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
Vvi4g1504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1505 . . . . Adu10g01768 . . . . Aev08g0592 . Ahy20g1996 . Aip10g02341 . . . . . . Arst10g02263 . . . . . Bva05g01565 . . . Cca06g01165 . . . . Dod09g1809 . . . . . Gma01g01614 . . . . . . . . Lal17g0735 . . . . . . . . . Lapu9g01137 . Lasa5g03343 . . . . . . . . . Lja1g4515 . Mal2g1516 . Mepo3g06818 . . . . . Mtr3g3340 . . . Phco7g01710 . . . Psa2g3363 . Pste2g03717 . . . . . Pumo10g01657 . Pvu9g1546 . Rops10g01011 . . . Spst9g01768 . Ssu2g2147 . . Sto4g0296 Tpr3g3140 . . . Tsu07g01331 . Vian4g01078 . . . Vimu10g01760 . Viun9g01799 . Vivi3g02466 . Vra11g0873 .
Vvi4g1506 . . . . . . . . . . . Ahy20g1997 . Aip10g02342 . . . Amo20g2555 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto4g0295 . . . . . . . . . . . . . . . . . .
Vvi4g1507 . . . . Adu10g01774 Adu03g03045 Aed5g2121 . . . Ahy13g3073 Ahy20g2004 Aip03g03477 Aip10g02347 . Alju06g2130 Amo13g3753 Amo20g2563 Apr1g0454 . Arst3g04012 Arst3g04012 . Bach2g00021 . Bisa08g2451 Bva05g01563 . . . Cca09g02256 . . Dere03g0374 Dod04g2530 Dod09g1814 . Enph6g0320 . Glsi02g0347 . . . . . . . . . . Lal17g0737 . . . . . . . . . Lapu9g01136 Lapu3g03429 . Lasa7g04519 . . . . Lele21g1510 Lele22g1501 Lele23g0503 Lele24g1456 Lja1g4511 Lja4g0602 Mal2g1512 Mal7g4733 Mepo3g06822 Mepo2g04411 Mesa9g04342 Mesa13g00711 . . Mtr3g3343 Mtr8g3277 . . Phco7g01711 Phco4g03087 . . . . Pste2g03721 Pste3g01576 Pte3g00062 . Pte2g02597 Pte3g00062 . Pumo6g00677 Pvu9g1547 Pvu2g2792 . Rops2g00789 . Seca12g06282 Spst9g01770 Spst3g01311 Ssu5g2857 . Sto3g3193 . Tpr3g3144 Tpr3g0825 . Trre7g05198 Tsu07g01329 Tsu02g00660 . Vian1g03660 . Vifa2g03184 Vimu10g01756 Vimu11g04181 . Viun3g00855 Vivi3g02460 Vivi5g04463 . .
Vvi4g1508 . . . . . . Aed5g2123 . Aev03g2909 Aev08g0590 Ahy13g3072 Ahy20g2013 Aip03g03476 Aip10g02357 . . Amo13g3750 Amo20g2573 Apr1g0453 . . . . . . . . . . . Cca09g02257 . . . Dod04g2531 Dod09g1815 . . . . . . . . . . . . Lal21g0662 . Lal17g0738 . . . Lan3g0719 . Lan3g0719 . . . . . . . . . . . . . . . Lja1g4510 Lja4g0601 Mal2g1511 Mal7g4734 . . . . . . Mtr3g3344 Mtr8g3278 . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g2858 . Sto3g3194 . Tpr3g3145 Tpr3g0824 . . Tsu07g01327 Tsu02g00659 . . . . . . . . . . . .
