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
Vvi1g1571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal3g3079 . . . . . . . Mtr7g2277 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr6g1043 . . . Tsu07g02877 . . . . . . . . . . . . .
Vvi1g1572 . . . . Adu03g02917 . . . . . . . . . . . . . . . Arst3g03849 . . . Bisa08g1646 . Bva06g01680 Bva05g00101 . . . . Dere03g0530 . . . . . . . . . Gma08g02396 . . . . . Lal6g1645 . Lal18g0570 . . . Lan8g0126 . Lan8g0126 . . . . . Lasa7g04631 . . . . . . . . . . Lja4g0500 . Mal7g4843 Mepo2g04528 . Mesa13g00594 . . . . Mtr8g3381 Phac2g04241 . Phco4g03200 . . . . Psa7g0902 Pste3g01298 . . . . . Pumo6g00574 . Pvu2g2898 . Rops2g00668 . Seca12g06386 . . . . . . . . Tpr3g0725 Trre7g05319 . . Tsu02g00551 Vian1g03753 . Vifa6g03400 . Vimu11g04308 . Viun3g00693 . Vivi5g05730 . . .
Vvi1g1573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal3g3081 . . . . . . . Mtr7g2279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr6g1044 . . . Tsu07g02878 . . . . . . . . . . . . .
Vvi1g1575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1576 . . . . . . . . . . . . . . . . . . . . Arst3g03852 Arst3g03850 . Bach2g02315 . . Bva06g01679 Bva05g00102 . . Cca07g02359 . . . . . . . . . . . Gma08g02395 . . . . . . . . . . . . . . . . . . Lapu9g00916 Lasa7g04629 Lasa5g03501 . . . . . . . . . . . Mal7g4841 . Mepo3g06946 . Mesa9g04494 . . . Mtr8g3380 Phac2g04240 . . Phco7g01892 . . . Psa7g0903 . Pste2g00234 Pte2g02518 . Pte3g00116 Pte1g02041 . Pumo10g01823 Pvu2g2896 Pvu9g1666 . Rops10g00867 . Seca4g01795 Spst3g01195 . Ssu3g0243 . . . . Tpr3g0726 . Trre5g04750 . Tsu02g00552 . . . . Vimu11g04301 Vimu10g01636 . Viun9g01587 Vivi5g05728 Vivi3g02253 Vra4g1215 .
Vvi1g1577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g2518 . . . . . . . . . . . . . . . . . . .
Vvi1g1578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1579 Acco04g2338 . Accr8g00415 . . . . . . . . . . . Alju06g2302 . . . . . Arst3g03863 Arst3g03863 . . Bisa08g1652 . Bva06g01678 Bva05g00103 . . Cca07g02357 . Dere03g0523 . . . Enph6g0437 . Glsi02g0482 . . . Gma08g02393 . . . . . Lal6g1644 . . . . . Lan8g0127 . . . . . Lapu3g03507 Lapu9g00913 . Lasa5g03497 Lele21g1628 Lele22g1611 Lele23g0383 . . . . . . Lja4g0503 . . . Mepo3g06943 . Mesa9g04474 Mibi09g0466 . . . . Phac9g02673 Phco4g03196 Phco7g01897 Prci4g2610 . . . Pste3g01324 Pste2g00225 Pte2g02521 . . Pte1g02042 Pumo6g00578 Pumo10g01816 Pvu2g2891 Pvu9g1662 Rops2g00674 Rops10g00872 . Seca4g01801 Spst3g01198 Spst9g01781 Ssu3g0244 . . . . . . Trre5g04755 . . Vian1g03749 . . . Vimu11g04296 . Viun3g00700 Viun9g01597 . Vivi3g02256 Vra4g1214 .
