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
Vvi16g0989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal8g2900 . . . . . . . Mtr6g1297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr2g4284 . . . Tsu06g02975 . . . . . . . . . . . .
Vvi16g0991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0992 . . . . Adu05g03434 . Aed1g2309 Aed7g0643 Aev05g2872 Aev09g2191 Ahy15g3594 Ahy19g3584 Aip05g03912 Aip09g04042 . . . . . Apr6g0645 Arst5g04406 . Bach1g01113 . . . Bva03g01312 Bva04g01189 . . Cca02g02212 Cca08g00725 . . Dod02g2984 Dod06g0837 . . . . Gma20g01527 . . . Gso20g1309 . . . . Lal2g0946 Lal9g0828 . . Lal13g0057 . . . . . . . . . . . . . . . . . . Lja2g2674 Lja5g0669 Mal1g2103 . . . . . . . Mtr1g3701 Mtr6g1292 . . . . . . Psa6g4471 . Pste9g01120 . . . . . . . Pvu4g1136 . . . Seca10g03849 . Spst4g03259 . Ssu7g0829 . . . Tpr1g0796 Tpr2g4283 . . Tsu01g04370 Tsu06g02974 Vian8g01003 . Vifa1g04413 . Vimu8g02230 . Viun4g02060 . Vivi2g05368 . Vra8g2197 Vra1g1783
Vvi16g0993 . . . . . . . Aed7g0644 Aev05g2870 . Ahy15g3596 . Aip05g03913 . . . . . . Apr6g0644 . . . . . . Bva03g01311 . . . . Cca08g00726 . . Dod02g2982 . . . . . Gma16g00291 . . . Gso16g0263 . . . . . . . . . . . . . . . . . . Lasa6g04033 . . . . . . . . Lja2g2675 . Mal1g2104 . . Mepo4g04200 . Mesa1g04585 . . Mtr1g3700 Mtr6g1291 . Phac7g01145 . Phco6g02435 . . . . . Pste4g02832 . . . . . . . Pvu7g0766 . Rops6g02679 . Seca10g03850 . . . . . . Tpr1g0800 Tpr2g4169 . . . Tsu06g02973 . . . Vifa3g02864 . . . Viun7g03190 . Vivi1g04452 . Vra1g1782
Vvi16g0994 . . . . Adu05g03435 . . Aed7g0645 Aev05g2868 . Ahy15g3597 . Aip05g03914 . . . . . . Apr6g0643 Arst5g04410 . . . . . . Bva04g01191 . . . Cca08g00728 . . Dod02g2980 . . . . . Gma16g01535 . . . Gso16g1459 . . . . Lal2g0949 . . . . . . . . . . . . . . . . . . . . . . Lja2g2676 . . Mal8g2902 . . . . . . . Mtr6g1301 . . Phco5g00784 . . . . . Pste9g01119 . . . . . Pumo6g02524 . Pvu4g1134 . Rops5g01065 . Seca10g03831 . Spst4g03260 . . . . . . Tpr2g4289 Trre11g01236 . . Tsu06g02983 Vian8g01000 . Vifa1g04402 . Vimu8g02233 . Viun4g02044 . Vivi2g05371 . . .
Vvi16g0995 . . . . . . . Aed7g0648 Aev05g2864 . Ahy15g3600 Ahy19g3585 Aip05g03917 Aip09g04043 . . . . . Apr6g0642 . . . . . . Bva03g01309 . . . . Cca08g00731 . . . . . . . . Gma16g01533 . . . Gso16g1456 . . . . . Lal9g0830 . . . . . . . . . Lapu4g00694 . . . . . . . . . . . Lja2g2688 . . Mal8g2904 . . . . . . . Mtr6g1303 . . . . . . . . Pste9g01117 . . . . . Pumo6g02520 . Pvu4g1133 . Rops5g01064 . Seca10g03830 . Spst4g03261 . . . Sto10g2329 . . Tpr2g4290 Trre11g01237 . . Tsu06g02984 . . Vifa1g04401 . Vimu8g02234 . Viun4g02041 . Vivi2g05372 . . .
