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
Vvi3g0883 . . . . . . Aed1g2048 . Aev09g2438 . Ahy19g3357 . Aip09g03825 . . . Amo19g4243 . Apr8g2387 . . . . . . . . . Car04g01385 . Cca02g02465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g0622 . . . . . . . Mtr1g3991 . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0545 . . Sto10g0395 . Tpr1g0518 . . . Tsu01g04664 . . . . . . . . . . . .
Vvi3g0884 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto13g2585 . . . . . . . . . . . . . . . . . .
Vvi3g0886 . . . . Adu09g02570 . Aed1g2049 . Aev09g2437 . Ahy19g3360 . Aip09g03826 . . . . . . . Arst9g03400 . . . . . . . Car04g01384 . Cca02g02464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02246 . Lasa6g04378 . . . . . . . . . . . . . Mepo4g04487 . . . . . . . . . Phco6g02718 . . . Psa6g4827 . . . . Pte9g01339 . . . . Pvu7g0488 . Rops6g03019 . Seca8g07653 . Spst10g01221 . . . . Sto10g0397 . . Trre1g05732 . . . Vian3g00442 . Vifa3g03250 . Vimu3g03319 . . . Vivi1g04022 . . .
Vvi3g0887 . . . . . Adu05g01339 Aed1g2050 . . Aev05g1242 . Ahy15g1309 . Aip05g01380 . . . . Apr8g2386 . . Arst5g01712 . . . . . . Car04g01383 . Cca02g02463 Cca06g02024 . . . Dod02g1385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g00048 . . Psa6g4817 . . . . . . Pte19g00455 . . . Pvu2g0513 . Rops1g02450 . Seca10g00066 . . . . . Sto10g0398 . . . . . . . . . Vifa3g03251 . . . . . . . Vra11g0051
Vvi3g0888 . . . . Adu09g02567 . Aed1g2051 . Aev09g2436 . Ahy19g3364 . Aip09g03829 . . . . . . . Arst9g03397 . . . . . . . Car04g01382 . Cca02g02462 . . . Dod06g0526 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa6g04377 . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g4816 . . . . . . . . . Pvu7g0489 . Rops6g03018 . . . Spst10g01220 . . . . Sto10g0401 . . . . . . . . Vifa3g03249 . Vimu3g03316 . Viun7g03543 . Vivi1g04025 . . .
Vvi3g0889 . . . . . Adu05g01338 . Aed11g1939 . Aev05g1241 . Ahy15g1306 . Aip05g01377 . . . . . . . Arst5g01709 . . . . Bva13g00431 Bva14g00516 . Car08g00041 . Cca06g02023 . . . Dod02g1383 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g02535 . . . . . . . . . . . . . Mepo5g00049 . Mesa17g00045 . . . . . . . Phco4g00049 . . . . . . . . . Pte19g00456 . Pumo8g02586 . Pvu2g0512 . Rops1g02449 . Seca10g00067 . Spst2g00051 . Ssu2g3138 Sto2g0469 Sto10g0402 . . . Trre9g00049 . . . . . Vifa1g04019 . . . Viun2g02911 . Vivi2g04244 . Vra11g0052
Vvi3g0890 . . . . Adu09g02566 . . . Aev09g2435 Aev05g1240 Ahy19g3365 Ahy15g1305 Aip09g03830 Aip05g01376 . . Amo19g4238 . Apr8g2385 . Arst9g03396 . . . . . . Bva14g00517 Car04g01379 . Cca02g02461 Cca06g02022 . . Dod06g0527 Dod02g1382 . . . . . . . . . . . . . . . . Lal12g0368 . . . . . . . . . Lasa6g04375 . . . . . . . . . Lja5g0470 . . Mal1g0625 Mepo4g04485 . Mesa1g04911 . . . . Mtr1g3988 . . Phco6g02716 . . . . . Pste4g01339 . . Pte9g01337 . . Pumo3g00707 . Pvu7g0492 . . . Seca8g07651 . Spst10g01219 . Ssu7g0546 Ssu2g3136 . . . Tpr1g0522 Trre1g05730 . . Tsu01g04662 Vian3g00445 . Vifa3g03245 . Vimu3g03314 . Viun7g03539 . Vivi1g04046 . . .