Vvi1g1580 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa6g05046 . . . . . . . . . . . . . . . . . . . . . . . Phco6g03240 . . . . . Pste4g00008 . . . . . . . Pvu7g0003 . . . . . Spst10g01751 . . . Sto3g2520 . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g1571 Chr1 22452109 22455815 +
Mal Mal3g3079 Chr3 105758025 105760157 +
Mtr Mtr7g2277 Chr7 39173120 39175803 +
Tpr Tpr6g1043 Chr6 9754943 9757667 +
Tsu Tsu07g02877 Chr07 33957717 33960311 +
Vvi Vvi1g1572 Chr1 22457479 22458836 -
Adu Adu03g02917 Chr03 110605013 110609016 -
Arst Arst3g03849 Chr3 109309856 109314525 -
Bisa Bisa08g1646 Chr08 38426867 38428482 -
Bva Bva06g01680 Chr06 11796027 11798960 +
Bva Bva05g00101 Chr05 509322 512179 -
Dere Dere03g0530 Chr03 9253386 9254558 +
Gma Gma08g02396 Chr08 23697289 23701133 +
Lal Lal6g1645 Chr6 19224680 19228672 +
Lal Lal18g0570 Chr18 4782810 4786660 +
Lan Lan8g0126 Chr8 2015247 2019889 -
Lan Lan8g0126 Chr8 2015247 2019889 -
Lasa Lasa7g04631 Chr7 674103340 674105538 +
Lja Lja4g0500 Chr4 4086729 4089837 -
Mal Mal7g4843 Chr7 116919609 116921601 +
Mepo Mepo2g04528 Chr2 53705533 53707751 +
Mesa Mesa13g00594 Chr13 7048765 7050632 -
Mtr Mtr8g3381 Chr8 44309325 44311569 +
Phac Phac2g04241 Chr2 41025299 41027242 +
Phco Phco4g03200 Chr4 52722277 52724233 +
Psa Psa7g0902 Chr7 68270755 68273095 -
Pste Pste3g01298 Chr3 8145603 8148097 -
Pumo Pumo6g00574 Chr6 7235430 7236167 -
Pvu Pvu2g2898 Chr2 44542507 44544591 +
Rops Rops2g00668 Chr2 9462455 9464830 -
Seca Seca12g06386 Chr12 155866271 155868528 +
Tpr Tpr3g0725 Chr3 6972578 6975181 -
Trre Trre7g05319 Chr7 59398027 59400428 +
Tsu Tsu02g00551 Chr02 4660899 4663334 -
Vian Vian1g03753 Chr1 60450008 60452271 +
Vifa Vifa6g03400 Chr6 1115831112 1115833459 +
Vimu Vimu11g04308 Chr11 64446272 64448081 +
Viun Viun3g00693 Chr3 4293209 4294987 -
Vivi Vivi5g05730 Chr5 160842252 160844955 +
Vvi Vvi1g1573 Chr1 22467217 22468084 +
Vvi Vvi1g1574 Chr1 22469075 22482650 -
Mal Mal3g3081 Chr3 105780292 105788745 -
Mtr Mtr7g2279 Chr7 39181594 39190250 -
Tpr Tpr6g1044 Chr6 9761046 9771274 -
Tsu Tsu07g02878 Chr07 33968235 33976427 -
Vvi Vvi1g1575 Chr1 22493353 22493848 -
Vvi Vvi1g1576 Chr1 22511435 22524037 +
Arst Arst3g03852 Chr3 109387648 109395437 +
Arst Arst3g03850 Chr3 109387647 109395437 +
Bach Bach2g02315 Chr2 29676050 29682365 +
Bva Bva06g01679 Chr06 11785346 11791556 -
Bva Bva05g00102 Chr05 514464 521271 +
Cca Cca07g02359 Chr07 52199492 52205820 -
Gma Gma08g02395 Chr08 23679944 23685668 -
Lapu Lapu9g00916 Chr9 13751634 13760724 -
Lasa Lasa7g04629 Chr7 673820621 673825227 -
Lasa Lasa5g03501 Chr5 568743766 568749180 -
Mal Mal7g4841 Chr7 116873497 116879712 -
Mepo Mepo3g06946 Chr3 83096775 83104714 -
Mesa Mesa9g04494 Chr9 78470966 78477062 -
Mtr Mtr8g3380 Chr8 44287210 44294823 -
Phac Phac2g04240 Chr2 41002122 41010585 -
Phco Phco7g01892 Chr7 22433759 22441884 +
Psa Psa7g0903 Chr7 68349002 68355578 +
Pste Pste2g00234 Chr2 1401112 1409547 -
Pte Pte2g02518 Chr2 44349667 44357332 +
Pte Pte3g00116 Chr3 1122780 1128838 -
Pte Pte1g02041 Chr1 41511070 41518498 +
Pumo Pumo10g01823 Chr10 23956238 23963347 -
