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
Vvi16g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1040 . . . . . Adu09g02323 Aed1g2318 . . Aev09g2178 . Ahy19g3592 . Aip09g04051 . . . . . . . Arst9g03065 . . . . . . . . Cca02g02202 . . . . Dod06g0850 . . . . Gma10g02181 . . . Gso10g2050 . . . . . . . . Lal13g0063 . . . . . . . Lapu7g01999 . Lasa6g04019 . . . . . . . . . Lja5g0681 Mal1g2115 . . Mepo4g04189 . Mesa1g04570 . . Mtr1g3690 . . Phac7g01160 . Phco6g02424 . Prci1g1128 Psa6g4454 . . Pste4g02798 . . Pte16g00334 . . . . Pvu7g0776 . Rops6g02669 . Seca8g07329 . Spst10g00912 Ssu7g0844 . . . Tpr1g0814 . . Trre1g05323 Tsu01g04357 . . Vian3g00678 . Vifa3g02847 . Vimu3g02982 . Viun7g03179 . Vivi1g04464 Vra8g2187 .
Vvi16g1041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1042 . . . . . . . Aed7g0675 . . . . . . . . . . . . . . . . . . . . . . . Cca08g00752 . . . . . . . . Gma20g01537 . . . Gso20g1317 . . . . Lal2g0962 Lal9g0851 . . . . . . . . . . . . . . . . . . . . . Lja2g2703 . Mal1g2116 . . . . . . . Mtr1g3689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr1g0815 . . . Tsu01g04356 . . . . . . . . . . . . .
Vvi16g1043 . . . . . . . Aed11g1751 . Aev09g2176 . Ahy19g3593 . Aip09g04052 . . . . . Apr6g0612 . . . . . . Bva03g02480 . . . . Cca06g01827 . . . Dod06g0852 . . . . Gma10g02180 . . . Gso10g2049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g2117 . . . . . . . Mtr1g3688 . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2903 Sto10g2316 . Tpr1g0816 . . . Tsu01g04355 . . . . . . . . . . . . Vra11g0249
Vvi16g1044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal2g0965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g4449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1045 Acco10g2509 . Accr4g00267 . Adu08g00462 . Aed1g2320 Aed7g0676 . . . . . . Alju08g0272 . . . . Apr6g0611 Arst8g00592 . Bach12g00950 . Bisa09g0959 . Bva03g02481 . . . Cca02g02201 Cca08g00753 Dere04g1178 . . . Enph1g1799 . Glsi08g0993 . Gma10g02179 . . . Gso10g2048 . . . . Lal2g0967 Lal9g0852 . . Lal13g0064 . . . . . . Lapu9g01379 . Lasa5g02969 . Lele01g0216 Lele02g0214 Lele03g0222 Lele04g0216 . . . . Lja1g4890 . . . Mepo3g06506 . Mesa9g04030 . Mibi05g0226 . . . Phac9g01084 . Phco7g01387 . Prci15g0330 . . . Pste2g03383 Pste4g02776 . . Pte16g00335 Pte9g00406 Pumo10g01372 Pumo3g01051 Pvu9g1420 Pvu7g0786 Rops10g02053 . Seca4g02508 Seca10g03759 Spst9g01428 Spst10g00909 Ssu7g0846 Ssu9g0004 Sto10g2307 . . . Trre5g03790 . . . Vian4g01412 Vian3g00681 Vifa2g02757 . Vimu10g01596 Vimu3g02979 Viun9g02240 Viun7g03174 Vivi3g02896 . Vra8g2184 .
Vvi16g1046 . . . . . . . Aed7g0678 Aev05g2833 Aev09g2168 Ahy15g3621 Ahy19g3594 Aip05g03936 Aip09g04053 . . . . . Apr6g0610 . . . . . . Bva03g02482 . . . Cca02g02200 Cca08g00755 . . Dod02g2957 Dod06g0856 . . . . Gma10g02178 . . . Gso10g2047 . . . Lal1g0851 Lal2g0968 . Lal24g0062 . Lal13g0065 Lan13g0827 Lan13g0827 . Lan13g0827 . Lan13g0827 . Lapu7g01980 . Lasa6g04016 . . . . . . . . Lja2g2706 Lja5g0682 Mal1g2119 . . Mepo4g04186 . Mesa1g04566 . . Mtr1g3686 . . . . Phco6g02406 . . . . . Pste4g02772 . . Pte16g00336 . . Pumo3g01052 . Pvu7g0793 . Rops6g02659 . Seca10g03757 . Spst10g00907 Ssu7g0847 Ssu9g0005 Sto10g2302 . Tpr1g0818 . . Trre1g05317 Tsu01g04353 . . Vian3g00682 . Vifa3g02842 . Vimu3g02977 . Viun7g03170 . Vivi1g04471 Vra8g2182 Vra1g1710
Vvi16g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02949 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0908 . . . . . . . . . . . . . . . . . . Sto9g2785 . . . . . . . . . . . . . . . . . . .
