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
Vvi3g0043 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0046 . . . . . Adu03g00542 Aed5g0346 Aed9g0077 Aev04g3408 . Ahy13g0766 . Aip03g00806 . . . Amo13g0809 . . Apr5g1806 Arst3g00717 Arst3g00717 . . . . Bva13g01770 . Car06g03830 . Cca04g00373 Cca07g00090 . . Dod03g3213 . . . . . Gma04g00075 . Gma11g01018 Gma12g00332 Gso4g0072 . Gso4g0072 Gso4g0072 Lal1g0193 Lal2g0118 Lal9g0136 . . . Lan13g0199 Lan13g0199 Lan13g0199 . . . . Lapu11g00809 . Lasa7g02187 . . . . . . . . . . Mal7g2626 . . . . Mesa13g02674 . . Mtr4g2168 . . . Phco7g00108 Phco9g00448 . . Psa7g3206 . . Pste1g01618 Pte3g01858 . . . . Pumo10g00748 Pvu9g0032 Pvu11g0402 Rops10g02642 Rops3g00483 Seca4g00139 Seca6g00814 Spst9g00102 Spst2g02591 Ssu3g2907 . Sto2g0812 . Tpr3g2390 . . Trre7g02706 Tsu02g02498 . . Vian5g01542 . Vifa6g01115 Vimu10g03674 Vimu5g02423 Viun9g03904 Viun11g02506 . Vivi5g02869 . Vra5g1806
Vvi3g0047 . . . . . Adu03g00543 . . . . Ahy13g0113 . Aip03g00129 . . . Amo13g5815 . . . . Arst3g00719 . . . . Bva13g01771 . . . . . . . . . . . . . . . Gma11g01013 Gma12g00330 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco9g00445 . . . . . Pste1g01611 . . . . . . . Pvu11g0400 . . . . . Spst2g02593 . . Sto2g0813 . . . . . . . . . . . . Vimu5g02425 . . . . . .
Vvi3g0048 . . . . . . Aed5g0343 Aed9g0076 Aev04g3411 . Ahy13g0768 . Aip03g00808 . . . Amo13g0811 . . Apr5g1807 . . . . . . Bva13g01774 . Car06g03831 . Cca04g00372 Cca07g00088 . . Dod03g3216 . . . . . Gma04g00074 Gma06g00067 Gma11g01012 Gma12g00329 . . . . . Lal2g0117 Lal9g0135 . . . . . . . . . . . . . . . . . . . . . Lja1g2342 . Mal7g2628 . . . . . . . Mtr4g2169 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu3g2910 . Sto2g0815 Sto10g0122 Tpr3g2392 . . . Tsu02g02499 . . . . . . . . . . . . Vra5g1809
Vvi3g0049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0050 . . . . . . . Aed9g0075 Aev04g3412 . Ahy13g0769 . Aip03g00809 . . . Amo13g0812 . . Apr5g1808 Arst3g00724 . . . . . Bva13g01776 . . . . Cca07g00087 . . Dod03g3217 . . . . . Gma04g00073 Gma06g00066 . . Gso4g0071 Gso4g0071 . . . . . . . . . . . . . . . . Lasa5g04821 . . . . . . . . . . . . . Mepo3g08014 . Mesa9g05675 . . . . . Phac9g02062 . Phco7g00106 . . . . . . . Pte3g01856 . . . . . Pvu9g0030 . . . Seca4g00133 . Spst9g00099 . . . . Sto10g0121 . . Trre5g05919 . . . . . . . Vimu10g03679 . Viun9g03907 . Vivi3g00007 . . Vra5g1810
Vvi3g0051 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g01777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g02445 . Lasa5g04819 . . . . . . . . . Lja1g2345 . . . Mepo3g08016 . Mesa9g05677 . . . . . . . Phco7g00104 . . . . . . . Pte3g01855 . . . . . Pvu9g0028 . . . Seca4g00131 . Spst9g00097 . . . . Sto10g0120 . . Trre5g05922 . . . . . . . . . Viun9g03908 . Vivi3g00006 . . .
