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
Vvi4g0514 . . . . Adu08g02518 . . . . . . . . . . . . . . . Arst8g03470 . . . . . . . Car05g02967 . . . . . . . . . . . . . . Gma06g00616 . . . . . . . . . . . . . . . . Lapu9g01882 . Lasa5g04075 . . . . . . . . . . . Mal2g0868 . Mepo3g07444 . Mesa9g05053 . . . Mtr3g3924 . Phac9g00402 . Phco7g00768 . . . . . Pste2g01772 . . . . . Pumo10g00067 . Pvu9g0964 . . . Seca4g00964 . Spst9g00799 . . . . . Tpr7g0628 . . . Tsu07g00642 . Vian4g01961 . Vifa2g04028 . Vimu10g02946 . Viun9g03060 . Vivi3g01324 . . .
Vvi4g0515 . . . . . . Aed4g1805 . . Aev08g2620 . Ahy18g2676 . Aip08g03059 . . . . . . . . . . . . Bva10g00364 . . . Cca03g01559 . . . . Dod09g0923 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3869 . . . . . . . . . . . . . . . . . Psa5g0668 . . . . . . . . . . . . . . . . . Ssu1g3447 . Sto5g0844 . . . . . . . . . . . . . . . . . Vra5g1195 .
Vvi4g0516 . . . . . Adu06g02808 . Aed6g1144 . . Ahy16g3105 . Aip06g03335 . . . . . . Apr9g0169 . Arst6g03643 . . . . . Bva06g02405 . Car04g03174 . Cca05g00534 . . Dod08g1670 . . . . . . Gma17g01994 . . . . . . . . . Lal25g1067 . . . . . . . . . Lapu8g00611 . Lasa6g00608 . . . . . . . . . Lja5g2836 . Mal1g5512 . Mepo4g00643 . Mesa1g00675 . . . Mtr1g0214 . Phac1g00700 . Phco2g00601 . . . Psa6g0679 . Pste8g01115 . . Pte3g01120 . . Pumo9g00643 . Pvu1g0531 . Rops9g01895 . . . . . Ssu5g0584 . Sto9g3298 . Tpr1g3387 . Trre1g00709 . Tsu01g00701 . Vian7g00414 . . . Vimu1g02597 . Viun8g00789 . Vivi4g05080 . Vra6g1561
Vvi4g0517 . . . . . . . . . Aev08g0547 Ahy16g3106 Ahy20g2086 Aip06g03336 Aip10g02455 . . . Amo20g2701 . Apr9g0170 . . . . . . . . . . . . . . Dod08g1671 Dod09g1865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g2837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3299 . . . . . . . . . . . . . . . . . .
Vvi4g0518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0520 Acco10g2003 . Accr4g00782 . Adu08g02520 . . . . Aev08g2619 . Ahy18g2678 . Aip08g03062 Alju08g0795 . . . . . Arst8g03473 . Bach12g00507 . Bisa09g1206 . Bva10g00366 Bva06g02404 Car05g02966 . . . Dere04g0568 . . Dod09g0922 Enph1g1390 . Glsi08g1582 . . . Gma04g00628 Gma06g00615 . . . . Lal21g0342 . . . . . Lan3g1068 . . . . . Lapu9g01883 . Lasa5g04074 . Lele01g0631 . Lele03g0631 Lele04g0636 . . . . Lja1g3870 . Mal2g0870 . Mepo3g07443 . Mesa9g05052 . Mibi05g0717 . Mtr3g3923 . . . Phco7g00766 . Prci15g0998 . . . . . Pte3g01121 . . . . . Pvu9g0963 . . . . . Spst9g00797 . . . Sto5g0847 Sto9g3300 Tpr7g0629 . Trre5g05209 . Tsu07g00643 . . . . . Vimu10g02951 . . . Vivi3g01326 . . .
Vvi4g0521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0522 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0849 . . . . . . . . . . . . . . . . . . .