Vvi16g1048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aed Aed11g1751 Chr11 21024898 21030499 -
Cca Cca06g01827 Chr06 33689350 33695068 -
Ssu Ssu2g2903 Chr2 90351614 90364026 -
Vra Vra11g0249 Chr11 1706428 1712352 +
Psa Psa6g0908 Chr6 34165701 34168958 -
Apr Apr6g0612 Chr6 8858015 8865928 +
Vvi Vvi16g1039 Chr16 18743092 18743343 -
Vvi Vvi16g1040 Chr16 18744239 18747522 -
Adu Adu09g02323 Chr09 110164868 110167517 +
Aed Aed1g2318 Chr1 19204958 19208498 -
Aev Aev09g2178 Chr09 24658386 24661067 +
Ahy Ahy19g3592 Chr19 158524355 158527055 -
Aip Aip09g04051 Chr09 146772970 146775639 -
Arst Arst9g03065 Chr9 108062857 108065566 +
Cca Cca02g02202 Chr02 42530931 42534083 +
Dod Dod06g0850 Chr06 10582904 10586179 -
Gma Gma10g02181 Chr10 49399935 49405265 +
Gso Gso10g2050 Chr10 47518659 47524078 +
Lal Lal13g0063 Chr13 385318 388823 -
Lapu Lapu7g01999 Chr7 36235917 36239354 +
Lasa Lasa6g04019 Chr6 612151660 612153723 +
Lja Lja5g0681 Chr5 6121383 6125355 -
Mal Mal1g2115 Chr1 27651247 27654426 -
Mepo Mepo4g04189 Chr4 51803517 51806019 +
Mesa Mesa1g04570 Chr1 71651683 71654061 +
Mtr Mtr1g3690 Chr1 48584335 48588706 +
Phac Phac7g01160 Chr7 7313163 7316628 -
Phco Phco6g02424 Chr6 45646235 45672558 +
Prci Prci1g1128 Chr1 18301200 18322620 +
Psa Psa6g4454 Chr6 391085016 391089036 +
Pste Pste4g02798 Chr4 19718301 19722517 +
Pte Pte16g00334 Chr16 4365339 4368352 -
Pvu Pvu7g0776 Chr7 6987320 6991000 -
Rops Rops6g02669 Chr6 48044097 48048644 +
Seca Seca8g07329 Chr8 170011619 170015514 +
Spst Spst10g00912 Chr10 9923253 9926262 +
Ssu Ssu7g0844 Chr7 16976456 16981557 -
Tpr Tpr1g0814 Chr1 6804392 6807697 -
Trre Trre1g05323 Chr1 59109973 59112975 +
Tsu Tsu01g04357 Chr01 51489379 51490833 +
Vian Vian3g00678 Chr3 6860027 6862937 -
Vifa Vifa3g02847 Chr3 799562815 799565713 +
Vimu Vimu3g02982 Chr3 43891755 43895692 +
Viun Viun7g03179 Chr7 34364620 34367902 +
Vivi Vivi1g04464 Chr1 95125146 95130430 -
Vra Vra8g2187 Chr8 40264645 40268691 +
Vvi Vvi16g1041 Chr16 18748451 18748738 -
Vvi Vvi16g1042 Chr16 18748878 18753944 -
Aed Aed7g0675 Chr7 4968780 4979960 -
Cca Cca08g00752 Chr08 14585773 14593452 -
Gma Gma20g01537 Chr20 42380938 42391921 -
Gso Gso20g1317 Chr20 43197537 43205262 -
Lal Lal2g0962 Chr2 6449429 6455211 -
Lal Lal9g0851 Chr9 6255110 6263473 -
Lja Lja2g2703 Chr2 38986537 38995015 -
Mal Mal1g2116 Chr1 27657056 27662848 -
Mtr Mtr1g3689 Chr1 48575948 48582559 +
Tpr Tpr1g0815 Chr1 6809619 6817469 -
Tsu Tsu01g04356 Chr01 51481646 51488617 +
Vvi Vvi16g1043 Chr16 18756190 18759112 -
Aed Aed11g1751 Chr11 21024898 21030499 -
Aev Aev09g2176 Chr09 24650142 24655490 +
Ahy Ahy19g3593 Chr19 158527637 158532589 -
Aip Aip09g04052 Chr09 146776255 146781118 -
Apr Apr6g0612 Chr6 8858015 8865928 +