Vvi4g1509 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1510 . . . . Adu10g01786 Adu03g03043 Aed5g2124 . Aev03g2910 Aev08g0589 Ahy13g3071 Ahy20g2014 Aip03g03475 Aip10g02358 . . Amo13g3749 Amo20g2574 Apr1g0452 . Arst3g04009 Arst3g04009 . . . . Bva05g01560 . . . Cca09g02258 . . . Dod04g2532 Dod09g1816 . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g01133 . Lasa5g03349 . . . . . . . . . Lja1g4509 . Mal2g1509 . Mepo3g06825 . Mesa9g04345 . . . Mtr3g3346 . . . Phco7g01715 Phco4g03089 . . . . Pste2g03725 . . . Pte2g02596 . Pumo10g01693 Pumo6g00674 Pvu9g1551 Pvu2g2795 Rops10g01006 . Seca4g01961 . Spst9g01949 Spst3g01308 Ssu5g2859 . . . Tpr3g3148 . Trre5g04315 . Tsu07g01323 . Vian4g01075 Vian1g03662 Vifa2g03190 Vifa2g03190 Vimu10g01751 Vimu11g04183 Viun9g01790 Viun3g00852 Vivi3g02453 . . .
Vvi4g1511 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1513 . . . . . . . . . . . . . . . . . . . . . Arst1g00869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo3g04466 . Mesa9g01523 . . . . . . . Phco11g02105 . . . . . Pste7g01168 . . . . . Pumo1g00974 Pvu8g2168 Pvu6g0373 . Rops11g02956 . Seca6g03105 . . . . . . . . . Trre5g01450 . . . Vian6g00153 . Vifa2g00854 . Vimu2g02945 . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1504 Chr4 22597368 22598974 -
Vvi Vvi4g1505 Chr4 22605368 22630739 -
Adu Adu10g01768 Chr10 81626199 81630862 -
Aev Aev08g0592 Chr08 3388057 3392551 +
Ahy Ahy20g1996 Chr20 113162583 113167601 -
Aip Aip10g02341 Chr10 106008964 106013624 -
Arst Arst10g02263 Chr10 80562902 80567965 -
Bva Bva05g01565 Chr05 12847186 12853118 +
Cca Cca06g01165 Chr06 26038404 26048348 +
Dod Dod09g1809 Chr09 39646398 39648046 -
Gma Gma01g01614 Chr01 51830497 51837257 +
Lal Lal17g0735 Chr17 5210095 5227174 -
Lapu Lapu9g01137 Chr9 24875315 24881306 +
Lasa Lasa5g03343 Chr5 555909229 555914628 -
Lja Lja1g4515 Chr1 58826426 58832074 +
Mal Mal2g1516 Chr2 18161735 18168951 +
Mepo Mepo3g06818 Chr3 81936067 81941991 -
Mtr Mtr3g3340 Chr3 47339604 47345417 -
Phco Phco7g01710 Chr7 17132921 17138291 -
Psa Psa2g3363 Chr2 378473035 378476786 +
Pste Pste2g03717 Chr2 41018623 41027224 -
Pumo Pumo10g01657 Chr10 21766758 21774320 -
Pvu Pvu9g1546 Chr9 21839338 21844619 -
Rops Rops10g01011 Chr10 21680937 21686179 +
Spst Spst9g01768 Chr9 19539153 19541929 -
Ssu Ssu2g2147 Chr2 77412030 77415897 +
Sto Sto4g0296 Chr4 2285884 2294332 +
Tpr Tpr3g3140 Chr3 34629904 34636500 -
Tsu Tsu07g01331 Chr07 11654341 11660015 +
Vian Vian4g01078 Chr4 17338500 17340456 +
Vimu Vimu10g01760 Chr10 24611451 24616872 +
Viun Viun9g01799 Chr9 27512761 27518427 +
Vivi Vivi3g02466 Chr3 41351544 41357645 +