Vvi3g0052 . . . . . . Aed5g0341 . Aev04g3413 . Ahy13g0770 . Aip03g00810 . . . . . . . . . . . . . Bva13g01779 . . . Cca04g00370 . . . Dod03g3218 . . . . . . . . . . . . . . Lal2g0115 . . . . . . . . . . . Lapu11g00813 . Lasa7g02196 . . . . . . . . . . Mal7g2631 . . Mepo2g02392 . Mesa13g02669 . . Mtr4g2172 . . Phac11g00572 . Phco9g00441 . . Psa7g3201 . . Pste1g01588 . . . . . Pumo11g01882 . Pvu11g0397 . Rops3g00479 . Seca6g00800 . Spst2g02596 Ssu3g2916 . Sto2g0824 . Tpr3g2414 . . Trre7g02697 Tsu02g02503 . . Vian5g01547 . Vifa6g01103 . Vimu5g02428 . Viun11g02512 . Vivi5g02878 . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0043 Chr3 574566 578799 +
Vvi Vvi3g0044 Chr3 579750 583120 -
Vvi Vvi3g0045 Chr3 584654 586269 -
Vvi Vvi3g0046 Chr3 592606 594260 +
Adu Adu03g00542 Chr03 5096709 5099021 +
Aed Aed5g0346 Chr5 2439071 2440476 -
Aed Aed9g0077 Chr9 539872 541881 -
Aev Aev04g3408 Chr04 32711726 32714045 +
Ahy Ahy13g0766 Chr13 8028732 8031030 +
Aip Aip03g00806 Chr03 7810321 7812710 +
Amo Amo13g0809 Chr13 10069946 10070737 +
Apr Apr5g1806 Chr5 21363216 21365655 +
Arst Arst3g00717 Chr3 5106815 5109557 +
Arst Arst3g00717 Chr3 5106815 5109557 +
Bva Bva13g01770 Chr13 14310398 14313896 +
Car Car06g03830 Chr06 69987325 69991416 +
Cca Cca04g00373 Chr04 3781375 3784634 -
Cca Cca07g00090 Chr07 1202524 1204869 -
Dod Dod03g3213 Chr03 64738476 64742021 +
Gma Gma04g00075 Chr04 647904 650022 -
Gma Gma11g01018 Chr11 8628322 8631571 -
Gma Gma12g00332 Chr12 2753134 2755577 -
Gso Gso4g0072 Chr4 638736 640832 -
Gso Gso4g0072 Chr4 638736 640832 -
Gso Gso4g0072 Chr4 638736 640832 -
Lal Lal1g0193 Chr1 1157077 1159903 -
Lal Lal2g0118 Chr2 715536 718074 -
Lal Lal9g0136 Chr9 879175 881985 -
Lan Lan13g0199 Chr13 1249026 1251673 -
Lan Lan13g0199 Chr13 1249026 1251673 -
Lan Lan13g0199 Chr13 1249026 1251673 -
Lapu Lapu11g00809 Chr11 10890509 10893561 +
Lasa Lasa7g02187 Chr7 500859596 500861356 +
Mal Mal7g2626 Chr7 88253966 88256565 +
Mesa Mesa13g02674 Chr13 31295019 31297778 -
Mtr Mtr4g2168 Chr4 35239182 35247158 +
Phco Phco7g00108 Chr7 701066 702951 -
Phco Phco9g00448 Chr9 3221222 3223801 -
Psa Psa7g3206 Chr7 239272179 239274852 -
Pste Pste1g01618 Chr1 4992392 4994904 -
Pte Pte3g01858 Chr3 29574772 29576963 -
Pumo Pumo10g00748 Chr10 9543766 9545857 +
Pvu Pvu9g0032 Chr9 582544 583548 -
Pvu Pvu11g0402 Chr11 3385903 3388808 -
Rops Rops10g02642 Chr10 45752704 45755176 +
Rops Rops3g00483 Chr3 6242880 6245832 -
Seca Seca4g00139 Chr4 2093947 2096565 -
Seca Seca6g00814 Chr6 27783474 27787252 -
Spst Spst9g00102 Chr9 750237 752041 -
Spst Spst2g02591 Chr2 25652312 25654658 +
Ssu Ssu3g2907 Chr3 83897184 83899299 +
Sto Sto2g0812 Chr2 7023700 7024704 +
Tpr Tpr3g2390 Chr3 22663409 22667962 +
Trre Trre7g02706 Chr7 23166596 23169056 -
Tsu Tsu02g02498 Chr02 25641850 25645011 +
