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
Vvi4g1394 . Acco11g2469 . Accr9g00035 . Adu05g00327 Aed11g1119 . Aev05g0330 . Ahy15g0306 . Aip05g00298 . . Alju09g2471 . . . Apr7g0273 . Arst5g00410 . Bach4g00818 . Bisa11g1915 Bva08g00957 . . . Cca06g01175 . . Dere09g1187 Dod02g0362 . . Enph13g0778 . Glsi05g1226 Gma11g00791 Gma01g01621 . . . . . . . . . . . . . . . . . . . Lapu2g01021 . Lasa2g03538 . . . . Lele49g0018 Lele50g0021 Lele51g0020 Lele52g0022 Lja2g0638 . Mal6g0895 . . Mepo5g01106 . Mesa17g01164 . Mibi12g2153 Mtr5g0982 . . Phac2g01841 . Phco4g00759 . Prci10g0037 Psa2g3364 . . Pste1g03369 . . . Pte12g00560 . Pumo8g01644 . Pvu2g1208 . Rops1g01446 . Seca10g01105 . Spst2g01005 Ssu2g2155 . Sto6g4029 . Tpr2g1211 . . Trre9g01408 . . . Vian10g00892 . Vifa1g06333 . Vimu7g03192 . Viun2g01722 . Vivi2g02762 Vra11g0865 .
Vvi4g1395 . . . . . . . . . . . Ahy20g1954 . Aip10g02293 . . . Amo20g2475 Apr3g0446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal17g0705 . . . . . . . . . . . . . . . . . . . . . Lja1g4552 . Mal2g1563 . . . . . . . Mtr3g3306 . . . Phco8g00299 . . . . . . . . . . . . . Pvu3g2806 . . . . . Spst3g03682 . . . . Sto4g0329 Tpr3g3103 . . . Tsu07g01366 . . . . . Vimu11g00916 . . . . . . .
Vvi4g1396 . . . . Adu10g01720 . Aed5g2090 . . . Ahy13g3107 . Aip03g03523 Aip10g02294 . . . Amo20g2478 Apr1g0491 . Arst3g04063 . . . . . . . . . Cca09g02225 . . . . Dod09g1773 . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g01165 . Lasa5g03281 . . . . . . . . . Lja1g4551 . Mal2g1562 . Mepo3g06785 . Mesa9g04302 . . . Mtr3g3307 . . . Phco7g01679 . . . Psa5g1508 . . . . . . . Pumo10g01623 . Pvu9g1516 . . . Seca4g02020 . Spst9g01690 . Ssu5g2821 . Sto3g3150 . Tpr3g3105 . Trre5g04240 . Tsu07g01365 . Vian4g01112 . . . Vimu10g01807 . . . Vivi3g02513 . . .
Vvi4g1397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto4g0328 . . . . . . . . . . . . . . . . . .
Vvi4g1398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1399 . . . . . Adu03g03096 Aed5g2091 . Aev03g2878 . Ahy13g3106 . Aip03g03522 . . . . . . . . Arst3g04062 . . . . . . . . Cca09g02226 . . . Dod04g2499 . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g03402 . Lasa7g04448 . . . . . . . . . Lja4g0635 . Mal7g4693 . Mepo2g04374 . . . . . Mtr8g3239 . Phac2g04048 . Phco4g03044 . . . . . Pste3g01671 . . Pte2g02615 . . Pumo6g00711 . Pvu2g2762 . . . Seca12g06235 . Spst3g01352 Ssu5g2822 . . . . Tpr3g0861 . Trre7g05148 . Tsu02g00700 . Vian1g03629 . . . Vimu11g04135 . Viun3g00896 . Vivi5g04383 . .
