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
Vvi1g0851 . . . . . . . Aed7g1661 . Aev03g0539 . Ahy13g3712 . Aip03g04150 . . . Amo13g3894 . Apr3g0813 . . . . . . Bva08g01301 Bva11g01108 . Car07g01979 . Cca11g00655 . . . Dod04g0039 . . . . . . Gma08g02721 . . . . . . . . Lal23g1047 . Lal15g0494 . . . . . . . . . . . . . . . . . . . Lja4g2830 . Mal5g2883 . . . . . . . Mtr8g1946 . . . . . . . Psa4g2911 . . . . . . . . . . . . . . . . . Ssu5g1055 . . . . . . . Tsu04g03204 . . . . . . . . . . . .
Vvi1g0852 . Acco12g0693 . Accr10g01333 . Adu03g03780 . Aed7g1662 . Aev03g0538 . Ahy13g3713 . Aip03g04151 . Alju12g1402 . . . Apr3g0814 . . . . . Bisa01g1615 . . . Car07g01980 . Cca11g00654 . Dere13g1221 . Dod04g0036 . Enph14g1126 . Glsi09g1081 . . Gma08g02722 . . . . . . . . . . . . . . . . . . . . . . . . . Lele53g0947 Lele54g0927 Lele55g0526 Lele56g0514 . Lja4g2831 . Mal5g2890 . Mepo1g02656 . . . Mibi10g1335 . Mtr8g1943 . Phac11g02822 . Phco8g02854 . Prci5g1685 . . . Pste7g00709 . . . . . . . Pvu3g0549 . Rops2g02738 . Seca12g03733 . Spst3g02535 . Ssu5g1054 . . . Tpr4g4792 . Trre15g02075 . Tsu04g03206 . . . . . Vimu11g03272 . Viun3g03272 . . . .
Vvi1g0853 Acco11g0982 . Accr9g01305 . Adu05g01501 . Aed11g0216 . Aev05g1295 . Ahy15g1448 . Aip05g01528 . Alju09g1015 . . . Apr7g1618 . Arst5g01921 . . . Bisa11g2298 . Bva08g01297 . Car02g00605 . Cca06g00801 . Dere09g1587 . Dod02g1484 . Enph13g0137 . Glsi05g0836 . Gma02g00291 Gma01g00303 . . Gso2g0272 Gso2g0272 . . . . . Lal23g1045 Lal16g0551 Lal15g0497 . . . . . . Lapu2g01569 . . . Lele49g1068 Lele50g1157 Lele51g1083 Lele52g1121 . . . . Lja2g0997 . Mal6g1674 . Mepo5g01615 . Mesa17g01803 . . . Mtr5g1428 . . . Phco4g01467 . Prci10g1759 . . . Pste1g02105 . . . . . Pumo8g01199 . Pvu2g0754 . Rops1g00877 . Seca10g01508 . Spst2g01436 . Ssu2g1755 . . Sto6g4352 Tpr2g1763 . Trre9g02213 . Tsu05g01515 . Vian10g01155 . Vifa1g04715 . Vimu7g03743 . Viun2g01200 . Vivi2g01399 . . .
Vvi1g0854 Acco11g0980 . Accr9g01307 . Adu05g01502 . Aed11g0217 . Aev05g1296 . Ahy15g1449 . Aip05g01530 . Alju09g1014 . . . Apr7g1617 Apr3g0816 Arst5g01923 . . . Bisa11g2299 . Bva08g01296 . Car02g00606 . Cca06g00800 . Dere09g1589 . Dod02g1485 . Enph13g0135 . Glsi05g0833 . Gma02g00290 Gma01g00304 Gma08g02726 . Gso2g0271 Gso2g0271 Gso2g0271 . . . . . Lal16g0552 Lal15g0498 . . . . . . Lapu2g01568 . Lasa2g00438 . Lele49g1069 Lele50g1158 Lele51g1084 Lele52g1122 . . . . Lja2g0998 . Mal6g1676 . Mepo5g01616 . Mesa17g01804 . . . Mtr5g1429 . . . Phco4g01469 . . . . . Pste1g02107 . . Pte12g01244 . . Pumo8g01198 . Pvu2g0755 . Rops1g00878 . Seca10g01510 . Spst2g01437 . . . . Sto6g4353 Tpr2g1764 . Trre9g02212 . Tsu05g01517 . Vian10g01154 . Vifa1g04717 . Vimu7g03744 . Viun2g01199 . . . . .
