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
Vvi1g1321 . . . . Adu10g00732 . . . . Aev03g1427 . Ahy20g1020 . Aip10g01076 . . . Amo20g0951 . . Arst10g00937 . . . . . Bva06g01774 Bva05g00023 . . . . . . . Dod04g0571 . . . . . . . Gma18g00096 . . . . . . . . . . . . . . . . . . Lasa5g02654 . . . . . . . . . . . . . Mepo3g06252 . Mesa9g03713 . . . Mtr3g2837 . . . Phco2g02946 . . . Psa5g2199 . Pste7g02367 . . . . . Pumo1g00421 . Pvu1g2667 . Rops11g03756 . Seca6g01754 . Spst1g01923 . . . . . Tpr2g4717 . Trre5g03165 . . . Vian2g03155 . Vifa2g02489 . Vimu6g01546 . Viun1g03420 . Vivi3g03309 . . .
Vvi1g1322 . . . . Adu10g00731 . . . . Aev03g1426 . Ahy20g1016 . Aip10g01075 . . . Amo20g0944 . . Arst10g00935 . . . . . Bva06g01773 . . . . . . . . Dod04g0572 . . . . . . . Gma18g00094 . . . . . . . . . . . . . . . . . . Lasa5g02651 . . . . . . . . . . . . . Mepo3g06251 . Mesa9g03712 . . . Mtr3g2836 . . . Phco2g02947 . . . . . Pste7g02369 . . Pte2g02699 . . Pumo1g00422 . Pvu1g2668 . Rops11g03754 . Seca6g01753 . Spst1g01922 . . . . . Tpr2g4716 . Trre5g03164 . . . Vian2g03156 . Vifa2g02488 . Vimu6g01545 . Viun1g03422 . Vivi3g03310 . . .
Vvi1g1323 . . . . . . . . . Aev03g2474 . Ahy13g4447 . Aip03g04932 . . . Amo13g5555 . . . . . . . . Bva06g01772 Bva05g00024 . . . . . . . Dod04g2000 . . . . . . Gma08g00939 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g4151 . . . . . . . Mtr8g2772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g1332 . . . Tsu02g01231 . . . . . . . . . . . .
Vvi1g1324 . . . . . . . . . Aev03g2475 . Ahy13g4448 . Aip03g04933 . . . Amo13g5552 . . . . . . . . Bva06g01771 . . . . . . . . Dod04g2001 . . . . . . Gma08g00940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g4153 . . . . . . . Mtr8g2773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g1331 . . . Tsu02g01230 . . . . . . . . . . . .
Vvi1g1325 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma08g00942 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g4154 . . . . . . . Mtr8g2774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g1330 . . . Tsu02g01229 . . . . . . . . . . . .
Vvi1g1328 Acco04g0152 . Accr8g02398 . . . . . . Aev03g2477 . Ahy13g4449 . Aip03g04934 Alju06g0176 . . Amo13g5551 . . . . . . Bisa08g0269 . Bva06g01770 Bva05g00025 . . . . Dere03g1882 . . Dod04g0574 Enph6g0961 . Glsi12g2699 . . . . Gma18g00093 . . . . . . . . . . . . . . . . . . Lasa5g02649 . Lele21g0129 Lele22g0131 Lele23g1922 Lele24g0121 . . . . . . . . Mepo3g06250 . Mesa9g03708 . Mibi09g2301 . Mtr3g2834 . . . Phco2g02949 . Prci4g0219 . . . Pste7g02370 . . . . . Pumo1g00424 . Pvu1g2670 . Rops11g03753 . Seca6g01750 . Spst1g01920 . . . Sto3g2919 . Tpr2g4704 . Trre5g03160 . . . Vian2g03158 . Vifa2g02484 . Vimu6g01544 . Viun1g03425 . Vivi3g03316 . . .
Vvi1g1329 . . . . Adu10g00728 . . . . Aev03g1414 . Ahy20g1012 . Aip10g01072 . . . Amo20g0942 . . Arst10g00931 . . . . . Bva06g01769 Bva05g00026 . . . . . . . Dod04g0584 . . . . . . . Gma18g00092 . . . . . . . . . . . . . . . . Lapu6g00104 . Lasa5g02648 . . . . . . . . . . . . . Mepo3g06248 . Mesa9g03707 . . . Mtr3g2833 . . . Phco2g02950 . . . . . Pste7g02371 . . . . . Pumo1g00425 . Pvu1g2671 . Rops11g03752 . Seca6g01749 . . . . . . . Tpr2g4703 . Trre5g03158 . . . Vian2g03159 . Vifa2g02483 . Vimu6g01543 . Viun1g03426 . Vivi3g03318 . . .