Vvi3g0891 . . . . Adu09g02565 . Aed1g2053 . Aev09g2434 Aev05g0758 Ahy19g3366 Ahy15g0517 Aip09g03831 Aip05g00516 . . Amo19g4237 . Apr8g2384 . Arst9g03395 . . . . . . Bva14g00518 Car04g01362 . Cca02g02460 . . . Dod06g0528 Dod02g0836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g0486 . . . . . . . . . . . . . Phco6g02715 . . . . . . . . . . . Pumo3g00709 . Pvu7g0493 . Rops6g03015 . . . Spst10g01218 . Ssu7g0547 . Sto2g0426 . . . . . . . . . . . Vimu3g03313 . Viun7g03537 . . . . .
Vvi3g0892 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vifa Vifa3g03251 Chr3 928894403 928895117 -
Vvi Vvi3g0883 Chr3 8744237 8744878 +
Aed Aed1g2048 Chr1 17215873 17216790 +
Aev Aev09g2438 Chr09 26364425 26365186 -
Ahy Ahy19g3357 Chr19 156485320 156486204 -
Aip Aip09g03825 Chr09 144843506 144844291 -
Amo Amo19g4243 Chr19 159172254 159182574 +
Apr Apr8g2387 Chr8 34160293 34160958 -
Car Car04g01385 Chr04 14095852 14096556 -
Cca Cca02g02465 Chr02 45798894 45799945 -
Mal Mal1g0622 Chr1 7162311 7163024 +
Mtr Mtr1g3991 Chr1 51527006 51527719 -
Ssu Ssu7g0545 Chr7 10088319 10088840 +
Sto Sto10g0395 Chr10 3188168 3192621 -
Tpr Tpr1g0518 Chr1 4376878 4377576 +
Tsu Tsu01g04664 Chr01 54000594 54001310 -
Vvi Vvi3g0884 Chr3 8763803 8765911 -
Vvi Vvi3g0885 Chr3 8766129 8766881 -
Sto Sto13g2585 Chr13 31958612 31961181 +
Vvi Vvi3g0886 Chr3 8776002 8776646 +
Adu Adu09g02570 Chr09 113243717 113244505 +
Aed Aed1g2049 Chr1 17227172 17227909 +
Aev Aev09g2437 Chr09 26359281 26359937 -
Ahy Ahy19g3360 Chr19 156506151 156506942 -
Aip Aip09g03826 Chr09 144858869 144859660 -
Arst Arst9g03400 Chr9 111140501 111141307 +
Car Car04g01384 Chr04 14091775 14092476 -
Cca Cca02g02464 Chr02 45769217 45769909 -
Lapu Lapu7g02246 Chr7 38796149 38796892 +
Lasa Lasa6g04378 Chr6 637568364 637569074 -
Mepo Mepo4g04487 Chr4 54642158 54642902 +
Phco Phco6g02718 Chr6 48690147 48694662 -
Psa Psa6g4827 Chr6 420989293 420990326 +
Pte Pte9g01339 Chr9 34803356 34804033 -
Pvu Pvu7g0488 Chr7 3862712 3863884 +
Rops Rops6g03019 Chr6 53234453 53235139 -
Seca Seca8g07653 Chr8 173840919 173849472 -
Spst Spst10g01221 Chr10 12981664 12982443 -
Sto Sto10g0397 Chr10 3198973 3200677 -
Trre Trre1g05732 Chr1 62291718 62292248 +
Vian Vian3g00442 Chr3 4159100 4159843 -
Vifa Vifa3g03250 Chr3 928783373 928784086 -
Vimu Vimu3g03319 Chr3 46661412 46661796 +
Vivi Vivi1g04022 Chr1 85035623 85036563 +
Vvi Vvi3g0887 Chr3 8793246 8793890 +
Adu Adu05g01339 Chr05 20164393 20165180 -
Aed Aed1g2050 Chr1 17232034 17232573 +
Aev Aev05g1242 Chr05 8734388 8735101 -
Ahy Ahy15g1309 Chr15 21346437 21347516 -
Aip Aip05g01380 Chr05 20592766 20593725 -
Apr Apr8g2386 Chr8 34156317 34156844 -
Arst Arst5g01712 Chr5 20212736 20213737 -