Vvi1g0855 . . . . Adu05g01505 . . . Aev05g1303 . Ahy15g1452 . Aip05g01533 . . . . . Apr7g1615 . . . . . . . . . Car02g00608 . . . . . Dod02g1486 . . . . . . Gma01g00307 . . . . . . . . . . . . . . . . . . Lapu2g01567 . Lasa7g00564 . . . . . . . . . Lja2g0999 . Mal6g1680 . . . . Mesa9g02999 . . Mtr5g1433 . Phac2g01110 . Phco4g01472 . . . . . Pste1g02118 . . . . . Pumo8g01196 . Pvu2g0756 Pvu9g1279 . . . . Spst2g01441 Spst9g01280 . . . . . . . . Tsu05g01520 . Vian10g01153 Vian4g01553 Vifa1g04725 . Vimu7g03747 . . . . . . .
Vvi1g0856 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0859 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0860 . . . . . . . . . . . . . . . . . . . . . . . Bach2g02101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g00752 . Lasa5g02233 . . . . . . . . . . . . . . . . . . . . . . . Phco7g02162 . . . . . Pste2g00184 . . . . . . . Pvu9g1870 . Rops10g00630 . Seca4g03119 . Spst9g02249 . . . . . . . . . . . Vian4g00827 . Vifa2g02059 . Vimu10g01174 . Viun9g01164 . Vivi3g03872 . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0851 Chr1 9031126 9033960 +
Aed Aed7g1661 Chr7 19920872 19924312 +
Aev Aev03g0539 Chr03 3932506 3935508 -
Ahy Ahy13g3712 Chr13 135938074 135941091 +
Aip Aip03g04150 Chr03 125409727 125412574 +
Amo Amo13g3894 Chr13 130642787 130644388 -
Apr Apr3g0813 Chr3 21294775 21298043 +
Bva Bva08g01301 Chr08 6802012 6805401 -
Bva Bva11g01108 Chr11 12361012 12364215 +
Car Car07g01979 Chr07 23176741 23183577 +
Cca Cca11g00655 Chr11 10756819 10760325 -
Dod Dod04g0039 Chr04 463320 466154 -
Gma Gma08g02721 Chr08 42672378 42675191 +
Lal Lal23g1047 Chr23 12227584 12232459 -
Lal Lal15g0494 Chr15 3403768 3407776 +
Lja Lja4g2830 Chr4 47667208 47671081 +
Mal Mal5g2883 Chr5 85899937 85903697 +
Mtr Mtr8g1946 Chr8 29199697 29203950 -
Psa Psa4g2911 Chr4 233466563 233469196 +
Ssu Ssu5g1055 Chr5 33182038 33184911 -
Tsu Tsu04g03204 Chr04 40410621 40414740 +
Vvi Vvi1g0852 Chr1 9035382 9038904 -
Acco Acco12g0693 Chr12 6446159 6449528 +
Accr Accr10g01333 Chr10 36384037 36387101 +
Adu Adu03g03780 Chr03 126504099 126506938 +
Aed Aed7g1662 Chr7 19925879 19930236 -
Aev Aev03g0538 Chr03 3928704 3931216 +
Ahy Ahy13g3713 Chr13 135943672 135946583 -
Aip Aip03g04151 Chr03 125415357 125418020 -
Alju Alju12g1402 Chr12 35246880 35251083 -
Apr Apr3g0814 Chr3 21301545 21304931 -
Bisa Bisa01g1615 Chr01 27671425 27677299 +
Car Car07g01980 Chr07 23184167 23187922 -
Cca Cca11g00654 Chr11 10750983 10754809 +
Dere Dere13g1221 Chr13 16913103 16916480 +
Dod Dod04g0036 Chr04 458083 461050 +
Enph Enph14g1126 Chr14 12868223 12873776 +
Glsi Glsi09g1081 Chr09 7554010 7557468 +
Gma Gma08g02722 Chr08 42678642 42682696 -