Bva Bva03g02480 Chr03 20944475 20951600 -
Cca Cca06g01827 Chr06 33689350 33695068 -
Dod Dod06g0852 Chr06 10597164 10599729 -
Gma Gma10g02180 Chr10 49392808 49399801 +
Gso Gso10g2049 Chr10 47511406 47519157 +
Mal Mal1g2117 Chr1 27667974 27673476 -
Mtr Mtr1g3688 Chr1 48569401 48573548 +
Ssu Ssu2g2903 Chr2 90351614 90364026 -
Sto Sto10g2316 Chr10 33355013 33362196 +
Tpr Tpr1g0816 Chr1 6818703 6823740 -
Tsu Tsu01g04355 Chr01 51470322 51480467 +
Vra Vra11g0249 Chr11 1706428 1712352 +
Vvi Vvi16g1044 Chr16 18768815 18776853 -
Lal Lal2g0965 Chr2 6483802 6488937 -
Psa Psa6g4449 Chr6 390989784 390994645 +
Vvi Vvi16g1045 Chr16 18793359 18798293 +
Acco Acco10g2509 Chr10 36344491 36346634 +
Accr Accr4g00267 Chr4 2652607 2654706 -
Adu Adu08g00462 Chr08 8383553 8386298 -
Aed Aed1g2320 Chr1 19244312 19248623 +
Aed Aed7g0676 Chr7 4999246 5002251 +
Alju Alju08g0272 Chr08 1981700 1983711 -
Apr Apr6g0611 Chr6 8813747 8818905 -
Arst Arst8g00592 Chr8 8355488 8357836 -
Bach Bach12g00950 Chr12 6728451 6730262 +
Bisa Bisa09g0959 Chr09 14003369 14005456 -
Bva Bva03g02481 Chr03 20965850 20969068 +
Cca Cca02g02201 Chr02 42510735 42513912 -
Cca Cca08g00753 Chr08 14674010 14679915 +
Dere Dere04g1178 Chr04 13158052 13160416 +
Enph Enph1g1799 Chr1 42971583 42973494 +
Glsi Glsi08g0993 Chr08 7349019 7350349 -
Gma Gma10g02179 Chr10 49364140 49367885 -
Gso Gso10g2048 Chr10 47482674 47486390 -
Lal Lal2g0967 Chr2 6501531 6504732 +
Lal Lal9g0852 Chr9 6275028 6279088 +
Lal Lal13g0064 Chr13 391786 396379 +
Lapu Lapu9g01379 Chr9 28014088 28018303 -
Lasa Lasa5g02969 Chr5 522551503 522553236 -
Lele Lele01g0216 Chr01 1230733 1232827 -
Lele Lele02g0214 Chr02 1186111 1188331 -
Lele Lele03g0222 Chr03 1207276 1209350 -
Lele Lele04g0216 Chr04 1284266 1285676 -
Lja Lja1g4890 Chr1 67103483 67105303 -
Mepo Mepo3g06506 Chr3 79073384 79076070 +
Mesa Mesa9g04030 Chr9 72801553 72804830 +
Mibi Mibi05g0226 Chr05 2319837 2321997 -
Phac Phac9g01084 Chr9 8310979 8314550 +
Phco Phco7g01387 Chr7 12652411 12655826 +
Prci Prci15g0330 Chr15 2160897 2163911 -
Pste Pste2g03383 Chr2 33923823 33929336 +
Pste Pste4g02776 Chr4 19572847 19576460 -
Pte Pte16g00335 Chr16 4399499 4401509 +
Pte Pte9g00406 Chr9 4881079 4885150 +
Pumo Pumo10g01372 Chr10 18219784 18224884 +
Pumo Pumo3g01051 Chr3 16124214 16127813 +
Pvu Pvu9g1420 Chr9 20168679 20172056 +
Pvu Pvu7g0786 Chr7 7135571 7139366 +
Rops Rops10g02053 Chr10 37387133 37389199 +
Seca Seca4g02508 Chr4 42841170 42848397 +
Seca Seca10g03759 Chr10 75327989 75332465 -
Spst Spst9g01428 Chr9 14243617 14246596 +
Spst Spst10g00909 Chr10 9887061 9890093 -
Ssu Ssu7g0846 Chr7 17073313 17075727 +
Ssu Ssu9g0004 Chr9 2040009 2043487 +
Sto Sto10g2307 Chr10 33200446 33203436 -
Trre Trre5g03790 Chr5 38355037 38357702 +