Vra Vra11g0873 Chr11 7367415 7373142 -
Vvi Vvi4g1506 Chr4 22635781 22636790 +
Ahy Ahy20g1997 Chr20 113318854 113319703 +
Aip Aip10g02342 Chr10 106150146 106151146 +
Amo Amo20g2555 Chr20 119956617 119957617 +
Sto Sto4g0295 Chr4 2280343 2281844 -
Vvi Vvi4g1507 Chr4 22650810 22697617 +
Adu Adu10g01774 Chr10 82115299 82124605 +
Adu Adu03g03045 Chr03 114240667 114248155 -
Aed Aed5g2121 Chr5 23500607 23509693 +
Ahy Ahy13g3073 Chr13 123474061 123481604 -
Ahy Ahy20g2004 Chr20 113751825 113759133 +
Aip Aip03g03477 Chr03 113544127 113550488 -
Aip Aip10g02347 Chr10 106561545 106570987 +
Alju Alju06g2130 Chr06 47363101 47369581 +
Amo Amo13g3753 Chr13 126687227 126693420 -
Amo Amo20g2563 Chr20 120182180 120191698 +
Apr Apr1g0454 Chr1 5569696 5587062 -
Arst Arst3g04012 Chr3 112955601 112963154 -
Arst Arst3g04012 Chr3 112955601 112963154 -
Bach Bach2g00021 Chr2 325878 338615 -
Bisa Bisa08g2451 Chr08 58131201 58179641 -
Bva Bva05g01563 Chr05 12828850 12841163 -
Cca Cca09g02256 Chr09 47784758 47800596 +
Dere Dere03g0374 Chr03 7412464 7434764 +
Dod Dod04g2530 Chr04 49140420 49149566 +
Dod Dod09g1814 Chr09 39768377 39783764 +
Enph Enph6g0320 Chr6 6529371 6547124 +
Glsi Glsi02g0347 Chr02 2230129 2244455 +
Lal Lal17g0737 Chr17 5240450 5253138 +
Lapu Lapu9g01136 Chr9 24838998 24860078 -
Lapu Lapu3g03429 Chr3 57536622 57566514 +
Lasa Lasa7g04519 Chr7 665935329 665946594 +
Lele Lele21g1510 Chr21 23361649 23372851 +
Lele Lele22g1501 Chr22 20711346 20717310 +
Lele Lele23g0503 Chr23 3688247 3690309 -
Lele Lele24g1456 Chr24 20452814 20460651 +
Lja Lja1g4511 Chr1 58712594 58723919 -
Lja Lja4g0602 Chr4 4974607 4982650 -
Mal Mal2g1512 Chr2 18073316 18084392 +
Mal Mal7g4733 Chr7 115635345 115645384 +
Mepo Mepo3g06822 Chr3 81978954 81982911 -
Mepo Mepo2g04411 Chr2 52640393 52651560 +
Mesa Mesa9g04342 Chr9 76531389 76544273 -
Mesa Mesa13g00711 Chr13 8412131 8421932 -
Mtr Mtr3g3343 Chr3 47378826 47385609 -
Mtr Mtr8g3277 Chr8 43249838 43261261 +
Phco Phco7g01711 Chr7 17156721 17171701 +
Phco Phco4g03087 Chr4 51834975 51851314 +
Pste Pste2g03721 Chr2 41226781 41239424 +
Pste Pste3g01576 Chr3 9851190 9865082 -
Pte Pte3g00062 Chr3 755202 764338 +
Pte Pte2g02597 Chr2 45055934 45065089 -
Pte Pte3g00062 Chr3 755202 764338 +
Pumo Pumo6g00677 Chr6 8508262 8525534 -
Pvu Pvu9g1547 Chr9 21855166 21871260 +
Pvu Pvu2g2792 Chr2 43671358 43687889 +
Rops Rops2g00789 Chr2 11301060 11318923 -
Seca Seca12g06282 Chr12 154716330 154730689 +
Spst Spst9g01770 Chr9 19567178 19577448 +
Spst Spst3g01311 Chr3 16545002 16546492 -
Ssu Ssu5g2857 Chr5 74878301 74892342 +
Sto Sto3g3193 Chr3 36738587 36740509 +