Lele Lele53g0947 Chr53 19081400 19084984 -
Lele Lele54g0927 Chr54 15726146 15728792 -
Lele Lele55g0526 Chr55 3388473 3391606 +
Lele Lele56g0514 Chr56 3756412 3758970 -
Lja Lja4g2831 Chr4 47685822 47690192 -
Mal Mal5g2890 Chr5 86069593 86075035 -
Mepo Mepo1g02656 Chr1 28132669 28136902 +
Mibi Mibi10g1335 Chr10 33885047 33888921 -
Mtr Mtr8g1943 Chr8 29183375 29187155 +
Phac Phac11g02822 Chr11 39703626 39705660 -
Phco Phco8g02854 Chr8 41985690 41998755 +
Prci Prci5g1685 Chr5 35336058 35339942 +
Pste Pste7g00709 Chr7 6490464 6493877 +
Pvu Pvu3g0549 Chr3 6670113 6674050 +
Rops Rops2g02738 Chr2 46342342 46345962 +
Seca Seca12g03733 Chr12 95863613 95867419 +
Spst Spst3g02535 Chr3 73388795 73392001 -
Ssu Ssu5g1054 Chr5 33173997 33179499 +
Tpr Tpr4g4792 Chr4 56904265 56908140 +
Trre Trre15g02075 Chr15 16905887 16909326 +
Tsu Tsu04g03206 Chr04 40449088 40454226 -
Vimu Vimu11g03272 Chr11 52920533 52924284 +
Viun Viun3g03272 Chr3 39703407 39707137 +
Vvi Vvi1g0853 Chr1 9040679 9082566 +
Acco Acco11g0982 Chr11 21699597 21712700 -
Accr Accr9g01305 Chr9 17448215 17465194 +
Adu Adu05g01501 Chr05 25210973 25218539 +
Aed Aed11g0216 Chr11 1770653 1778694 +
Aev Aev05g1295 Chr05 9154114 9162094 +
Ahy Ahy15g1448 Chr15 26731997 26740043 +
Aip Aip05g01528 Chr05 25661171 25669309 +
Alju Alju09g1015 Chr09 32200815 32213424 -
Apr Apr7g1618 Chr7 23326424 23335980 -
Arst Arst5g01921 Chr5 25258266 25266047 +
Bisa Bisa11g2298 Chr11 47043384 47054957 +
Bva Bva08g01297 Chr08 6762760 6770449 -
Car Car02g00605 Chr02 7258438 7269990 +
Cca Cca06g00801 Chr06 20920208 20936682 -
Dere Dere09g1587 Chr09 20205856 20221714 +
Dod Dod02g1484 Chr02 17727070 17735693 +
Enph Enph13g0137 Chr13 6955325 6967661 -
Glsi Glsi05g0836 Chr05 58732383 58742014 -
Gma Gma02g00291 Chr02 3056888 3067453 -
Gma Gma01g00303 Chr01 3466627 3476968 +
Gso Gso2g0272 Chr2 2958306 2969319 -
Gso Gso2g0272 Chr2 2958306 2969319 -
Lal Lal23g1045 Chr23 12201932 12211496 -
Lal Lal16g0551 Chr16 3544749 3555786 +
Lal Lal15g0497 Chr15 3430802 3441835 +
Lapu Lapu2g01569 Chr2 29164139 29175749 -
Lele Lele49g1068 Chr49 6903600 6921718 +
Lele Lele50g1157 Chr50 7784677 7804494 +
Lele Lele51g1083 Chr51 7003572 7017200 +
Lele Lele52g1121 Chr52 7651486 7667912 +
Lja Lja2g0997 Chr2 9397504 9406422 +
Mal Mal6g1674 Chr6 31370989 31383628 +
Mepo Mepo5g01615 Chr5 17145929 17157338 +
Mesa Mesa17g01803 Chr17 25700155 25710577 +
Mtr Mtr5g1428 Chr5 15031200 15042922 +
Phco Phco4g01467 Chr4 13177039 13187837 +
Prci Prci10g1759 Chr10 13243966 13255553 +
Pste Pste1g02105 Chr1 6610310 6622611 +
Pumo Pumo8g01199 Chr8 43384877 43396330 -
Pvu Pvu2g0754 Chr2 10363693 10374800 +
Rops Rops1g00877 Chr1 21211101 21225281 +