Vvi16g0996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Gma Gma16g00291 Chr16 3085917 3088477 -
Vvi Vvi16g0989 Chr16 18105390 18107713 +
Vvi Vvi16g0990 Chr16 18108464 18109397 +
Mal Mal8g2900 Chr8 77455650 77456489 -
Mtr Mtr6g1297 Chr6 19437040 19438545 +
Tpr Tpr2g4284 Chr2 46200842 46201711 +
Tsu Tsu06g02975 Chr06 39098327 39099378 -
Vvi Vvi16g0991 Chr16 18109594 18119836 +
Vvi Vvi16g0992 Chr16 18120458 18125792 +
Adu Adu05g03434 Chr05 106782866 106784019 +
Aed Aed1g2309 Chr1 19151591 19153055 +
Aed Aed7g0643 Chr7 4753169 4755008 +
Aev Aev05g2872 Chr05 29611900 29613052 -
Aev Aev09g2191 Chr09 24726179 24727036 -
Ahy Ahy15g3594 Chr15 158692601 158693945 +
Ahy Ahy19g3584 Chr19 158476023 158476836 +
Aip Aip05g03912 Chr05 147303138 147304808 +
Aip Aip09g04042 Chr09 146723935 146724612 +
Apr Apr6g0645 Chr6 9425521 9426584 -
Arst Arst5g04406 Chr5 105443788 105444822 +
Bach Bach1g01113 Chr1 24201391 24202140 -
Bva Bva03g01312 Chr03 12745472 12746636 -
Bva Bva04g01189 Chr04 8113900 8114744 +
Cca Cca02g02212 Chr02 42641076 42642065 -
Cca Cca08g00725 Chr08 13689608 13690504 +
Dod Dod02g2984 Chr02 63433605 63435029 -
Dod Dod06g0837 Chr06 10440896 10441733 +
Gma Gma20g01527 Chr20 42298846 42299774 +
Gso Gso20g1309 Chr20 43114656 43115640 +
Lal Lal2g0946 Chr2 6349230 6350790 +
Lal Lal9g0828 Chr9 6028486 6029917 +
Lal Lal13g0057 Chr13 360632 361808 +
Lja Lja2g2674 Chr2 37826320 37827649 +
Lja Lja5g0669 Chr5 6032042 6033234 +
Mal Mal1g2103 Chr1 27546164 27565410 +
Mtr Mtr1g3701 Chr1 48675494 48676665 -
Mtr Mtr6g1292 Chr6 19330500 19331605 -
Psa Psa6g4471 Chr6 391769425 391771024 -
Pste Pste9g01120 Chr9 8403166 8412091 -
Pvu Pvu4g1136 Chr4 34866518 34867929 -
Seca Seca10g03849 Chr10 80315490 80316296 -
Spst Spst4g03259 Chr4 72311133 72311984 +
Ssu Ssu7g0829 Chr7 16636705 16640716 +
Tpr Tpr1g0796 Chr1 6714083 6715584 +
Tpr Tpr2g4283 Chr2 46195390 46196361 -
Tsu Tsu01g04370 Chr01 51561119 51562512 -
Tsu Tsu06g02974 Chr06 39096174 39097221 -
Vian Vian8g01003 Chr8 26621274 26622112 -
Vifa Vifa1g04413 Chr1 686821575 686822063 -
Vimu Vimu8g02230 Chr8 29059983 29061187 +
Viun Viun4g02060 Chr4 36276732 36279465 -
Vivi Vivi2g05368 Chr2 178523843 178524602 +
Vra Vra8g2197 Chr8 40335901 40337070 -
Vra Vra1g1783 Chr1 33909185 33910237 +
Vvi Vvi16g0993 Chr16 18132576 18133672 +
Aed Aed7g0644 Chr7 4756746 4757996 +
Aev Aev05g2870 Chr05 29598842 29600812 -
Ahy Ahy15g3596 Chr15 158709141 158710322 +
Aip Aip05g03913 Chr05 147322065 147323295 +
Apr Apr6g0644 Chr6 9418733 9420056 -
Bva Bva03g01311 Chr03 12742012 12742984 -
Cca Cca08g00726 Chr08 13726069 13727478 +
Dod Dod02g2982 Chr02 63414168 63415773 -
Gma Gma16g00291 Chr16 3085917 3088477 -
Gso Gso16g0263 Chr16 3014976 3017410 -
Lasa Lasa6g04033 Chr6 613038001 613038625 -
Lja Lja2g2675 Chr2 37880151 37881613 +
Mal Mal1g2104 Chr1 27569809 27570822 +
Mepo Mepo4g04200 Chr4 51870963 51872049 -
Mesa Mesa1g04585 Chr1 71773213 71774772 -
Mtr Mtr1g3700 Chr1 48653510 48654905 -
Mtr Mtr6g1291 Chr6 19311983 19312912 -
Phac Phac7g01145 Chr7 7179278 7180550 +
Phco Phco6g02435 Chr6 45780629 45786719 -
Pste Pste4g02832 Chr4 19926124 19930767 -