Tpr Tpr3g3144 Chr3 34661514 34680855 -
Tpr Tpr3g0825 Chr3 7770597 7781120 -
Trre Trre7g05198 Chr7 58540662 58549281 +
Tsu Tsu07g01329 Chr07 11634253 11644966 +
Tsu Tsu02g00660 Chr02 5573174 5588473 -
Vian Vian1g03660 Chr1 59397631 59412585 +
Vifa Vifa2g03184 Chr2 915789847 915811105 -
Vimu Vimu10g01756 Chr10 24553508 24556015 -
Vimu Vimu11g04181 Chr11 63380368 63390383 +
Viun Viun3g00855 Chr3 5238235 5246572 -
Vivi Vivi3g02460 Chr3 41238540 41245971 +
Vivi Vivi5g04463 Chr5 142531070 142542921 +
Vvi Vvi4g1508 Chr4 22707276 22712802 +
Aed Aed5g2123 Chr5 23518434 23519742 +
Aev Aev03g2909 Chr03 28436224 28459188 +
Aev Aev08g0590 Chr08 3378586 3381057 -
Ahy Ahy13g3072 Chr13 123467001 123472897 -
Ahy Ahy20g2013 Chr20 114022081 114025101 +
Aip Aip03g03476 Chr03 113536611 113543934 -
Aip Aip10g02357 Chr10 106825867 106827897 +
Amo Amo13g3750 Chr13 126640313 126642673 -
Amo Amo20g2573 Chr20 120515985 120519140 +
Apr Apr1g0453 Chr1 5562701 5565889 -
Cca Cca09g02257 Chr09 47802513 47806238 +
Dod Dod04g2531 Chr04 49152495 49155203 +
Dod Dod09g1815 Chr09 39786128 39789997 +
Lal Lal21g0662 Chr21 5101151 5105120 +
Lal Lal17g0738 Chr17 5254474 5259475 +
Lan Lan3g0719 Chr3 13150337 13154599 -
Lan Lan3g0719 Chr3 13150337 13154599 -
Lja Lja1g4510 Chr1 58707805 58711296 -
Lja Lja4g0601 Chr4 4968877 4972616 -
Mal Mal2g1511 Chr2 18067263 18071064 -
Mal Mal7g4734 Chr7 115648406 115650652 +
Mtr Mtr3g3344 Chr3 47396421 47401473 +
Mtr Mtr8g3278 Chr8 43264281 43267422 +
Ssu Ssu5g2858 Chr5 74895344 74898046 +
Sto Sto3g3194 Chr3 36743949 36747022 +
Tpr Tpr3g3145 Chr3 34687885 34692698 +
Tpr Tpr3g0824 Chr3 7765470 7768966 -
Tsu Tsu07g01327 Chr07 11616651 11620998 -
Tsu Tsu02g00659 Chr02 5566447 5569953 -
Vvi Vvi4g1509 Chr4 22723777 22725378 -
Vvi Vvi4g1510 Chr4 22733201 22739947 +
Adu Adu10g01786 Chr10 82323018 82325668 -
Adu Adu03g03043 Chr03 114139722 114141895 +
Aed Aed5g2124 Chr5 23520471 23522623 -
Aev Aev03g2910 Chr03 28459699 28461727 -
Aev Aev08g0589 Chr08 3375867 3377837 +
Ahy Ahy13g3071 Chr13 123454598 123457442 +
Ahy Ahy20g2014 Chr20 114029322 114032080 -
Aip Aip03g03475 Chr03 113523170 113526584 +
Aip Aip10g02358 Chr10 106832241 106834952 -
Amo Amo13g3749 Chr13 126628326 126630681 +
Amo Amo20g2574 Chr20 120523282 120526088 -
Apr Apr1g0452 Chr1 5558481 5561411 +
Arst Arst3g04009 Chr3 112854282 112856984 +
Arst Arst3g04009 Chr3 112854282 112856984 +
Bva Bva05g01560 Chr05 12821166 12823536 +
Cca Cca09g02258 Chr09 47808627 47812486 -
Dod Dod04g2532 Chr04 49153983 49157961 -
Dod Dod09g1816 Chr09 39791001 39792607 -
Lapu Lapu9g01133 Chr9 24819696 24822826 +
Lasa Lasa5g03349 Chr5 556506658 556508835 -
