 Gso6g2120 Lal9g0491 . Lal2g0555 Lal20g0299 . Lal11g1394 Lan8g1413 . Lan8g1413 Lan8g1413 . Lan8g1413 . . . . . . . . . . . . . Lja3g4488 Mal4g1027 Mal5g2395 . . . . . . Mtr2g2698 Mtr8g1696 . . . Phco9g01744 . . Psa5g5675 . . Pste1g03920 . . . . . . . Pvu11g1611 . . . . . . . Ssu3g1867 Sto7g0315 Sto4g2915 Tpr7g3601 Tpr7g2030 . . Tsu02g04482 Tsu08g02024 . . . . . Vimu5g00391 . . . Vivi7g00204 . Vra2g1304
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Car Car07g02152 Chr07 28814592 28834200 -
Vvi Vvi19g0340 Chr19 3625081 3626699 -
Vvi Vvi19g0341 Chr19 3626949 3634812 -
Sto Sto4g2909 Chr4 29648218 29648926 -
Vvi Vvi19g0342 Chr19 3640098 3649935 +
Aed Aed1g0655 Chr1 7852148 7857082 +
Aed Aed5g1100 Chr5 9328769 9338311 -
Aev Aev10g2390 Chr10 23527796 23539600 -
Ahy Ahy18g1252 Chr18 21904802 21911603 -
Aip Aip08g01334 Chr08 20892713 20899301 -
Amo Amo18g1449 Chr18 27393373 27399878 -
Apr Apr2g0352 Chr2 4209183 4215298 -
Apr Apr5g0074 Chr5 704371 710598 -
Bva Bva09g00809 Chr09 4156319 4161342 -
Bva Bva07g01799 Chr07 16411665 16417439 +
Car Car01g02090 Chr01 46339608 46345467 +
Car Car07g02152 Chr07 28814592 28834200 -
Cca Cca10g01054 Chr10 13007503 13013089 -
Cca Cca04g01373 Chr04 17929400 17936362 -
Dod Dod10g1045 Chr10 28690307 28696659 +
Gma Gma06g02324 Chr06 44047119 44053643 +
Gma Gma12g01356 Chr12 21011696 21017758 -
Gma Gma12g02067 Chr12 41397945 41402781 -
Gma Gma13g02491 Chr13 39768477 39775807 +
Gso Gso6g2113 Chr6 40029133 40035948 +
Gso Gso6g2113 Chr6 40029133 40035948 +
Gso Gso6g2113 Chr6 40029133 40035948 +
Gso Gso6g2113 Chr6 40029133 40035948 +
Lal Lal9g0493 Chr9 3315695 3321260 -
Lal Lal20g0302 Chr20 2324082 2328991 -
Lal Lal11g1396 Chr11 17419132 17425162 -
Lan Lan8g1411 Chr8 21153439 21159500 +
Lan Lan8g1411 Chr8 21153439 21159500 +
Lan Lan8g1411 Chr8 21153439 21159500 +
Mal Mal4g1035 Chr4 14306763 14312464 -
Mal Mal5g2390 Chr5 65415541 65422164 +
Mtr Mtr2g2691 Chr2 40020386 40026035 +
Mtr Mtr8g1692 Chr8 25000935 25008528 +
Psa Psa5g5664 Chr5 492401309 492405533 +
Ssu Ssu8g1096 Chr8 19295967 19300742 -
Ssu Ssu3g1864 Chr3 58174845 58180904 +
Sto Sto4g2910 Chr4 29653494 29657055 +
Tpr Tpr7g3596 Chr7 44566418 44572151 +
Tsu Tsu02g04472 Chr02 53620913 53625933 +
Tsu Tsu08g02043 Chr08 26923581 26932385 -
Vra Vra2g1308 Chr2 20751382 20762889 -
Vvi Vvi19g0343 Chr19 3653823 3655253 +
Adu Adu10g00332 Chr10 3868944 3870103 +
Aed Aed1g0656 Chr1 7860354 7862151 +
Aev Aev10g2388 Chr10 23517195 23518457 -
Ahy Ahy18g1251 Chr18 21888094 21889493 -
Aip Aip08g01333 Chr08 20882944 20884286 -
Amo Amo18g1448 Chr18 27376596 27378041 -
Apr Apr2g0351 Chr2 4192528 4193861 -
Arst Arst10g00438 Chr10 3518607 3519919 +
Bach Bach7g00697 Chr7 17852323 17853844 +