Vvi4g1400 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1394 Chr4 20870430 20881039 -
Acco Acco11g2469 Chr11 37756037 37765439 -
Accr Accr9g00035 Chr9 391907 401371 +
Adu Adu05g00327 Chr05 3477073 3485035 +
Aed Aed11g1119 Chr11 16751590 16760928 +
Aev Aev05g0330 Chr05 2380606 2388934 +
Ahy Ahy15g0306 Chr15 3591979 3600147 +
Aip Aip05g00298 Chr05 3197814 3205740 +
Alju Alju09g2471 Chr09 47577365 47586826 -
Apr Apr7g0273 Chr7 8075913 8085076 -
Arst Arst5g00410 Chr5 3497439 3504412 +
Bach Bach4g00818 Chr4 5434305 5444554 -
Bisa Bisa11g1915 Chr11 41389692 41399731 -
Bva Bva08g00957 Chr08 4863255 4868694 -
Cca Cca06g01175 Chr06 26136538 26147522 +
Dere Dere09g1187 Chr09 15629167 15641943 -
Dod Dod02g0362 Chr02 4908995 4918212 +
Enph Enph13g0778 Chr13 14127784 14145426 +
Glsi Glsi05g1226 Chr05 61775351 61784739 +
Gma Gma11g00791 Chr11 6588674 6597923 -
Gma Gma01g01621 Chr01 51897915 51908296 +
Lapu Lapu2g01021 Chr2 9622795 9634733 +
Lasa Lasa2g03538 Chr2 540435494 540445876 -
Lele Lele49g0018 Chr49 116378 124511 +
Lele Lele50g0021 Chr50 167248 169542 +
Lele Lele51g0020 Chr51 124573 135510 +
Lele Lele52g0022 Chr52 150438 157066 +
Lja Lja2g0638 Chr2 5722087 5731032 -
Mal Mal6g0895 Chr6 13410841 13420917 +
Mepo Mepo5g01106 Chr5 11089716 11099668 -
Mesa Mesa17g01164 Chr17 14944050 14953756 -
Mibi Mibi12g2153 Chr12 37996812 38006810 -
Mtr Mtr5g0982 Chr5 9771960 9781887 -
Phac Phac2g01841 Chr2 20568068 20578260 -
Phco Phco4g00759 Chr4 5850622 5860305 +
Prci Prci10g0037 Chr10 294714 315412 +
Psa Psa2g3364 Chr2 378479937 378491024 +
Pste Pste1g03369 Chr1 15525920 15531856 -
Pte Pte12g00560 Chr12 5014228 5017412 -
Pumo Pumo8g01644 Chr8 52079851 52088788 +
Pvu Pvu2g1208 Chr2 23712377 23722385 -
Rops Rops1g01446 Chr1 31954975 31966417 +
Seca Seca10g01105 Chr10 10639470 10642214 -
Spst Spst2g01005 Chr2 8658164 8658691 -
Ssu Ssu2g2155 Chr2 77492597 77507958 +
Sto Sto6g4029 Chr6 44027556 44037383 -
Tpr Tpr2g1211 Chr2 14186612 14196398 -
Trre Trre9g01408 Chr9 12016996 12026870 -
Vian Vian10g00892 Chr10 9000772 9010695 -
Vifa Vifa1g06333 Chr1 987326602 987342586 +
Vimu Vimu7g03192 Chr7 27001441 27011251 -
Viun Viun2g01722 Chr2 26704642 26713191 +
Vivi Vivi2g02762 Chr2 122833427 122844672 +
Vra Vra11g0865 Chr11 7297322 7307587 -
Vvi Vvi4g1395 Chr4 20883072 20883491 +
Ahy Ahy20g1954 Chr20 109765724 109766407 +
Aip Aip10g02293 Chr10 102990922 102991341 +
Amo Amo20g2475 Chr20 115943134 115943553 +
Apr Apr3g0446 Chr3 9020556 9020978 -
Lal Lal17g0705 Chr17 4991038 4991445 +
Lja Lja1g4552 Chr1 59456014 59456430 -
Mal Mal2g1563 Chr2 18797660 18798067 -
Mtr Mtr3g3306 Chr3 47021136 47021537 +
Phco Phco8g00299 Chr8 2740083 2740496 +
Pvu Pvu3g2806 Chr3 49867624 49868040 -
Spst Spst3g03682 Chr3 86877595 86878005 +
Sto Sto4g0329 Chr4 2572810 2573184 -
Tpr Tpr3g3103 Chr3 34162905 34163306 +
Tsu Tsu07g01366 Chr07 12028851 12029249 -
Vimu Vimu11g00916 Chr11 9479382 9479783 -
Vvi Vvi4g1396 Chr4 20885557 20886362 -
Adu Adu10g01720 Chr10 79300592 79302206 -
Aed Aed5g2090 Chr5 23300206 23301407 -
Ahy Ahy13g3107 Chr13 125069939 125070970 +
Aip Aip03g03523 Chr03 115067296 115068124 +
Aip Aip10g02294 Chr10 103033126 103034135 -
Amo Amo20g2478 Chr20 116006598 116008086 -
Apr Apr1g0491 Chr1 6006603 6007598 +
Arst Arst3g04063 Chr3 114159745 114160617 +
Cca Cca09g02225 Chr09 47453686 47454976 -
Dod Dod09g1773 Chr09 39387308 39388987 -
Lapu Lapu9g01165 Chr9 25191802 25192783 +
Lasa Lasa5g03281 Chr5 550590633 550591355 -