Vian Vian4g01412 Chr4 28566150 28569278 -
Vian Vian3g00681 Chr3 6931109 6933547 +
Vifa Vifa2g02757 Chr2 762924100 762927027 +
Vimu Vimu10g01596 Chr10 18127078 18133879 -
Vimu Vimu3g02979 Chr3 43846502 43848807 -
Viun Viun9g02240 Chr9 31843790 31846965 -
Viun Viun7g03174 Chr7 34305161 34307794 -
Vivi Vivi3g02896 Chr3 48225932 48229248 +
Vra Vra8g2184 Chr8 40214570 40217372 -
Vvi Vvi16g1046 Chr16 18814460 18822012 -
Aed Aed7g0678 Chr7 5020668 5021776 -
Aev Aev05g2833 Chr05 29342817 29343593 +
Aev Aev09g2168 Chr09 24606865 24609388 +
Ahy Ahy15g3621 Chr15 158979341 158980725 -
Ahy Ahy19g3594 Chr19 158537764 158544333 -
Aip Aip05g03936 Chr05 147587780 147589045 -
Aip Aip09g04053 Chr09 146786483 146793745 -
Apr Apr6g0610 Chr6 8782662 8784398 +
Bva Bva03g02482 Chr03 20976956 20978093 -
Cca Cca02g02200 Chr02 42503627 42504770 +
Cca Cca08g00755 Chr08 14798889 14800675 -
Dod Dod02g2957 Chr02 62651819 62653124 +
Dod Dod06g0856 Chr06 10669707 10673348 -
Gma Gma10g02178 Chr10 49355251 49356029 +
Gso Gso10g2047 Chr10 47473734 47474512 +
Lal Lal1g0851 Chr1 5933873 5935441 -
Lal Lal2g0968 Chr2 6507881 6508543 -
Lal Lal24g0062 Chr24 378836 380779 -
Lal Lal13g0065 Chr13 392828 396379 -
Lan Lan13g0827 Chr13 9112179 9113531 -
Lan Lan13g0827 Chr13 9112179 9113531 -
Lan Lan13g0827 Chr13 9112179 9113531 -
Lan Lan13g0827 Chr13 9112179 9113531 -
Lapu Lapu7g01980 Chr7 36054828 36056583 +
Lasa Lasa6g04016 Chr6 611836126 611837154 +
Lja Lja2g2706 Chr2 39291888 39293325 -
Lja Lja5g0682 Chr5 6127815 6128948 -
Mal Mal1g2119 Chr1 27713489 27717446 -
Mepo Mepo4g04186 Chr4 51775445 51776676 +
Mesa Mesa1g04566 Chr1 71583628 71584397 +
Mtr Mtr1g3686 Chr1 48541897 48546017 +
Phco Phco6g02406 Chr6 45448502 45449336 +
Pste Pste4g02772 Chr4 19543742 19544968 +
Pte Pte16g00336 Chr16 4414056 4415210 -
Pumo Pumo3g01052 Chr3 16136343 16138076 -
Pvu Pvu7g0793 Chr7 7209285 7210535 -
Rops Rops6g02659 Chr6 47868960 47870289 +
Seca Seca10g03757 Chr10 74993050 74994542 +
Spst Spst10g00907 Chr10 9877042 9880409 +
Ssu Ssu7g0847 Chr7 17091023 17091797 -
Ssu Ssu9g0005 Chr9 2078130 2079076 -
Sto Sto10g2302 Chr10 33170836 33171501 +
Tpr Tpr1g0818 Chr1 6835976 6839445 -
Trre Trre1g05317 Chr1 59053943 59054738 +
Tsu Tsu01g04353 Chr01 51454226 51457616 +
Vian Vian3g00682 Chr3 6959168 6960088 -
Vifa Vifa3g02842 Chr3 797641627 797642644 +
Vimu Vimu3g02977 Chr3 43836161 43836886 +
Viun Viun7g03170 Chr7 34276733 34278115 +
Vivi Vivi1g04471 Chr1 95269768 95271679 -
Vra Vra8g2182 Chr8 40193958 40195432 +
Vra Vra1g1710 Chr1 31881678 31883076 +
Vvi Vvi16g1047 Chr16 18826205 18829719 +
Bva Bva06g02949 Chr06 18361938 18362290 +
Psa Psa6g0908 Chr6 34165701 34168958 -
Sto Sto9g2785 Chr9 29560172 29561749 +
Vvi Vvi16g1048 Chr16 18833877 18834365 +