Vian Vian5g01542 Chr5 37995377 37997894 +
Vifa Vifa6g01115 Chr6 363542693 363545241 -
Vimu Vimu10g03674 Chr10 45825883 45827572 +
Vimu Vimu5g02423 Chr5 34897754 34900219 +
Viun Viun9g03904 Chr9 43240033 43242061 +
Viun Viun11g02506 Chr11 38485955 38488633 +
Vivi Vivi5g02869 Chr5 115867429 115870155 +
Vra Vra5g1806 Chr5 24081744 24083709 +
Vvi Vvi3g0047 Chr3 596303 598436 -
Adu Adu03g00543 Chr03 5105465 5107760 -
Ahy Ahy13g0113 Chr13 1222751 1228938 +
Aip Aip03g00129 Chr03 1163720 1169863 +
Amo Amo13g5815 Chr13 160436244 160444709 +
Arst Arst3g00719 Chr3 5111726 5113754 -
Bva Bva13g01771 Chr13 14314598 14317677 -
Gma Gma11g01013 Chr11 8607770 8609771 +
Gma Gma12g00330 Chr12 2741777 2745309 +
Phco Phco9g00445 Chr9 3211710 3213839 +
Pste Pste1g01611 Chr1 4974752 4977187 +
Pvu Pvu11g0400 Chr11 3376440 3378947 +
Spst Spst2g02593 Chr2 25665880 25667933 -
Sto Sto2g0813 Chr2 7031799 7033824 -
Vimu Vimu5g02425 Chr5 34905887 34907953 -
Vvi Vvi3g0048 Chr3 607518 613614 +
Aed Aed5g0343 Chr5 2405481 2413777 -
Aed Aed9g0076 Chr9 531051 535774 -
Aev Aev04g3411 Chr04 32724438 32729447 +
Ahy Ahy13g0768 Chr13 8059700 8067082 +
Aip Aip03g00808 Chr03 7834966 7842248 +
Amo Amo13g0811 Chr13 10103497 10109588 +
Apr Apr5g1807 Chr5 21367668 21374594 +
Bva Bva13g01774 Chr13 14336901 14344264 +
Car Car06g03831 Chr06 70004393 70011456 +
Cca Cca04g00372 Chr04 3746280 3754184 -
Cca Cca07g00088 Chr07 1184533 1190453 -
Dod Dod03g3216 Chr03 64772148 64780299 +
Gma Gma04g00074 Chr04 635383 641184 -
Gma Gma06g00067 Chr06 618614 624208 -
Gma Gma11g01012 Chr11 8589179 8594938 -
Gma Gma12g00329 Chr12 2725252 2730734 -
Lal Lal2g0117 Chr2 703532 712095 -
Lal Lal9g0135 Chr9 871386 878890 -
Lja Lja1g2342 Chr1 27137683 27143328 +
Mal Mal7g2628 Chr7 88317441 88322727 +
Mtr Mtr4g2169 Chr4 35254014 35260973 +
Ssu Ssu3g2910 Chr3 83932296 83943141 +
Sto Sto2g0815 Chr2 7074776 7080606 +
Sto Sto10g0122 Chr10 932124 937048 -
Tpr Tpr3g2392 Chr3 22712477 22718956 +
Tsu Tsu02g02499 Chr02 25667455 25674195 +
Vra Vra5g1809 Chr5 24095521 24102044 +
Vvi Vvi3g0049 Chr3 614561 614683 +
Vvi Vvi3g0050 Chr3 615804 618883 +
Aed Aed9g0075 Chr9 527541 530325 -
Aev Aev04g3412 Chr04 32730613 32732481 +
Ahy Ahy13g0769 Chr13 8068340 8070702 +
Aip Aip03g00809 Chr03 7843572 7845637 +
Amo Amo13g0812 Chr13 10110742 10113727 +
Apr Apr5g1808 Chr5 21375187 21377780 +
Arst Arst3g00724 Chr3 5147169 5149385 +
Bva Bva13g01776 Chr13 14347623 14352619 +
Cca Cca07g00087 Chr07 1181124 1183164 -
Dod Dod03g3217 Chr03 64788029 64790961 +
Gma Gma04g00073 Chr04 631446 634283 -
Gma Gma06g00066 Chr06 614664 617794 -
Gso Gso4g0071 Chr4 622592 625273 -
Gso Gso4g0071 Chr4 622592 625273 -
Lasa Lasa5g04821 Chr5 697935369 697939516 -
Mepo Mepo3g08014 Chr3 93005787 93009952 +
Mesa Mesa9g05675 Chr9 92492672 92495780 +
Phac Phac9g02062 Chr9 19266193 19269537 +