Vvi4g0523 . Acco11g0045 . Accr9g02154 . . . . . . . . . . . Alju09g0065 . . . . . . . . . . . . . . . . . . . . . Enph13g0712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lele49g1642 Lele50g1743 Lele51g1646 Lele52g1705 . . . . . . . . . Mibi12g0051 . . . . . Phco4g02135 . Prci10g3003 . . . Pste3g02490 . . . . . . . Pvu2g1892 . . . . . Spst3g01907 . . . . . . . . . . . . . . . Vimu11g01689 . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Adu Adu06g02808 Chr06 105303621 105310097 -
Arst Arst6g03643 Chr6 104498067 104504588 -
Lapu Lapu8g00611 Chr8 23730766 23749014 -
Lasa Lasa6g00608 Chr6 21349029 21357673 +
Mepo Mepo4g00643 Chr4 8730598 8739652 +
Mesa Mesa1g00675 Chr1 8718468 8727450 +
Phac Phac1g00700 Chr1 5549990 5563109 +
Phco Phco2g00601 Chr2 5859381 5880132 +
Pste Pste8g01115 Chr8 5804090 5819085 -
Pte Pte3g01120 Chr3 9561598 9567659 -
Pumo Pumo9g00643 Chr9 11881373 11893031 +
Pvu Pvu1g0531 Chr1 5875242 5890904 +
Rops Rops9g01895 Chr9 34563994 34586163 -
Trre Trre1g00709 Chr1 5336075 5343235 +
Vian Vian7g00414 Chr7 10935225 10950875 -
Vimu Vimu1g02597 Chr1 37494991 37512005 -
Viun Viun8g00789 Chr8 6934456 6953368 +
Vivi Vivi4g05080 Chr4 181757126 181768952 -
Vvi Vvi4g0514 Chr4 4758775 4759346 +
Adu Adu08g02518 Chr08 41123960 41124639 +
Arst Arst8g03470 Chr8 45496555 45497293 +
Car Car05g02967 Chr05 74618972 74621775 -
Gma Gma06g00616 Chr06 5580522 5581801 -
Lapu Lapu9g01882 Chr9 33609332 33609883 +
Lasa Lasa5g04075 Chr5 626102841 626103400 -
Mal Mal2g0868 Chr2 10054494 10055102 +
Mepo Mepo3g07444 Chr3 87827636 87828991 -
Mesa Mesa9g05053 Chr9 85065374 85066340 -
Mtr Mtr3g3924 Chr3 53034753 53035647 -
Phac Phac9g00402 Chr9 2572814 2573969 -
Phco Phco7g00768 Chr7 5965857 5966439 -
Pste Pste2g01772 Chr2 18154432 18155488 -
Pumo Pumo10g00067 Chr10 1300081 1304104 +
Pvu Pvu9g0964 Chr9 14487565 14488282 -
Seca Seca4g00964 Chr4 15549433 15550471 +
Spst Spst9g00799 Chr9 6894738 6895338 -
Tpr Tpr7g0628 Chr7 5555718 5556706 +
Tsu Tsu07g00642 Chr07 5079923 5080571 +
Vian Vian4g01961 Chr4 36234236 36249610 +
Vifa Vifa2g04028 Chr2 1181258753 1181259386 -
Vimu Vimu10g02946 Chr10 40457970 40458543 +
Viun Viun9g03060 Chr9 38264064 38265163 +
Vivi Vivi3g01324 Chr3 21635209 21636144 +
Vvi Vvi4g0515 Chr4 4760940 4761762 +
Aed Aed4g1805 Chr4 22282260 22282727 -
Aev Aev08g2620 Chr08 24664765 24667313 -
Ahy Ahy18g2676 Chr18 129817519 129818426 +
Aip Aip08g03059 Chr08 120287010 120287568 +
Bva Bva10g00364 Chr10 4183986 4184892 +
Cca Cca03g01559 Chr03 34315761 34316623 +
Dod Dod09g0923 Chr09 29064525 29065505 -
Lja Lja1g3869 Chr1 48777658 48778975 +
Psa Psa5g0668 Chr5 53406826 53407821 +
Ssu Ssu1g3447 Chr1 88538503 88539145 +
Sto Sto5g0844 Chr5 5669278 5670383 +
Vra Vra5g1195 Chr5 18339944 18340964 +
Vvi Vvi4g0516 Chr4 4762451 4774620 -
Adu Adu06g02808 Chr06 105303621 105310097 -
Aed Aed6g1144 Chr6 16132697 16135502 -
Ahy Ahy16g3105 Chr16 146894357 146901109 -
Aip Aip06g03335 Chr06 130018258 130024873 -