Car Car04g01383 Chr04 14086031 14086726 -
Cca Cca02g02463 Chr02 45765662 45766300 -
Cca Cca06g02024 Chr06 35467446 35468117 -
Dod Dod02g1385 Chr02 16679631 16680481 -
Phco Phco4g00048 Chr4 325669 327052 +
Psa Psa6g4817 Chr6 420004127 420005006 +
Pte Pte19g00455 Chr19 3693168 3693897 +
Pvu Pvu2g0513 Chr2 4634989 4635636 -
Rops Rops1g02450 Chr1 47357693 47358364 -
Seca Seca10g00066 Chr10 622755 623423 +
Sto Sto10g0398 Chr10 3213306 3215462 +
Vifa Vifa3g03251 Chr3 928894403 928895117 -
Vra Vra11g0051 Chr11 398022 398844 +
Vvi Vvi3g0888 Chr3 8820035 8820694 +
Adu Adu09g02567 Chr09 113230558 113231085 -
Aed Aed1g2051 Chr1 17233256 17233762 +
Aev Aev09g2436 Chr09 26356665 26357228 -
Ahy Ahy19g3364 Chr19 156531528 156532259 +
Aip Aip09g03829 Chr09 144881466 144881993 +
Arst Arst9g03397 Chr9 111127342 111127875 -
Car Car04g01382 Chr04 14079292 14079993 -
Cca Cca02g02462 Chr02 45761044 45761574 -
Dod Dod06g0526 Chr06 6369430 6370106 +
Lasa Lasa6g04377 Chr6 637440740 637441372 -
Psa Psa6g4816 Chr6 420001039 420001794 +
Pvu Pvu7g0489 Chr7 3876555 3877440 +
Rops Rops6g03018 Chr6 53222989 53227601 -
Spst Spst10g01220 Chr10 12966192 12966884 -
Sto Sto10g0401 Chr10 3240900 3244104 +
Vifa Vifa3g03249 Chr3 928396178 928396702 +
Vimu Vimu3g03316 Chr3 46630375 46631516 -
Viun Viun7g03543 Chr7 36888521 36889568 +
Vivi Vivi1g04025 Chr1 85155367 85157968 +
Vvi Vvi3g0889 Chr3 8825672 8827044 +
Adu Adu05g01338 Chr05 20047696 20049501 -
Aed Aed11g1939 Chr11 22141595 22142827 -
Aev Aev05g1241 Chr05 8722961 8724226 -
Ahy Ahy15g1306 Chr15 21244412 21246258 -
Aip Aip05g01377 Chr05 20493603 20495404 -
Arst Arst5g01709 Chr5 20096410 20097923 -
Bva Bva13g00431 Chr13 1992792 1993469 +
Bva Bva14g00516 Chr14 2488762 2490549 +
Car Car08g00041 Chr08 381066 382838 +
Cca Cca06g02023 Chr06 35461595 35463406 -
Dod Dod02g1383 Chr02 16652033 16653863 -
Lasa Lasa2g02535 Chr2 504171602 504172867 +
Mepo Mepo5g00049 Chr5 494391 496056 +
Mesa Mesa17g00045 Chr17 469875 471122 +
Phco Phco4g00049 Chr4 331924 333171 +
Pte Pte19g00456 Chr19 3696483 3699051 +
Pumo Pumo8g02586 Chr8 63069192 63071099 -
Pvu Pvu2g0512 Chr2 4625148 4626860 -
Rops Rops1g02449 Chr1 47336732 47338237 -
Seca Seca10g00067 Chr10 645448 646689 +
Spst Spst2g00051 Chr2 452314 453564 +
Ssu Ssu2g3138 Chr2 93479456 93480550 -
Sto Sto2g0469 Chr2 4051615 4052184 -
Sto Sto10g0402 Chr10 3250039 3251379 +
Trre Trre9g00049 Chr9 559007 560263 +
Vifa Vifa1g04019 Chr1 617408798 617410069 -
Viun Viun2g02911 Chr2 33408967 33410722 -
Vivi Vivi2g04244 Chr2 155999416 156001061 -
Vra Vra11g0052 Chr11 401744 403634 +
Vvi Vvi3g0890 Chr3 8828565 8830100 -
Adu Adu09g02566 Chr09 113227345 113230291 +
Aev Aev09g2435 Chr09 26353515 26355143 +
Aev Aev05g1240 Chr05 8719512 8721065 +