Phco Phco7g00106 Chr7 687691 689905 -
Pte Pte3g01856 Chr3 29494889 29497824 -
Pvu Pvu9g0030 Chr9 561659 564352 -
Seca Seca4g00133 Chr4 1982115 1986367 -
Spst Spst9g00099 Chr9 732070 734376 -
Sto Sto10g0121 Chr10 928839 931105 -
Trre Trre5g05919 Chr5 58714921 58719001 +
Vimu Vimu10g03679 Chr10 45845933 45848130 +
Viun Viun9g03907 Chr9 43252974 43255627 +
Vivi Vivi3g00007 Chr3 104047 108319 -
Vra Vra5g1810 Chr5 24103197 24105761 +
Vvi Vvi3g0051 Chr3 624059 624325 -
Bva Bva13g01777 Chr13 14356490 14356762 -
Lapu Lapu9g02445 Chr9 38863683 38863931 -
Lasa Lasa5g04819 Chr5 697822158 697822427 +
Lja Lja1g2345 Chr1 27168631 27169142 -
Mepo Mepo3g08016 Chr3 93014393 93015002 -
Mesa Mesa9g05677 Chr9 92501520 92502510 -
Phco Phco7g00104 Chr7 683839 684087 +
Pte Pte3g01855 Chr3 29461994 29462835 +
Pvu Pvu9g0028 Chr9 558188 558603 +
Seca Seca4g00131 Chr4 1978710 1978964 +
Spst Spst9g00097 Chr9 726891 728891 +
Sto Sto10g0120 Chr10 925585 925857 +
Trre Trre5g05922 Chr5 58734986 58735258 -
Viun Viun9g03908 Chr9 43257412 43257997 -
Vivi Vivi3g00006 Chr3 98647 99232 +
Vvi Vvi3g0052 Chr3 624725 631913 +
Aed Aed5g0341 Chr5 2396172 2404180 +
Aev Aev04g3413 Chr04 32735509 32739267 +
Ahy Ahy13g0770 Chr13 8071934 8076107 +
Aip Aip03g00810 Chr03 7847705 7851243 +
Bva Bva13g01779 Chr13 14357316 14362267 +
Cca Cca04g00370 Chr04 3732759 3737981 +
Dod Dod03g3218 Chr03 64791920 64796291 +
Lal Lal2g0115 Chr2 690383 702680 -
Lapu Lapu11g00813 Chr11 10922487 10928140 -
Lasa Lasa7g02196 Chr7 502318275 502321866 -
Mal Mal7g2631 Chr7 88389590 88394784 -
Mepo Mepo2g02392 Chr2 33737761 33742854 -
Mesa Mesa13g02669 Chr13 31199339 31202818 +
Mtr Mtr4g2172 Chr4 35297985 35303262 -
Phac Phac11g00572 Chr11 3893534 3899089 +
Phco Phco9g00441 Chr9 3174649 3179832 +
Psa Psa7g3201 Chr7 238991805 238996310 +
Pste Pste1g01588 Chr1 4921852 4927329 +
Pumo Pumo11g01882 Chr11 50563110 50569655 -
Pvu Pvu11g0397 Chr11 3337855 3343477 +
Rops Rops3g00479 Chr3 6077238 6083359 +
Seca Seca6g00800 Chr6 27101827 27107912 +
Spst Spst2g02596 Chr2 25704676 25714287 -
Ssu Ssu3g2916 Chr3 83983776 83989404 -
Sto Sto2g0824 Chr2 7139606 7145592 +
Tpr Tpr3g2414 Chr3 22969938 22974303 -
Trre Trre7g02697 Chr7 23007462 23011825 +
Tsu Tsu02g02503 Chr02 25760681 25765039 -
Vian Vian5g01547 Chr5 38032919 38037358 -
Vifa Vifa6g01103 Chr6 361043808 361048241 +
Vimu Vimu5g02428 Chr5 34933190 34939772 -
Viun Viun11g02512 Chr11 38527597 38532455 -
Vivi Vivi5g02878 Chr5 116521398 116525436 -
Mal Mal7g2631 Chr7 88389590 88394784 -
Mtr Mtr4g2172 Chr4 35297985 35303262 -
Tpr Tpr3g2414 Chr3 22969938 22974303 -
Tsu Tsu02g02503 Chr02 25760681 25765039 -
Aed Aed9g0076 Chr9 531051 535774 -
Cca Cca07g00088 Chr07 1184533 1190453 -
Gma Gma04g00074 Chr04 635383 641184 -
Gma Gma06g00067 Chr06 618614 624208 -
Vra Vra5g1809 Chr5 24095521 24102044 +