Seca Seca10g01508 Chr10 16335207 16344099 +
Spst Spst2g01436 Chr2 13098660 13118124 +
Ssu Ssu2g1755 Chr2 67880436 67900306 -
Sto Sto6g4352 Chr6 46124547 46131566 +
Tpr Tpr2g1763 Chr2 20841933 20854236 +
Trre Trre9g02213 Chr9 24163656 24179552 -
Tsu Tsu05g01515 Chr05 14624595 14636478 +
Vian Vian10g01155 Chr10 18913039 18922730 -
Vifa Vifa1g04715 Chr1 736480551 736488516 +
Vimu Vimu7g03743 Chr7 32871776 32886333 +
Viun Viun2g01200 Chr2 22729645 22740437 -
Vivi Vivi2g01399 Chr2 59758609 59765824 +
Vvi Vvi1g0854 Chr1 9084035 9085728 -
Acco Acco11g0980 Chr11 21687764 21689897 +
Accr Accr9g01307 Chr9 17471042 17473192 -
Adu Adu05g01502 Chr05 25222885 25224974 -
Aed Aed11g0217 Chr11 1781081 1784685 -
Aev Aev05g1296 Chr05 9166233 9168384 -
Ahy Ahy15g1449 Chr15 26747304 26749446 -
Aip Aip05g01530 Chr05 25675957 25677884 -
Alju Alju09g1014 Chr09 32185926 32188111 +
Apr Apr7g1617 Chr7 23320328 23322228 +
Apr Apr3g0816 Chr3 21430642 21433623 -
Arst Arst5g01923 Chr5 25270110 25272181 -
Bisa Bisa11g2299 Chr11 47056124 47069043 -
Bva Bva08g01296 Chr08 6759741 6762063 +
Car Car02g00606 Chr02 7274593 7277398 -
Cca Cca06g00800 Chr06 20912642 20914962 +
Dere Dere09g1589 Chr09 20230642 20233144 -
Dod Dod02g1485 Chr02 17738267 17740908 -
Enph Enph13g0135 Chr13 6906066 6908300 +
Glsi Glsi05g0833 Chr05 58711723 58713734 +
Gma Gma02g00290 Chr02 3050830 3052925 +
Gma Gma01g00304 Chr01 3479692 3481863 -
Gma Gma08g02726 Chr08 42803878 42807717 -
Gso Gso2g0271 Chr2 2952744 2955256 +
Gso Gso2g0271 Chr2 2952744 2955256 +
Gso Gso2g0271 Chr2 2952744 2955256 +
Lal Lal16g0552 Chr16 3555853 3559147 -
Lal Lal15g0498 Chr15 3443209 3445783 -
Lapu Lapu2g01568 Chr2 29159361 29161491 +
Lasa Lasa2g00438 Chr2 58500516 58502727 -
Lele Lele49g1069 Chr49 6925712 6927946 -
Lele Lele50g1158 Chr50 7809034 7811329 -
Lele Lele51g1084 Chr51 7021421 7023645 -
Lele Lele52g1122 Chr52 7672460 7674777 -
Lja Lja2g0998 Chr2 9409673 9411934 -
Mal Mal6g1676 Chr6 31396708 31399048 -
Mepo Mepo5g01616 Chr5 17161288 17163996 -
Mesa Mesa17g01804 Chr17 25717330 25720278 -
Mtr Mtr5g1429 Chr5 15046555 15049282 -
Phco Phco4g01469 Chr4 13193495 13197966 -
Pste Pste1g02107 Chr1 6632278 6634328 -
Pte Pte12g01244 Chr12 34355463 34357901 +
Pumo Pumo8g01198 Chr8 43379114 43381539 +
Pvu Pvu2g0755 Chr2 10379815 10381996 -
Rops Rops1g00878 Chr1 21229059 21231165 -
Seca Seca10g01510 Chr10 16350235 16351300 -
Spst Spst2g01437 Chr2 13122348 13125912 -
Sto Sto6g4353 Chr6 46137291 46138813 -
Tpr Tpr2g1764 Chr2 20868027 20871111 -
Trre Trre9g02212 Chr9 24158604 24160701 +
Tsu Tsu05g01517 Chr05 14643719 14646597 -
Vian Vian10g01154 Chr10 18906828 18908752 +