Pvu Pvu7g0766 Chr7 6859189 6860509 +
Rops Rops6g02679 Chr6 48185852 48187392 -
Seca Seca10g03850 Chr10 80347090 80347733 -
Tpr Tpr1g0800 Chr1 6724843 6725593 +
Tpr Tpr2g4169 Chr2 44499739 44500792 +
Tsu Tsu06g02973 Chr06 39092890 39093728 -
Vifa Vifa3g02864 Chr3 805305816 805306317 +
Viun Viun7g03190 Chr7 34436985 34437807 -
Vivi Vivi1g04452 Chr1 94831660 94832688 +
Vra Vra1g1782 Chr1 33905321 33906097 +
Vvi Vvi16g0994 Chr16 18138996 18139532 -
Adu Adu05g03435 Chr05 106789436 106790403 -
Aed Aed7g0645 Chr7 4763033 4764297 -
Aev Aev05g2868 Chr05 29590347 29590892 +
Ahy Ahy15g3597 Chr15 158716350 158717185 -
Aip Aip05g03914 Chr05 147329129 147329945 -
Apr Apr6g0643 Chr6 9405695 9406466 +
Arst Arst5g04410 Chr5 105465205 105466088 -
Bva Bva04g01191 Chr04 8127296 8128033 -
Cca Cca08g00728 Chr08 13783060 13783800 -
Dod Dod02g2980 Chr02 63376201 63377168 +
Gma Gma16g01535 Chr16 35680419 35681879 +
Gso Gso16g1459 Chr16 34813425 34814668 +
Lal Lal2g0949 Chr2 6370331 6370882 -
Lja Lja2g2676 Chr2 37910072 37914684 -
Mal Mal8g2902 Chr8 77484695 77485249 -
Mtr Mtr6g1301 Chr6 19521333 19522175 -
Phco Phco5g00784 Chr5 9304704 9305234 -
Pste Pste9g01119 Chr9 8378990 8379529 +
Pumo Pumo6g02524 Chr6 58856315 58857499 +
Pvu Pvu4g1134 Chr4 34757507 34758639 +
Rops Rops5g01065 Chr5 21698361 21699139 +
Seca Seca10g03831 Chr10 79742431 79742979 +
Spst Spst4g03260 Chr4 72321539 72323365 -
Tpr Tpr2g4289 Chr2 46289863 46290680 -
Trre Trre11g01236 Chr11 12025193 12025750 -
Tsu Tsu06g02983 Chr06 39182432 39183862 -
Vian Vian8g01000 Chr8 26553123 26553731 +
Vifa Vifa1g04402 Chr1 684534304 684534840 +
Vimu Vimu8g02233 Chr8 29104299 29104865 -
Viun Viun4g02044 Chr4 36182501 36183317 +
Vivi Vivi2g05371 Chr2 178608656 178609424 -
Vvi Vvi16g0995 Chr16 18150126 18152952 -
Aed Aed7g0648 Chr7 4771692 4773107 -
Aev Aev05g2864 Chr05 29574739 29579191 -
Ahy Ahy15g3600 Chr15 158728272 158732315 +
Ahy Ahy19g3585 Chr19 158478952 158482478 -
Aip Aip05g03917 Chr05 147341343 147344923 +
Aip Aip09g04043 Chr09 146726959 146729627 -
Apr Apr6g0642 Chr6 9396680 9404324 +
Bva Bva03g01309 Chr03 12735009 12738162 +
Cca Cca08g00731 Chr08 13809955 13814718 +
Gma Gma16g01533 Chr16 35664725 35669018 -
Gso Gso16g1456 Chr16 34797583 34802122 -
Lal Lal9g0830 Chr9 6042564 6046211 +
Lapu Lapu4g00694 Chr4 14729040 14734064 -
Lja Lja2g2688 Chr2 38183366 38187580 -
Mal Mal8g2904 Chr8 77492832 77497365 -
Mtr Mtr6g1303 Chr6 19543920 19548673 -
Pste Pste9g01117 Chr9 8357486 8359717 -
Pumo Pumo6g02520 Chr6 58790740 58797490 +
Pvu Pvu4g1133 Chr4 34753790 34757273 +
Rops Rops5g01064 Chr5 21692478 21696762 +
Seca Seca10g03830 Chr10 79721962 79726043 +
Spst Spst4g03261 Chr4 72323453 72326025 -
Sto Sto10g2329 Chr10 33566771 33570923 +
Tpr Tpr2g4290 Chr2 46291403 46300889 -
Trre Trre11g01237 Chr11 12027050 12034646 -
Tsu Tsu06g02984 Chr06 39184881 39191846 -
Vifa Vifa1g04401 Chr1 684526978 684533914 +
Vimu Vimu8g02234 Chr8 29105379 29108843 -
Viun Viun4g02041 Chr4 36168767 36172074 -
Vivi Vivi2g05372 Chr2 178610476 178613761 -
Vvi Vvi16g0996 Chr16 18165899 18166705 -
Vvi Vvi16g0997 Chr16 18178277 18179083 -
Vvi Vvi16g0998 Chr16 18215401 18216904 +