Vvi1g1330 . . . . . . . . . Aev03g2478 . Ahy13g4450 . Aip03g04935 . . . Amo13g5549 . . . . . . . . . . . . . . . . . Dod04g0585 . . . . . . Gma08g00943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g4155 . . . . . . . Mtr8g2775 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g2916 . . Tpr3g1329 . . . Tsu02g01228 . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g1321 Chr1 19401890 19415232 -
Adu Adu10g00732 Chr10 9105827 9110957 +
Aev Aev03g1427 Chr03 14696903 14699626 +
Ahy Ahy20g1020 Chr20 15087136 15092439 +
Aip Aip10g01076 Chr10 14362380 14367649 +
Amo Amo20g0951 Chr20 15866219 15871898 +
Arst Arst10g00937 Chr10 8753077 8758222 +
Bva Bva06g01774 Chr06 12278476 12282455 +
Bva Bva05g00023 Chr05 111968 116542 -
Dod Dod04g0571 Chr04 8159539 8160633 -
Gma Gma18g00096 Chr18 759045 763334 +
Lasa Lasa5g02654 Chr5 495844180 495849444 +
Mepo Mepo3g06252 Chr3 76665788 76671672 +
Mesa Mesa9g03713 Chr9 68763450 68768132 +
Mtr Mtr3g2837 Chr3 42359149 42364424 +
Phco Phco2g02946 Chr2 58374740 58379014 -
Psa Psa5g2199 Chr5 173216166 173222383 -
Pste Pste7g02367 Chr7 22374144 22380964 -
Pumo Pumo1g00421 Chr1 5883843 5889227 -
Pvu Pvu1g2667 Chr1 51413288 51418655 -
Rops Rops11g03756 Chr11 71255369 71259931 +
Seca Seca6g01754 Chr6 72523817 72528053 +
Spst Spst1g01923 Chr1 27509847 27514368 +
Tpr Tpr2g4717 Chr2 52550947 52556983 +
Trre Trre5g03165 Chr5 27220932 27226638 +
Vian Vian2g03155 Chr2 52041883 52046093 -
Vifa Vifa2g02489 Chr2 653997429 654002166 +
Vimu Vimu6g01546 Chr6 14495151 14499131 +
Viun Viun1g03420 Chr1 41279967 41284811 -
Vivi Vivi3g03309 Chr3 55924241 55930031 -
Vvi Vvi1g1322 Chr1 19418638 19449374 -
Adu Adu10g00731 Chr10 9062773 9071847 +
Aev Aev03g1426 Chr03 14673543 14693401 +
Ahy Ahy20g1016 Chr20 15017709 15027409 +
Aip Aip10g01075 Chr10 14292823 14302173 +
Amo Amo20g0944 Chr20 15765349 15775123 +
Arst Arst10g00935 Chr10 8709965 8719274 +
Bva Bva06g01773 Chr06 12269047 12277875 +
Dod Dod04g0572 Chr04 8168235 8181467 -
Gma Gma18g00094 Chr18 740998 751122 +
Lasa Lasa5g02651 Chr5 495534385 495543232 +
Mepo Mepo3g06251 Chr3 76654063 76663502 +
Mesa Mesa9g03712 Chr9 68751082 68760570 +
Mtr Mtr3g2836 Chr3 42346655 42356324 +
Phco Phco2g02947 Chr2 58388042 58400115 -
Pste Pste7g02369 Chr7 22406661 22421667 -
Pte Pte2g02699 Chr2 45877724 45886247 -
Pumo Pumo1g00422 Chr1 5900796 5911075 -
Pvu Pvu1g2668 Chr1 51425356 51435643 -
Rops Rops11g03754 Chr11 71240599 71252688 +
Seca Seca6g01753 Chr6 72483179 72503843 +
Spst Spst1g01922 Chr1 27492754 27509818 +
Tpr Tpr2g4716 Chr2 52536845 52546731 +
Trre Trre5g03164 Chr5 27202902 27211493 +
Vian Vian2g03156 Chr2 52046340 52063605 -
Vifa Vifa2g02488 Chr2 652974242 652987334 +
Vimu Vimu6g01545 Chr6 14469644 14482207 +
Viun Viun1g03422 Chr1 41299812 41309986 -
Vivi Vivi3g03310 Chr3 55940606 55949288 -
Vvi Vvi1g1323 Chr1 19466437 19474945 +