Lja Lja1g4551 Chr1 59416206 59417527 +
Mal Mal2g1562 Chr2 18793670 18794457 +
Mepo Mepo3g06785 Chr3 81599725 81600849 -
Mesa Mesa9g04302 Chr9 76057289 76058227 -
Mtr Mtr3g3307 Chr3 47022732 47023933 -
Phco Phco7g01679 Chr7 16569434 16570395 -
Psa Psa5g1508 Chr5 115818688 115819815 +
Pumo Pumo10g01623 Chr10 21322442 21327055 -
Pvu Pvu9g1516 Chr9 21464094 21465806 -
Seca Seca4g02020 Chr4 34496690 34497393 +
Spst Spst9g01690 Chr9 17279724 17280667 -
Ssu Ssu5g2821 Chr5 74266953 74267972 -
Sto Sto3g3150 Chr3 36368323 36369925 -
Tpr Tpr3g3105 Chr3 34168380 34169491 -
Trre Trre5g04240 Chr5 44253979 44254984 -
Tsu Tsu07g01365 Chr07 12027158 12027949 +
Vian Vian4g01112 Chr4 18151076 18152038 -
Vimu Vimu10g01807 Chr10 25533597 25534521 +
Vivi Vivi3g02513 Chr3 42113037 42114019 +
Vvi Vvi4g1397 Chr4 20891604 20894151 -
Sto Sto4g0328 Chr4 2568399 2571165 +
Vvi Vvi4g1398 Chr4 20894725 20897159 -
Vvi Vvi4g1399 Chr4 20897782 20900213 -
Adu Adu03g03096 Chr03 115440638 115444000 +
Aed Aed5g2091 Chr5 23302901 23305572 -
Aev Aev03g2878 Chr03 28206975 28210034 -
Ahy Ahy13g3106 Chr13 125065530 125068909 +
Aip Aip03g03522 Chr03 115062910 115066445 +
Arst Arst3g04062 Chr3 114155251 114158420 +
Cca Cca09g02226 Chr09 47457847 47461469 -
Dod Dod04g2499 Chr04 48801005 48804686 -
Lapu Lapu3g03402 Chr3 57266697 57270502 -
Lasa Lasa7g04448 Chr7 661792798 661794879 -
Lja Lja4g0635 Chr4 5255566 5259525 +
Mal Mal7g4693 Chr7 115096954 115100703 -
Mepo Mepo2g04374 Chr2 52321656 52325167 -
Mtr Mtr8g3239 Chr8 42909290 42913106 -
Phac Phac2g04048 Chr2 39764452 39767988 -
Phco Phco4g03044 Chr4 51464715 51467890 -
Pste Pste3g01671 Chr3 10550889 10554251 +
Pte Pte2g02615 Chr2 45182768 45186226 +
Pumo Pumo6g00711 Chr6 8925201 8928798 +
Pvu Pvu2g2762 Chr2 43368131 43371549 -
Seca Seca12g06235 Chr12 154235244 154246751 -
Spst Spst3g01352 Chr3 16977190 16980211 +
Ssu Ssu5g2822 Chr5 74273190 74276363 -
Tpr Tpr3g0861 Chr3 8087615 8091313 +
Trre Trre7g05148 Chr7 58108892 58111798 -
Tsu Tsu02g00700 Chr02 5892311 5895334 +
Vian Vian1g03629 Chr1 59020476 59023577 -
Vimu Vimu11g04135 Chr11 62996705 62999836 -
Viun Viun3g00896 Chr3 5525523 5528843 +
Vivi Vivi5g04383 Chr5 141449969 141453008 -
Vvi Vvi4g1400 Chr4 20906331 20914980 -
Vvi Vvi4g1401 Chr4 20929977 20930219 -
Vvi Vvi4g1402 Chr4 20937407 20940046 +
Vvi Vvi4g1403 Chr4 20951304 20953335 -
Lal Lal17g0705 Chr17 4991038 4991445 +
Lja Lja1g4552 Chr1 59456014 59456430 -
Sto Sto4g0329 Chr4 2572810 2573184 -
Adu Adu10g01720 Chr10 79300592 79302206 -
Apr Apr1g0491 Chr1 6006603 6007598 +
Arst Arst3g04063 Chr3 114159745 114160617 +
Lapu Lapu9g01165 Chr9 25191802 25192783 +
Lasa Lasa5g03281 Chr5 550590633 550591355 -
Lja Lja1g4551 Chr1 59416206 59417527 +
Mepo Mepo3g06785 Chr3 81599725 81600849 -
Mesa Mesa9g04302 Chr9 76057289 76058227 -
Phco Phco7g01679 Chr7 16569434 16570395 -
Pumo Pumo10g01623 Chr10 21322442 21327055 -
Pvu Pvu9g1516 Chr9 21464094 21465806 -
Seca Seca4g02020 Chr4 34496690 34497393 +
Spst Spst9g01690 Chr9 17279724 17280667 -
Sto Sto3g3150 Chr3 36368323 36369925 -
Trre Trre5g04240 Chr5 44253979 44254984 -
Vian Vian4g01112 Chr4 18151076 18152038 -
Vimu Vimu10g01807 Chr10 25533597 25534521 +
Vivi Vivi3g02513 Chr3 42113037 42114019 +
Ahy Ahy13g3107 Chr13 125069939 125070970 +
Aip Aip03g03523 Chr03 115067296 115068124 +
Mal Mal2g1562 Chr2 18793670 18794457 +
Mtr Mtr3g3307 Chr3 47022732 47023933 -
Tpr Tpr3g3105 Chr3 34168380 34169491 -
Tsu Tsu07g01365 Chr07 12027158 12027949 +