Bva Bva09g00808 Chr09 4151066 4152825 -
Bva Bva07g01800 Chr07 16419976 16421238 +
Car Car01g02091 Chr01 46349935 46351539 +
Cca Cca10g01053 Chr10 12980587 12983608 -
Dod Dod10g1046 Chr10 28705311 28706943 +
Gma Gma12g02066 Chr12 41390208 41391531 -
Gma Gma13g02492 Chr13 39781121 39782920 +
Lal Lal1g1654 Chr1 18958275 18959847 +
Lal Lal20g0301 Chr20 2316016 2317603 -
Lasa Lasa1g05069 Chr1 820783153 820784290 +
Lja Lja3g4490 Chr3 86644457 86645897 -
Mal Mal4g1034 Chr4 14298172 14299353 -
Mtr Mtr2g2692 Chr2 40032984 40034585 +
Phac Phac6g02738 Chr6 24813271 24814783 +
Phco Phco11g00347 Chr11 2254467 2255493 -
Psa Psa5g5665 Chr5 492411660 492414018 +
Pumo Pumo2g00902 Chr2 13673760 13675119 +
Pvu Pvu6g1982 Chr6 29879779 29881123 -
Rops Rops11g00489 Chr11 6686457 6687647 -
Seca Seca6g04962 Chr6 117022526 117023959 +
Spst Spst6g00707 Chr6 6396528 6397651 -
Ssu Ssu8g1095 Chr8 19272429 19274073 -
Sto Sto7g0313 Chr7 2194961 2196084 +
Sto Sto4g2911 Chr4 29659668 29660911 +
Tsu Tsu02g04473 Chr02 53632592 53634031 +
Vifa Vifa1g10559 Chr1 1777306283 1777307125 +
Vimu Vimu2g00583 Chr2 3418661 3419647 -
Viun Viun6g02863 Chr6 32089375 32090780 +
Vvi Vvi19g0344 Chr19 3659071 3664283 -
Aed Aed5g1099 Chr5 9314904 9321148 +
Apr Apr5g0073 Chr5 699148 703548 +
Bva Bva07g01801 Chr07 16422441 16431009 -
Car Car07g02151 Chr07 28806736 28813647 +
Cca Cca04g01372 Chr04 17911944 17928042 +
Gma Gma06g02325 Chr06 44056499 44066397 -
Gso Gso6g2115 Chr6 40042426 40047512 -
Lal Lal1g0558 Chr1 3606883 3611817 +
Mal Mal5g2391 Chr5 65424407 65429300 -
Mtr Mtr8g1693 Chr8 25010956 25015021 -
Ssu Ssu3g1866 Chr3 58191013 58197416 -
Sto Sto4g2912 Chr4 29663551 29667984 -
Tsu Tsu08g02042 Chr08 26909808 26915931 +
Vra Vra2g1307 Chr2 20744676 20751104 +
Vvi Vvi19g0345 Chr19 3665807 3667741 -
Vvi Vvi19g0346 Chr19 3676945 3682036 -
Acco Acco06g2259 Chr06 17893186 17904620 -
Accr Accr5g00862 Chr5 33525492 33538353 +
Adu Adu10g00340 Chr10 3928451 3935055 -
Alju Alju03g1138 Chr03 39450103 39461315 +
Arst Arst10g00445 Chr10 3578117 3584348 -
Bach Bach7g00700 Chr7 17860761 17871105 -
Bisa Bisa07g0799 Chr07 20824763 20836756 -
Dere Dere02g2571 Chr02 28432608 28444739 +
Enph Enph4g0639 Chr4 20207090 20221578 +
Glsi Glsi11g2479 Chr11 17501066 17512064 -
Lapu Lapu6g01199 Chr6 11851130 11863161 +
Lasa Lasa1g00355 Chr1 22910785 22919679 +
Lele Lele13g0689 Chr13 18953127 18968110 +
Lele Lele14g0588 Chr14 17359667 17369268 +
Lele Lele15g1794 Chr15 10865001 10874824 -
Lele Lele16g1825 Chr16 10826679 10837868 -
Mepo Mepo6g00355 Chr6 3657469 3667621 +
Mesa Mesa5g04306 Chr5 72182688 72189307 -
Mibi Mibi06g0897 Chr06 28087418 28098450 +
Phac Phac6g02744 Chr6 24848263 24860692 -
Phco Phco11g00343 Chr11 2225700 2238187 +
Prci Prci3g0888 Chr3 11352303 11365035 +