Pvu Pvu2g2896 Chr2 44522671 44523137 -
Pvu Pvu9g1666 Chr9 23396369 23402117 -
Rops Rops10g00867 Chr10 19681298 19691115 +
Seca Seca4g01795 Chr4 29622749 29630770 +
Spst Spst3g01195 Chr3 15469826 15476052 +
Ssu Ssu3g0243 Chr3 4345308 4351770 +
Tpr Tpr3g0726 Chr3 6988574 6996213 +
Trre Trre5g04750 Chr5 49338488 49344041 +
Tsu Tsu02g00552 Chr02 4673473 4678991 +
Vimu Vimu11g04301 Chr11 64352582 64358625 -
Vimu Vimu10g01636 Chr10 20790760 20801410 +
Viun Viun9g01587 Chr9 23435836 23444147 +
Vivi Vivi5g05728 Chr5 160787091 160793236 -
Vivi Vivi3g02253 Chr3 37085029 37092403 +
Vra Vra4g1215 Chr4 19104131 19111853 -
Vvi Vvi1g1577 Chr1 22527863 22542626 -
Sto Sto3g2518 Chr3 29213162 29219093 -
Vvi Vvi1g1578 Chr1 22551857 22561690 +
Vvi Vvi1g1579 Chr1 22568108 22570236 +
Acco Acco04g2338 Chr04 39641071 39644840 -
Accr Accr8g00415 Chr8 6426424 6428286 +
Alju Alju06g2302 Chr06 49409667 49411564 -
Arst Arst3g03863 Chr3 109536695 109538976 +
Arst Arst3g03863 Chr3 109536695 109538976 +
Bisa Bisa08g1652 Chr08 38610390 38612104 +
Bva Bva06g01678 Chr06 11780672 11782758 -
Bva Bva05g00103 Chr05 522496 523054 +
Cca Cca07g02357 Chr07 52158938 52162730 -
Dere Dere03g0523 Chr03 9095932 9100756 -
Enph Enph6g0437 Chr6 7694445 7697040 -
Glsi Glsi02g0482 Chr02 3071301 3072363 -
Gma Gma08g02393 Chr08 23649421 23651961 -
Lal Lal6g1644 Chr6 19205330 19207783 -
Lan Lan8g0127 Chr8 2041464 2043255 +
Lapu Lapu3g03507 Chr3 58409382 58412914 -
Lapu Lapu9g00913 Chr9 13696490 13698526 -
Lasa Lasa5g03497 Chr5 568115033 568115991 -
Lele Lele21g1628 Chr21 24240294 24243413 -
Lele Lele22g1611 Chr22 21628301 21644118 -
Lele Lele23g0383 Chr23 2773051 2774713 +
Lja Lja4g0503 Chr4 4110477 4111860 +
Mepo Mepo3g06943 Chr3 83077093 83078993 -
Mesa Mesa9g04474 Chr9 78136949 78138574 -
Mibi Mibi09g0466 Chr09 6051260 6054317 +
Phac Phac9g02673 Chr9 25341047 25343070 -
Phco Phco4g03196 Chr4 52672219 52675078 -
Phco Phco7g01897 Chr7 22595755 22597747 +
Prci Prci4g2610 Chr4 38355096 38357677 -
Pste Pste3g01324 Chr3 8275559 8278199 +
Pste Pste2g00225 Chr2 1282192 1284212 -
Pte Pte2g02521 Chr2 44381119 44383882 +
Pte Pte1g02042 Chr1 41523867 41525572 +
Pumo Pumo6g00578 Chr6 7338894 7343231 +
Pumo Pumo10g01816 Chr10 23872349 23874904 -
Pvu Pvu2g2891 Chr2 44487105 44490185 -
Pvu Pvu9g1662 Chr9 23312039 23314113 -
Rops Rops2g00674 Chr2 9588312 9591923 +
Rops Rops10g00872 Chr10 19733177 19734594 -
Seca Seca4g01801 Chr4 29658690 29660762 +
Spst Spst3g01198 Chr3 15525370 15525846 +
Spst Spst9g01781 Chr9 20082605 20084341 +
Ssu Ssu3g0244 Chr3 4364514 4368053 +
Trre Trre5g04755 Chr5 49380658 49381940 +
Vian Vian1g03749 Chr1 60361779 60365122 -
Vimu Vimu11g04296 Chr11 64321144 64321620 -
Viun Viun3g00700 Chr3 4347736 4352111 +
Viun Viun9g01597 Chr9 23608570 23610508 +
Vivi Vivi3g02256 Chr3 37181479 37182935 +
Vra Vra4g1214 Chr4 19096208 19099616 -
Vvi Vvi1g1580 Chr1 22579786 22583532 +
Bva Bva05g00104 Chr05 525184 527861 +
Lasa Lasa6g05046 Chr6 683417088 683442551 +
Phco Phco6g03240 Chr6 52814526 52816606 +
Pste Pste4g00008 Chr4 69967 70658 -
Pvu Pvu7g0003 Chr7 20696 22847 -
Spst Spst10g01751 Chr10 17893045 17894613 +
