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
Vvi3g0413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0414 . . . . . . . . . . . . . . . . . . . . . Arst5g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03337 . . . . . . . . . . . . . . . . . . . . . . . Phco4g00941 . . . . . . . . . . . . . Pvu2g0340 . Rops1g01625 . Seca10g00906 . Spst2g00837 . . . . . . . . . . . Vian10g00721 . Vifa1g06772 . Vimu7g02978 . Viun2g01942 . . . .
Vvi3g0415 . . . . . . . . . . Ahy20g0016 . Aip10g00015 . . . . . . . . Arst5g01037 . Bach4g00657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03336 . . . . . . . . Lja3g0499 . . . . Mepo5g00914 . . . . Mtr4g2112 . . . . Phco4g00942 . . . . . Pste1g02832 . . Pte2g00288 . . Pumo8g01807 . Pvu2g0339 . Rops1g01626 . . . Spst2g00836 . . . . . . . Trre9g01070 Tsu02g02418 . . Vian10g00720 . Vifa1g06776 . Vimu7g02977 . Viun2g01944 . Vivi2g03012 . .
Vvi3g0416 . . . . . . . . . . Ahy13g0706 . Aip03g00747 . . . Amo13g0735 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu11g00759 . Lasa7g02077 . . . . . . . . . . . . . Mepo2g02329 . . . . . . . . . . . . . . . . . . . . . Pumo10g00709 . Pvu11g0458 . Rops3g00559 . Seca4g03500 . Spst2g02538 . . Sto2g0725 . . . . Trre7g02824 . . . Vian5g01499 . . . Vimu5g02345 . Viun11g02445 . . . .
Vvi3g0417 . . . . . Adu05g00832 . . . . . . . . . . . . . . . Arst5g01036 . Bach4g00656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g00692 . Lasa2g03335 . . . . . . . . Lja3g0500 . Mal7g2557 . . Mepo5g00913 . . . . Mtr4g2111 . . Phac2g02584 . Phco4g00944 . . . . . Pste1g02829 . . Pte2g00290 . . Pumo8g01808 . Pvu2g0338 . Rops1g01627 . . . Spst2g00835 . . . . Tpr3g2314 . . Trre9g01068 . . . Vian10g00719 . . . Vimu7g02976 . Viun2g01945 . Vivi2g03013 . .
Vvi3g0418 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0419 . Acco11g2304 . Accr9g00194 . Adu05g00831 . . . . . . . . . Alju09g2315 . . . . . Arst5g01035 . Bach4g00655 . Bisa11g1708 . . . . . . . Dere04g0161 . . . Enph13g0917 . Glsi08g1964 . . . . . . . . . . . . . . . . . . . . . Lapu2g00690 . Lasa2g03334 . . . . Lele49g0143 Lele50g0164 Lele51g0158 Lele52g0162 . . . . . Mepo5g00912 . . . Mibi12g1998 . . . Phac2g02583 . Phco4g00945 . Prci10g0265 . . . Pste1g02824 . . . . . . . Pvu2g0337 . Rops1g01628 . . . Spst2g00834 . . Sto2g0721 . . . . Trre9g01067 . . . Vian10g00718 . . . Vimu7g02974 . Viun2g01946 . Vivi2g03014 . .
Vvi3g0420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca04g00429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja3g0501 . Mal7g2556 . . . . . . . Mtr4g2110 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g2846 . . . Tpr3g2313 . . . Tsu02g02417 . . . . . . . . . . . Vra2g0406 .
Vvi3g0421 . . . Accr9g00197 . Adu05g00829 . . . . . . . . . Alju09g2310 . . . . . Arst5g01029 . Bach4g00651 . Bisa11g1703 . . . . . . . Dere09g0935 . . . Enph13g0922 . Glsi05g1431 . . . . . . . . . . . . . . . . . . . . . Lapu2g00687 . Lasa2g03330 . . . . Lele49g0146 Lele50g0166 Lele51g0160 Lele52g0165 . . . . . . . . . Mibi12g1994 . . . Phac2g02572 . Phco4g00952 . Prci10g0269 . . . . . . . . . . . Pvu2g0329 . . . . . Spst2g00830 . . . . . . . . . . . . . . . . . . . Vivi2g03019 . .