Apr Apr9g0169 Chr9 2212823 2220674 -
Arst Arst6g03643 Chr6 104498067 104504588 -
Bva Bva06g02405 Chr06 15447353 15452152 +
Car Car04g03174 Chr04 60016827 60025783 -
Cca Cca05g00534 Chr05 12064130 12071818 +
Dod Dod08g1670 Chr08 39658992 39669826 -
Gma Gma17g01994 Chr17 35758449 35768414 -
Lal Lal25g1067 Chr25 13940616 13948137 +
Lapu Lapu8g00611 Chr8 23730766 23749014 -
Lasa Lasa6g00608 Chr6 21349029 21357673 +
Lja Lja5g2836 Chr5 55866190 55876891 -
Mal Mal1g5512 Chr1 130147685 130156894 -
Mepo Mepo4g00643 Chr4 8730598 8739652 +
Mesa Mesa1g00675 Chr1 8718468 8727450 +
Mtr Mtr1g0214 Chr1 2475118 2485049 -
Phac Phac1g00700 Chr1 5549990 5563109 +
Phco Phco2g00601 Chr2 5859381 5880132 +
Psa Psa6g0679 Chr6 23023551 23049927 +
Pste Pste8g01115 Chr8 5804090 5819085 -
Pte Pte3g01120 Chr3 9561598 9567659 -
Pumo Pumo9g00643 Chr9 11881373 11893031 +
Pvu Pvu1g0531 Chr1 5875242 5890904 +
Rops Rops9g01895 Chr9 34563994 34586163 -
Ssu Ssu5g0584 Chr5 12939657 12963367 +
Sto Sto9g3298 Chr9 33044232 33050297 -
Tpr Tpr1g3387 Chr1 38233735 38242579 -
Trre Trre1g00709 Chr1 5336075 5343235 +
Tsu Tsu01g00701 Chr01 6144416 6157120 +
Vian Vian7g00414 Chr7 10935225 10950875 -
Vimu Vimu1g02597 Chr1 37494991 37512005 -
Viun Viun8g00789 Chr8 6934456 6953368 +
Vivi Vivi4g05080 Chr4 181757126 181768952 -
Vra Vra6g1561 Chr6 30911389 30925794 -
Vvi Vvi4g0517 Chr4 4774850 4776688 +
Aev Aev08g0547 Chr08 3085785 3091653 -
Ahy Ahy16g3106 Chr16 146901162 146904790 +
Ahy Ahy20g2086 Chr20 117707529 117713533 +
Aip Aip06g03336 Chr06 130025068 130026903 +
Aip Aip10g02455 Chr10 110360301 110366272 +
Amo Amo20g2701 Chr20 124758191 124764025 +
Apr Apr9g0170 Chr9 2221821 2223823 +
Dod Dod08g1671 Chr08 39674259 39677315 +
Dod Dod09g1865 Chr09 40292914 40298821 +
Lja Lja5g2837 Chr5 55878959 55883240 +
Sto Sto9g3299 Chr9 33050633 33052465 +
Vvi Vvi4g0518 Chr4 4778576 4779248 -
Vvi Vvi4g0519 Chr4 4780648 4780977 +
Vvi Vvi4g0520 Chr4 4787471 4788523 -
Acco Acco10g2003 Chr10 32632921 32633970 +
Accr Accr4g00782 Chr4 7462363 7463412 -
Adu Adu08g02520 Chr08 41152333 41154107 -
Aev Aev08g2619 Chr08 24656167 24656988 +
Ahy Ahy18g2678 Chr18 129879985 129881804 -
Aip Aip08g03062 Chr08 120347150 120348938 -
Alju Alju08g0795 Chr08 5972833 5973882 -
Arst Arst8g03473 Chr8 45524998 45526748 -
Bach Bach12g00507 Chr12 3444155 3445204 +
Bisa Bisa09g1206 Chr09 17381481 17382530 +
Bva Bva10g00366 Chr10 4188394 4189720 -
Bva Bva06g02404 Chr06 15442621 15444118 +
Car Car05g02966 Chr05 74609898 74611563 +
Dere Dere04g0568 Chr04 5658848 5659897 +
Dod Dod09g0922 Chr09 29035991 29037713 +
Enph Enph1g1390 Chr1 39430483 39430743 +
Glsi Glsi08g1582 Chr08 11353377 11356529 -
Gma Gma04g00628 Chr04 5749126 5750166 +
Gma Gma06g00615 Chr06 5566758 5568518 +
Lal Lal21g0342 Chr21 2305092 2306147 +
Lan Lan3g1068 Chr3 22984929 22986548 -
Lapu Lapu9g01883 Chr9 33617621 33618763 -
Lasa Lasa5g04074 Chr5 625987596 625988645 +
Lele Lele01g0631 Chr01 3697519 3698497 -