Sto Sto3g2520 Chr3 29246851 29259479 +
Bva Bva05g00103 Chr05 522496 523054 +
Cca Cca07g02357 Chr07 52158938 52162730 -
Lal Lal6g1644 Chr6 19205330 19207783 -
Ssu Ssu3g0244 Chr3 4364514 4368053 +
Vra Vra4g1214 Chr4 19096208 19099616 -
Glsi Glsi02g0482 Chr02 3071301 3072363 -
Vivi Vivi3g02256 Chr3 37181479 37182935 +
Arst Arst3g03863 Chr3 109536695 109538976 +
Lapu Lapu9g00913 Chr9 13696490 13698526 -
Lasa Lasa5g03497 Chr5 568115033 568115991 -
Lja Lja4g0503 Chr4 4110477 4111860 +
Mepo Mepo3g06943 Chr3 83077093 83078993 -
Mesa Mesa9g04474 Chr9 78136949 78138574 -
Phac Phac9g02673 Chr9 25341047 25343070 -
Phco Phco7g01897 Chr7 22595755 22597747 +
Pste Pste2g00225 Chr2 1282192 1284212 -
Pte Pte1g02042 Chr1 41523867 41525572 +
Pumo Pumo10g01816 Chr10 23872349 23874904 -
Pvu Pvu9g1662 Chr9 23312039 23314113 -
Rops Rops10g00872 Chr10 19733177 19734594 -
Seca Seca4g01801 Chr4 29658690 29660762 +
Spst Spst9g01781 Chr9 20082605 20084341 +
Trre Trre5g04755 Chr5 49380658 49381940 +
Viun Viun9g01597 Chr9 23608570 23610508 +
Vivi Vivi3g02256 Chr3 37181479 37182935 +
Arst Arst3g03850 Chr3 109387647 109395437 +
Bach Bach2g02315 Chr2 29676050 29682365 +
Lapu Lapu9g00916 Chr9 13751634 13760724 -
Lasa Lasa5g03501 Chr5 568743766 568749180 -
Mal Mal7g4841 Chr7 116873497 116879712 -
Mepo Mepo3g06946 Chr3 83096775 83104714 -
Mesa Mesa9g04494 Chr9 78470966 78477062 -
Mtr Mtr8g3380 Chr8 44287210 44294823 -
Phco Phco7g01892 Chr7 22433759 22441884 +
Psa Psa7g0903 Chr7 68349002 68355578 +
Pste Pste2g00234 Chr2 1401112 1409547 -
Pte Pte3g00116 Chr3 1122780 1128838 -
Pte Pte1g02041 Chr1 41511070 41518498 +
Pumo Pumo10g01823 Chr10 23956238 23963347 -
Pvu Pvu9g1666 Chr9 23396369 23402117 -
Rops Rops10g00867 Chr10 19681298 19691115 +
Seca Seca4g01795 Chr4 29622749 29630770 +
Tpr Tpr3g0726 Chr3 6988574 6996213 +
Trre Trre5g04750 Chr5 49338488 49344041 +
Tsu Tsu02g00552 Chr02 4673473 4678991 +
Vimu Vimu10g01636 Chr10 20790760 20801410 +
Viun Viun9g01587 Chr9 23435836 23444147 +
Vivi Vivi3g02253 Chr3 37085029 37092403 +
Adu Adu03g02917 Chr03 110605013 110609016 -
Arst Arst3g03849 Chr3 109309856 109314525 -
Bisa Bisa08g1646 Chr08 38426867 38428482 -
Dere Dere03g0530 Chr03 9253386 9254558 +
Lasa Lasa7g04631 Chr7 674103340 674105538 +
Lja Lja4g0500 Chr4 4086729 4089837 -
Mal Mal7g4843 Chr7 116919609 116921601 +
Mepo Mepo2g04528 Chr2 53705533 53707751 +
Mesa Mesa13g00594 Chr13 7048765 7050632 -
Mtr Mtr8g3381 Chr8 44309325 44311569 +
Phac Phac2g04241 Chr2 41025299 41027242 +
Phco Phco4g03200 Chr4 52722277 52724233 +
Psa Psa7g0902 Chr7 68270755 68273095 -
Pste Pste3g01298 Chr3 8145603 8148097 -
Pumo Pumo6g00574 Chr6 7235430 7236167 -
Pvu Pvu2g2898 Chr2 44542507 44544591 +
Rops Rops2g00668 Chr2 9462455 9464830 -
Seca Seca12g06386 Chr12 155866271 155868528 +
Tpr Tpr3g0725 Chr3 6972578 6975181 -
Trre Trre7g05319 Chr7 59398027 59400428 +
Tsu Tsu02g00551 Chr02 4660899 4663334 -
Vian Vian1g03753 Chr1 60450008 60452271 +
Vifa Vifa6g03400 Chr6 1115831112 1115833459 +
Vimu Vimu11g04308 Chr11 64446272 64448081 +
Viun Viun3g00693 Chr3 4293209 4294987 -
Vivi Vivi5g05730 Chr5 160842252 160844955 +