Vvi3g0422 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0413 Chr3 3408845 3410915 +
Vvi Vvi3g0414 Chr3 3417114 3417959 -
Arst Arst5g01038 Chr5 10200629 10203148 +
Lasa Lasa2g03337 Chr2 531120728 531121986 +
Phco Phco4g00941 Chr4 7464455 7465791 -
Pvu Pvu2g0340 Chr2 3348728 3353321 -
Rops Rops1g01625 Chr1 34591554 34593283 -
Seca Seca10g00906 Chr10 8649335 8652273 +
Spst Spst2g00837 Chr2 7068756 7070052 +
Vian Vian10g00721 Chr10 6983104 6984444 +
Vifa Vifa1g06772 Chr1 1045907038 1045908398 -
Vimu Vimu7g02978 Chr7 25097400 25098721 +
Viun Viun2g01942 Chr2 28065193 28066750 -
Vvi Vvi3g0415 Chr3 3421853 3425512 -
Ahy Ahy20g0016 Chr20 163180 168452 -
Aip Aip10g00015 Chr10 196097 202755 -
Arst Arst5g01037 Chr5 10197396 10198968 +
Bach Bach4g00657 Chr4 4378225 4380154 +
Lasa Lasa2g03336 Chr2 531120728 531129519 +
Lja Lja3g0499 Chr3 5028269 5030853 -
Mepo Mepo5g00914 Chr5 8915420 8916909 +
Mtr Mtr4g2112 Chr4 34645859 34648325 +
Phco Phco4g00942 Chr4 7472062 7473396 +
Pste Pste1g02832 Chr1 11939631 11942578 +
Pte Pte2g00288 Chr2 2271920 2273912 -
Pumo Pumo8g01807 Chr8 54275820 54280827 -
Pvu Pvu2g0339 Chr2 3347036 3347720 +
Rops Rops1g01626 Chr1 34600922 34620964 -
Spst Spst2g00836 Chr2 7056291 7057587 -
Trre Trre9g01070 Chr9 8535674 8537357 +
Tsu Tsu02g02418 Chr02 24671914 24674893 +
Vian Vian10g00720 Chr10 6975751 6977093 +
Vifa Vifa1g06776 Chr1 1046235904 1046237291 +
Vimu Vimu7g02977 Chr7 25075041 25076403 -
Viun Viun2g01944 Chr2 28073884 28075495 -
Vivi Vivi2g03012 Chr2 129114222 129115897 -
Vvi Vvi3g0416 Chr3 3430195 3433729 -
Ahy Ahy13g0706 Chr13 7340045 7342886 +
Aip Aip03g00747 Chr03 7158624 7161345 +
Amo Amo13g0735 Chr13 9048378 9050961 +
Lapu Lapu11g00759 Chr11 10521526 10523442 +
Lasa Lasa7g02077 Chr7 489513048 489514337 -
Mepo Mepo2g02329 Chr2 33053468 33058176 +
Pumo Pumo10g00709 Chr10 9095119 9097276 +
Pvu Pvu11g0458 Chr11 3832449 3836748 -
Rops Rops3g00559 Chr3 6991807 6994131 +
Seca Seca4g03500 Chr4 60838241 60843089 -
Spst Spst2g02538 Chr2 25031501 25033264 +
Sto Sto2g0725 Chr2 6210780 6213140 +
Trre Trre7g02824 Chr7 24463853 24481260 -
Vian Vian5g01499 Chr5 37561768 37568353 +
Vimu Vimu5g02345 Chr5 34305821 34307462 +
Viun Viun11g02445 Chr11 38105657 38107464 +
Vvi Vvi3g0417 Chr3 3437265 3442553 -
Adu Adu05g00832 Chr05 10149688 10178274 +
Arst Arst5g01036 Chr5 10174384 10176106 +
Bach Bach4g00656 Chr4 4375323 4376906 +
Lapu Lapu2g00692 Chr2 6081489 6082797 -
Lasa Lasa2g03335 Chr2 531120728 531129519 +
Lja Lja3g0500 Chr3 5034155 5036445 +
Mal Mal7g2557 Chr7 87214414 87216932 -
Mepo Mepo5g00913 Chr5 8908742 8910623 +
Mtr Mtr4g2111 Chr4 34639637 34642450 -
Phac Phac2g02584 Chr2 26999536 27001387 -
Phco Phco4g00944 Chr4 7478245 7481659 +
Pste Pste1g02829 Chr1 11918292 11920153 +
Pte Pte2g00290 Chr2 2278740 2281718 +
Pumo Pumo8g01808 Chr8 54319253 54324052 -
Pvu Pvu2g0338 Chr2 3324496 3326039 -
Rops Rops1g01627 Chr1 34608998 34622277 -
Spst Spst2g00835 Chr2 7050199 7055140 +
Tpr Tpr3g2314 Chr3 21972304 21975741 -
Trre Trre9g01068 Chr9 8521414 8522983 +
Vian Vian10g00719 Chr10 6969143 6970478 -
Vimu Vimu7g02976 Chr7 25069489 25070801 -
Viun Viun2g01945 Chr2 28086906 28088493 +
Vivi Vivi2g03013 Chr2 129121175 129123149 -
Vvi Vvi3g0418 Chr3 3448953 3449315 +
Vvi Vvi3g0419 Chr3 3451599 3455674 -
Acco Acco11g2304 Chr11 36566996 36572633 +
Accr Accr9g00194 Chr9 2142819 2144091 -
Adu Adu05g00831 Chr05 10147332 10148912 +