Pste Pste2g01897 Chr2 19335507 19347213 +
Pumo Pumo2g00906 Chr2 13699725 13709964 -
Pvu Pvu6g1987 Chr6 29907570 29919566 -
Rops Rops11g00482 Chr11 6615642 6628401 +
Seca Seca6g04968 Chr6 117059639 117067996 -
Spst Spst6g00703 Chr6 6366703 6378288 +
Trre Trre3g00385 Chr3 2510529 2519330 +
Vian Vian6g01830 Chr6 35731948 35743202 -
Vifa Vifa1g10564 Chr1 1778362267 1778371719 -
Vimu Vimu2g00580 Chr2 3391635 3403788 +
Viun Viun6g02868 Chr6 32108399 32118564 -
Vvi Vvi19g0347 Chr19 3720814 3721275 +
Vvi Vvi19g0348 Chr19 3721754 3724328 -
Vvi Vvi19g0349 Chr19 3750407 3776369 +
Aed Aed1g0658 Chr1 7876952 7886854 +
Aed Aed5g1097 Chr5 9288957 9299885 -
Aev Aev10g2386 Chr10 23496531 23506666 -
Ahy Ahy18g1246 Chr18 21663608 21672237 -
Ahy Ahy13g1805 Chr13 29311110 29322927 -
Aip Aip08g01323 Chr08 20669359 20677285 -
Aip Aip03g01995 Chr03 28222776 28234442 -
Amo Amo13g2271 Chr13 38777213 38781977 -
Apr Apr2g0349 Chr2 4158875 4170685 -
Apr Apr5g0071 Chr5 673195 684863 -
Bva Bva09g00805 Chr09 4132636 4142440 -
Bva Bva07g01802 Chr07 16436607 16445896 +
Car Car01g02095 Chr01 46393799 46403866 +
Car Car07g02147 Chr07 28494567 28514028 +
Cca Cca10g01050 Chr10 12875045 12884800 -
Cca Cca04g01371 Chr04 17852644 17864484 -
Dod Dod10g1048 Chr10 28717948 28728821 +
Dod Dod03g1896 Chr03 40137021 40154667 +
Gma Gma06g02327 Chr06 44130611 44143707 +
Gma Gma12g01353 Chr12 20908821 20926729 -
Gma Gma12g02063 Chr12 41352095 41362664 -
Gma Gma13g02495 Chr13 39812037 39823083 +
Gso Gso6g2120 Chr6 40112890 40125690 +
Gso Gso6g2120 Chr6 40112890 40125690 +
Gso Gso6g2120 Chr6 40112890 40125690 +
Gso Gso6g2120 Chr6 40112890 40125690 +
Lal Lal9g0491 Chr9 3292227 3302160 -
Lal Lal2g0555 Chr2 3353781 3364055 -
Lal Lal20g0299 Chr20 2291633 2302649 -
Lal Lal11g1394 Chr11 17385235 17395152 -
Lan Lan8g1413 Chr8 21195955 21205690 +
Lan Lan8g1413 Chr8 21195955 21205690 +
Lan Lan8g1413 Chr8 21195955 21205690 +
Lan Lan8g1413 Chr8 21195955 21205690 +
Lja Lja3g4488 Chr3 86607029 86618859 -
Mal Mal4g1027 Chr4 14219077 14229436 -
Mal Mal5g2395 Chr5 65587925 65600398 +
Mtr Mtr2g2698 Chr2 40075315 40085852 +
Mtr Mtr8g1696 Chr8 25044792 25057984 +
Phco Phco9g01744 Chr9 41232911 41248152 +
Psa Psa5g5675 Chr5 492702335 492713806 -
Pste Pste1g03920 Chr1 20179066 20182167 -
Pvu Pvu11g1611 Chr11 41014856 41029550 +
Ssu Ssu3g1867 Chr3 58235686 58250541 +
Sto Sto7g0315 Chr7 2202522 2211157 +
Sto Sto4g2915 Chr4 29688345 29698761 +
Tpr Tpr7g3601 Chr7 44615915 44625235 +
Tpr Tpr7g2030 Chr7 25207134 25228028 -
Tsu Tsu02g04482 Chr02 53688879 53698666 +
Tsu Tsu08g02024 Chr08 26491575 26505926 -
Vimu Vimu5g00391 Chr5 3652928 3667560 +
Vivi Vivi7g00204 Chr7 11750098 11779002 +
Vra Vra2g1304 Chr2 20678803 20703741 -