Lja Lja1g4509 Chr1 58697883 58700598 +
Mal Mal2g1509 Chr2 18059711 18061771 +
Mepo Mepo3g06825 Chr3 81997891 82000505 -
Mesa Mesa9g04345 Chr9 76571561 76573702 -
Mtr Mtr3g3346 Chr3 47404707 47407372 -
Phco Phco7g01715 Chr7 17218362 17220454 -
Phco Phco4g03089 Chr4 51857680 51859865 -
Pste Pste2g03725 Chr2 41269117 41271698 -
Pte Pte2g02596 Chr2 45048087 45050494 +
Pumo Pumo10g01693 Chr10 22308382 22310992 -
Pumo Pumo6g00674 Chr6 8467629 8470154 +
Pvu Pvu9g1551 Chr9 21889332 21892137 -
Pvu Pvu2g2795 Chr2 43692995 43695737 -
Rops Rops10g01006 Chr10 21549934 21552538 +
Seca Seca4g01961 Chr4 32928783 32932109 +
Spst Spst9g01949 Chr9 28687233 28689461 +
Spst Spst3g01308 Chr3 16505774 16508007 +
Ssu Ssu5g2859 Chr5 74907951 74910275 -
Tpr Tpr3g3148 Chr3 34705279 34708348 -
Trre Trre5g04315 Chr5 45292699 45295186 -
Tsu Tsu07g01323 Chr07 11603521 11606313 +
Vian Vian4g01075 Chr4 17251404 17253577 +
Vian Vian1g03662 Chr1 59419309 59421410 -
Vifa Vifa2g03190 Chr2 916506917 916509234 -
Vifa Vifa2g03190 Chr2 916506917 916509234 -
Vimu Vimu10g01751 Chr10 24459877 24462067 +
Vimu Vimu11g04183 Chr11 63399036 63401202 -
Viun Viun9g01790 Chr9 27461328 27464090 +
Viun Viun3g00852 Chr3 5225439 5227981 +
Vivi Vivi3g02453 Chr3 41200296 41203247 +
Vvi Vvi4g1511 Chr4 22741778 22742118 -
Vvi Vvi4g1512 Chr4 22756099 22765929 +
Vvi Vvi4g1513 Chr4 22767813 22771992 -
Arst Arst1g00869 Chr1 8820107 8826211 +
Mepo Mepo3g04466 Chr3 55102906 55106029 +
Mesa Mesa9g01523 Chr9 35609362 35612164 +
Phco Phco11g02105 Chr11 17687873 17690886 -
Pste Pste7g01168 Chr7 10775648 10780649 +
Pumo Pumo1g00974 Chr1 15469261 15471941 -
Pvu Pvu8g2168 Chr8 52123094 52124539 +
Pvu Pvu6g0373 Chr6 14214300 14219443 +
Rops Rops11g02956 Chr11 51871224 51878858 -
Seca Seca6g03105 Chr6 97235479 97239103 -
Trre Trre5g01450 Chr5 10346393 10349212 -
Vian Vian6g00153 Chr6 4090685 4093349 -
Vifa Vifa2g00854 Chr2 223487806 223490578 +
Vimu Vimu2g02945 Chr2 28226114 28228869 -
Cca Cca06g01165 Chr06 26038404 26048348 +
Ssu Ssu2g2147 Chr2 77412030 77415897 +
Vra Vra11g0873 Chr11 7367415 7373142 -
Arst Arst1g00869 Chr1 8820107 8826211 +
Mepo Mepo3g04466 Chr3 55102906 55106029 +
Mesa Mesa9g01523 Chr9 35609362 35612164 +
Phco Phco11g02105 Chr11 17687873 17690886 -
Pste Pste7g01168 Chr7 10775648 10780649 +
Pumo Pumo1g00974 Chr1 15469261 15471941 -
Pvu Pvu6g0373 Chr6 14214300 14219443 +
Rops Rops11g02956 Chr11 51871224 51878858 -
Seca Seca6g03105 Chr6 97235479 97239103 -
Trre Trre5g01450 Chr5 10346393 10349212 -
Vian Vian6g00153 Chr6 4090685 4093349 -
Vifa Vifa2g00854 Chr2 223487806 223490578 +
Vimu Vimu2g02945 Chr2 28226114 28228869 -