Ahy Ahy19g3365 Chr19 156532343 156535283 -
Ahy Ahy15g1305 Chr15 21241098 21243638 +
Aip Aip09g03830 Chr09 144882223 144885151 -
Aip Aip05g01376 Chr05 20490341 20492906 +
Amo Amo19g4238 Chr19 159093351 159093677 +
Apr Apr8g2385 Chr8 34151000 34154331 +
Arst Arst9g03396 Chr9 111124128 111127112 +
Bva Bva14g00517 Chr14 2491523 2494509 -
Car Car04g01379 Chr04 14065777 14068878 -
Cca Cca02g02461 Chr02 45754676 45757973 +
Cca Cca06g02022 Chr06 35450366 35459490 +
Dod Dod06g0527 Chr06 6370965 6374772 -
Dod Dod02g1382 Chr02 16648247 16648759 +
Lal Lal12g0368 Chr12 2625115 2627182 +
Lasa Lasa6g04375 Chr6 636906966 636908645 -
Lja Lja5g0470 Chr5 4133393 4136651 +
Mal Mal1g0625 Chr1 7180819 7182456 +
Mepo Mepo4g04485 Chr4 54619964 54623221 -
Mesa Mesa1g04911 Chr1 75989540 75991183 -
Mtr Mtr1g3988 Chr1 51511033 51514219 -
Phco Phco6g02716 Chr6 48676751 48682546 +
Pste Pste4g01339 Chr4 9871976 9875315 +
Pte Pte9g01337 Chr9 34788781 34791984 +
Pumo Pumo3g00707 Chr3 10505461 10508690 -
Pvu Pvu7g0492 Chr7 3887528 3891774 -
Seca Seca8g07651 Chr8 173832762 173836119 -
Spst Spst10g01219 Chr10 12961281 12962876 +
Ssu Ssu7g0546 Chr7 10096706 10098325 -
Ssu Ssu2g3136 Chr2 93444197 93445765 +
Tpr Tpr1g0522 Chr1 4389765 4391677 +
Trre Trre1g05730 Chr1 62281553 62283205 -
Tsu Tsu01g04662 Chr01 53985420 53988616 -
Vian Vian3g00445 Chr3 4190057 4191640 -
Vifa Vifa3g03245 Chr3 927713927 927715561 -
Vimu Vimu3g03314 Chr3 46623554 46627576 +
Viun Viun7g03539 Chr7 36843138 36847180 +
Vivi Vivi1g04046 Chr1 85836722 85839691 -
Vvi Vvi3g0891 Chr3 8842961 8844144 +
Adu Adu09g02565 Chr09 113224511 113225870 -
Aed Aed1g2053 Chr1 17252460 17253934 +
Aev Aev09g2434 Chr09 26349531 26350882 -
Aev Aev05g0758 Chr05 5313904 5315097 -
Ahy Ahy19g3366 Chr19 156536987 156538330 +
Ahy Ahy15g0517 Chr15 6221364 6223327 +
Aip Aip09g03831 Chr09 144887166 144888525 +
Aip Aip05g00516 Chr05 6039904 6046530 +
Amo Amo19g4237 Chr19 159089071 159090286 -
Apr Apr8g2384 Chr8 34147843 34149205 -
Arst Arst9g03395 Chr9 111121363 111122654 -
Bva Bva14g00518 Chr14 2496344 2497538 +
Car Car04g01362 Chr04 13911614 13913865 +
Cca Cca02g02460 Chr02 45751130 45752577 -
Dod Dod06g0528 Chr06 6377072 6378840 +
Dod Dod02g0836 Chr02 10782404 10784884 -
Lja Lja5g0486 Chr5 4247502 4249742 -
Phco Phco6g02715 Chr6 48675317 48676592 -
Pumo Pumo3g00709 Chr3 10511639 10513486 +
Pvu Pvu7g0493 Chr7 3893892 3895449 +
Rops Rops6g03015 Chr6 53175397 53176886 +
Spst Spst10g01218 Chr10 12956669 12958181 -
Ssu Ssu7g0547 Chr7 10102038 10103378 +
Sto Sto2g0426 Chr2 3695650 3697589 +
Vimu Vimu3g03313 Chr3 46618432 46619705 -
Viun Viun7g03537 Chr7 36837139 36838416 -
Vvi Vvi3g0892 Chr3 8872386 8873296 +
Sto Sto2g0426 Chr2 3695650 3697589 +