Alju Alju09g2315 Chr09 46205777 46208750 +
Arst Arst5g01035 Chr5 10172004 10173910 +
Bach Bach4g00655 Chr4 4372328 4373819 +
Bisa Bisa11g1708 Chr11 38465341 38466802 +
Dere Dere04g0161 Chr04 1639064 1640540 -
Enph Enph13g0917 Chr13 15269542 15271194 -
Glsi Glsi08g1964 Chr08 13841828 13844234 +
Lapu Lapu2g00690 Chr2 6061261 6062981 +
Lasa Lasa2g03334 Chr2 531072520 531073805 +
Lele Lele49g0143 Chr49 875178 880248 -
Lele Lele50g0164 Chr50 973357 974413 -
Lele Lele51g0158 Chr51 913826 914879 -
Lele Lele52g0162 Chr52 970200 975103 -
Mepo Mepo5g00912 Chr5 8900148 8901868 +
Mibi Mibi12g1998 Chr12 36225177 36226553 +
Phac Phac2g02583 Chr2 26976658 26978542 -
Phco Phco4g00945 Chr4 7490510 7491864 +
Prci Prci10g0265 Chr10 1716889 1718484 -
Pste Pste1g02824 Chr1 11869261 11899649 +
Pvu Pvu2g0337 Chr2 3315744 3317348 -
Rops Rops1g01628 Chr1 34630760 34632734 -
Spst Spst2g00834 Chr2 7046323 7047711 +
Sto Sto2g0721 Chr2 6169364 6174358 +
Trre Trre9g01067 Chr9 8517035 8518181 +
Vian Vian10g00718 Chr10 6958721 6959993 +
Vimu Vimu7g02974 Chr7 25047102 25048664 +
Viun Viun2g01946 Chr2 28095368 28101036 +
Vivi Vivi2g03014 Chr2 129136251 129138146 -
Vvi Vvi3g0420 Chr3 3457811 3461238 -
Cca Cca04g00429 Chr04 4254784 4257152 -
Lja Lja3g0501 Chr3 5036915 5040387 -
Mal Mal7g2556 Chr7 87209444 87211743 +
Mtr Mtr4g2110 Chr4 34634615 34638084 +
Ssu Ssu3g2846 Chr3 83057490 83059933 +
Tpr Tpr3g2313 Chr3 21969466 21971839 +
Tsu Tsu02g02417 Chr02 24661128 24664319 +
Vra Vra2g0406 Chr2 3161058 3162871 -
Vvi Vvi3g0421 Chr3 3462578 3463477 +
Accr Accr9g00197 Chr9 2156284 2157177 +
Adu Adu05g00829 Chr05 10108574 10109488 -
Alju Alju09g2310 Chr09 46181925 46189209 -
Arst Arst5g01029 Chr5 10133290 10134846 -
Bach Bach4g00651 Chr4 4358264 4359773 -
Bisa Bisa11g1703 Chr11 38392025 38394767 -
Dere Dere09g0935 Chr09 12336256 12338882 -
Enph Enph13g0922 Chr13 15296819 15297712 +
Glsi Glsi05g1431 Chr05 63069010 63069987 +
Lapu Lapu2g00687 Chr2 6040339 6041541 -
Lasa Lasa2g03330 Chr2 530964827 530965723 -
Lele Lele49g0146 Chr49 888688 889716 +
Lele Lele50g0166 Chr50 979047 981104 +
Lele Lele51g0160 Chr51 919223 922029 +
Lele Lele52g0165 Chr52 983735 984631 +
Mibi Mibi12g1994 Chr12 36192890 36193786 -
Phac Phac2g02572 Chr2 26854643 26856172 -
Phco Phco4g00952 Chr4 7539996 7546160 +
Prci Prci10g0269 Chr10 1738635 1746818 +
Pvu Pvu2g0329 Chr2 3266161 3267456 -
Spst Spst2g00830 Chr2 7006500 7007796 -
Vivi Vivi2g03019 Chr2 129201711 129203344 +
Vvi Vvi3g0422 Chr3 3467087 3469928 +
Accr Accr9g00197 Chr9 2156284 2157177 +
Adu Adu05g00829 Chr05 10108574 10109488 -
Alju Alju09g2310 Chr09 46181925 46189209 -
Arst Arst5g01029 Chr5 10133290 10134846 -
Bach Bach4g00651 Chr4 4358264 4359773 -
Bisa Bisa11g1703 Chr11 38392025 38394767 -
Dere Dere09g0935 Chr09 12336256 12338882 -
Enph Enph13g0922 Chr13 15296819 15297712 +
Glsi Glsi05g1431 Chr05 63069010 63069987 +
Lapu Lapu2g00687 Chr2 6040339 6041541 -
Lasa Lasa2g03330 Chr2 530964827 530965723 -
Lele Lele49g0146 Chr49 888688 889716 +
Lele Lele50g0166 Chr50 979047 981104 +
Lele Lele51g0160 Chr51 919223 922029 +
Lele Lele52g0165 Chr52 983735 984631 +
Mibi Mibi12g1994 Chr12 36192890 36193786 -
Phac Phac2g02572 Chr2 26854643 26856172 -
Phco Phco4g00952 Chr4 7539996 7546160 +
Prci Prci10g0269 Chr10 1738635 1746818 +
Pvu Pvu2g0329 Chr2 3266161 3267456 -
Spst Spst2g00830 Chr2 7006500 7007796 -
Vivi Vivi2g03019 Chr2 129201711 129203344 +