Lele Lele03g0631 Chr03 3713020 3713998 -
Lele Lele04g0636 Chr04 3839622 3840616 -
Lja Lja1g3870 Chr1 48782680 48784204 -
Mal Mal2g0870 Chr2 10060640 10061689 -
Mepo Mepo3g07443 Chr3 87810692 87812573 +
Mesa Mesa9g05052 Chr9 85057682 85058731 +
Mibi Mibi05g0717 Chr05 6787210 6788259 -
Mtr Mtr3g3923 Chr3 53028225 53029775 +
Phco Phco7g00766 Chr7 5956685 5957823 +
Prci Prci15g0998 Chr15 6229187 6230828 -
Pte Pte3g01121 Chr3 9569146 9571495 -
Pvu Pvu9g0963 Chr9 14474998 14477090 +
Spst Spst9g00797 Chr9 6885987 6887036 +
Sto Sto5g0847 Chr5 5674544 5675593 -
Sto Sto9g3300 Chr9 33053535 33054584 -
Tpr Tpr7g0629 Chr7 5561731 5563248 -
Trre Trre5g05209 Chr5 53212392 53213435 +
Tsu Tsu07g00643 Chr07 5084356 5086157 -
Vimu Vimu10g02951 Chr10 40483046 40484095 -
Vivi Vivi3g01326 Chr3 21657151 21658559 -
Vvi Vvi4g0521 Chr4 4793095 4796263 -
Vvi Vvi4g0522 Chr4 4797333 4800003 -
Bva Bva06g02403 Chr06 15437682 15439897 +
Sto Sto5g0849 Chr5 5682772 5685353 -
Vvi Vvi4g0523 Chr4 4801184 4802305 +
Acco Acco11g0045 Chr11 691380 691979 +
Accr Accr9g02154 Chr9 46305865 46307031 -
Alju Alju09g0065 Chr09 803435 807761 +
Enph Enph13g0712 Chr13 13370064 13371224 -
Lele Lele49g1642 Chr49 18525122 18526291 -
Lele Lele50g1743 Chr50 22173582 22174739 -
Lele Lele51g1646 Chr51 17469236 17470405 -
Lele Lele52g1705 Chr52 20599022 20600173 -
Mibi Mibi12g0051 Chr12 1054983 1055540 +
Phco Phco4g02135 Chr4 41844417 41845604 -
Prci Prci10g3003 Chr10 38574901 38576186 -
Pste Pste3g02490 Chr3 17709081 17710262 -
Pvu Pvu2g1892 Chr2 33700259 33701446 -
Spst Spst3g01907 Chr3 43005248 43006429 -
Vimu Vimu11g01689 Chr11 21700097 21701855 +
Aev Aev08g0547 Chr08 3085785 3091653 -
Ahy Ahy20g2086 Chr20 117707529 117713533 +
Aip Aip10g02455 Chr10 110360301 110366272 +
Amo Amo20g2701 Chr20 124758191 124764025 +
Dod Dod09g1865 Chr09 40292914 40298821 +
Acco Acco10g2003 Chr10 32632921 32633970 +
Accr Accr4g00782 Chr4 7462363 7463412 -
Adu Adu08g02520 Chr08 41152333 41154107 -
Alju Alju08g0795 Chr08 5972833 5973882 -
Arst Arst8g03473 Chr8 45524998 45526748 -
Bach Bach12g00507 Chr12 3444155 3445204 +
Bisa Bisa09g1206 Chr09 17381481 17382530 +
Dere Dere04g0568 Chr04 5658848 5659897 +
Enph Enph1g1390 Chr1 39430483 39430743 +
Glsi Glsi08g1582 Chr08 11353377 11356529 -
Lapu Lapu9g01883 Chr9 33617621 33618763 -
Lasa Lasa5g04074 Chr5 625987596 625988645 +
Lele Lele01g0631 Chr01 3697519 3698497 -
Lele Lele03g0631 Chr03 3713020 3713998 -
Lele Lele04g0636 Chr04 3839622 3840616 -
Mepo Mepo3g07443 Chr3 87810692 87812573 +
Mesa Mesa9g05052 Chr9 85057682 85058731 +
Mibi Mibi05g0717 Chr05 6787210 6788259 -
Phco Phco7g00766 Chr7 5956685 5957823 +
Prci Prci15g0998 Chr15 6229187 6230828 -
Pte Pte3g01121 Chr3 9569146 9571495 -
Pte Pte3g01121 Chr3 9569146 9571495 -
Pvu Pvu9g0963 Chr9 14474998 14477090 +
Spst Spst9g00797 Chr9 6885987 6887036 +
Trre Trre5g05209 Chr5 53212392 53213435 +
Vimu Vimu10g02951 Chr10 40483046 40484095 -
Vivi Vivi3g01326 Chr3 21657151 21658559 -