Vifa Vifa1g04717 Chr1 737155472 737157509 -
Vimu Vimu7g03744 Chr7 32888754 32890614 -
Viun Viun2g01199 Chr2 22724317 22726826 +
Vvi Vvi1g0855 Chr1 9118167 9120059 +
Adu Adu05g01505 Chr05 25409176 25412825 +
Aev Aev05g1303 Chr05 9238360 9245189 +
Ahy Ahy15g1452 Chr15 27058576 27062305 +
Aip Aip05g01533 Chr05 25958420 25962045 +
Apr Apr7g1615 Chr7 23287899 23290915 -
Car Car02g00608 Chr02 7311100 7318352 +
Dod Dod02g1486 Chr02 17824537 17833539 +
Gma Gma01g00307 Chr01 3600355 3605631 +
Lapu Lapu2g01567 Chr2 29117907 29123302 -
Lasa Lasa7g00564 Chr7 22493575 22495354 -
Lja Lja2g0999 Chr2 9430367 9432551 +
Mal Mal6g1680 Chr6 31633342 31639624 +
Mesa Mesa9g02999 Chr9 59412356 59414396 -
Mtr Mtr5g1433 Chr5 15090741 15094261 +
Phac Phac2g01110 Chr2 7520039 7525458 +
Phco Phco4g01472 Chr4 13290035 13300849 +
Pste Pste1g02118 Chr1 6686562 6704222 +
Pumo Pumo8g01196 Chr8 43296219 43350673 -
Pvu Pvu2g0756 Chr2 10491217 10495199 +
Pvu Pvu9g1279 Chr9 18460113 18463900 +
Spst Spst2g01441 Chr2 13164723 13166734 +
Spst Spst9g01280 Chr9 12261417 12272422 +
Tsu Tsu05g01520 Chr05 14696160 14699891 +
Vian Vian10g01153 Chr10 18870998 18873558 -
Vian Vian4g01553 Chr4 30788689 30792138 -
Vifa Vifa1g04725 Chr1 739360440 739377076 +
Vimu Vimu7g03747 Chr7 32925471 32926974 +
Vvi Vvi1g0856 Chr1 9159672 9161483 +
Vvi Vvi1g0857 Chr1 9164169 9164537 +
Vvi Vvi1g0858 Chr1 9164598 9164912 +
Vvi Vvi1g0859 Chr1 9165038 9165184 +
Vvi Vvi1g0860 Chr1 9166959 9167945 +
Bach Bach2g02101 Chr2 28245646 28251030 +
Lapu Lapu9g00752 Chr9 10118057 10126686 -
Lasa Lasa5g02233 Chr5 463672023 463679176 -
Phco Phco7g02162 Chr7 38343290 38349994 -
Pste Pste2g00184 Chr2 911297 919597 +
Pvu Pvu9g1870 Chr9 26621633 26628943 -
Rops Rops10g00630 Chr10 15527518 15534913 +
Seca Seca4g03119 Chr4 53483713 53487999 -
Spst Spst9g02249 Chr9 52297089 52312790 -
Vian Vian4g00827 Chr4 10929562 10935542 +
Vifa Vifa2g02059 Chr2 534731074 534737993 -
Vimu Vimu10g01174 Chr10 11475038 11482154 +
Viun Viun9g01164 Chr9 10144480 10151372 +
Vivi Vivi3g03872 Chr3 66741513 66750766 +
Bach Bach2g02101 Chr2 28245646 28251030 +
Lapu Lapu9g00752 Chr9 10118057 10126686 -
Lasa Lasa5g02233 Chr5 463672023 463679176 -
Phco Phco7g02162 Chr7 38343290 38349994 -
Pste Pste2g00184 Chr2 911297 919597 +
Pvu Pvu9g1870 Chr9 26621633 26628943 -
Rops Rops10g00630 Chr10 15527518 15534913 +
Seca Seca4g03119 Chr4 53483713 53487999 -
Spst Spst9g02249 Chr9 52297089 52312790 -
Vian Vian4g00827 Chr4 10929562 10935542 +
Vifa Vifa2g02059 Chr2 534731074 534737993 -
Vimu Vimu10g01174 Chr10 11475038 11482154 +
Viun Viun9g01164 Chr9 10144480 10151372 +
Vivi Vivi3g03872 Chr3 66741513 66750766 +
Aed Aed11g0217 Chr11 1781081 1784685 -