Aev Aev03g2474 Chr03 25785757 25788884 +
Ahy Ahy13g4447 Chr13 144570148 144573605 +
Aip Aip03g04932 Chr03 133911625 133914961 +
Amo Amo13g5555 Chr13 157104495 157107913 -
Bva Bva06g01772 Chr06 12262547 12267669 -
Bva Bva05g00024 Chr05 116909 121646 +
Dod Dod04g2000 Chr04 43456035 43459111 +
Gma Gma08g00939 Chr08 7916312 7924582 +
Mal Mal7g4151 Chr7 108315927 108319609 +
Mtr Mtr8g2772 Chr8 38379580 38383765 +
Tpr Tpr3g1332 Chr3 11795059 11799234 -
Tsu Tsu02g01231 Chr02 10456425 10460646 -
Vvi Vvi1g1324 Chr1 19480236 19483305 +
Aev Aev03g2475 Chr03 25792638 25794656 +
Ahy Ahy13g4448 Chr13 144589933 144593718 +
Aip Aip03g04933 Chr03 133933574 133937333 +
Amo Amo13g5552 Chr13 157060905 157064290 -
Bva Bva06g01771 Chr06 12255940 12259697 -
Dod Dod04g2001 Chr04 43466048 43469931 +
Gma Gma08g00940 Chr08 7931334 7935107 +
Mal Mal7g4153 Chr7 108326422 108329098 +
Mtr Mtr8g2773 Chr8 38392567 38396495 +
Tpr Tpr3g1331 Chr3 11786704 11790621 -
Tsu Tsu02g01230 Chr02 10446848 10450592 -
Vvi Vvi1g1325 Chr1 19487523 19493345 +
Vvi Vvi1g1326 Chr1 19493811 19493984 -
Vvi Vvi1g1327 Chr1 19494496 19495470 -
Gma Gma08g00942 Chr08 7940285 7941199 -
Mal Mal7g4154 Chr7 108331856 108334947 -
Mtr Mtr8g2774 Chr8 38400697 38402215 -
Tpr Tpr3g1330 Chr3 11781762 11783638 +
Tsu Tsu02g01229 Chr02 10442582 10444142 +
Vvi Vvi1g1328 Chr1 19500264 19509123 +
Acco Acco04g0152 Chr04 1239758 1240194 +
Accr Accr8g02398 Chr8 47589759 47591964 -
Aev Aev03g2477 Chr03 25801833 25807116 +
Ahy Ahy13g4449 Chr13 144607024 144610645 +
Aip Aip03g04934 Chr03 133945030 133948656 +
Alju Alju06g0176 Chr06 1352944 1355060 +
Amo Amo13g5551 Chr13 157048912 157052681 -
Bisa Bisa08g0269 Chr08 4872125 4875645 +
Bva Bva06g01770 Chr06 12249640 12254369 -
Bva Bva05g00025 Chr05 122348 126194 +
Dere Dere03g1882 Chr03 30649444 30652582 +
Dod Dod04g0574 Chr04 8252504 8257472 +
Enph Enph6g0961 Chr6 12433156 12436438 +
Glsi Glsi12g2699 Chr12 40519114 40521855 -
Gma Gma18g00093 Chr18 730311 734604 -
Lasa Lasa5g02649 Chr5 495469658 495475114 -
Lele Lele21g0129 Chr21 808012 810557 +
Lele Lele22g0131 Chr22 757544 760126 +
Lele Lele23g1922 Chr23 22350628 22353850 -
Lele Lele24g0121 Chr24 768859 771440 +
Mepo Mepo3g06250 Chr3 76634964 76640303 -
Mesa Mesa9g03708 Chr9 68706896 68711601 -
Mibi Mibi09g2301 Chr09 42497317 42499859 -
Mtr Mtr3g2834 Chr3 42328526 42333673 -
Phco Phco2g02949 Chr2 58404373 58408529 +
Prci Prci4g0219 Chr4 1488223 1491347 +
Pste Pste7g02370 Chr7 22453610 22460907 +
Pumo Pumo1g00424 Chr1 5922224 5929204 +
Pvu Pvu1g2670 Chr1 51440567 51444783 +
Rops Rops11g03753 Chr11 71224504 71232430 -
Seca Seca6g01750 Chr6 72407068 72413604 -
Spst Spst1g01920 Chr1 27459585 27463929 -
Sto Sto3g2919 Chr3 33882728 33892560 -
Tpr Tpr2g4704 Chr2 52420135 52421411 -
Trre Trre5g03160 Chr5 27088730 27094109 -
Vian Vian2g03158 Chr2 52082522 52086442 +
Vifa Vifa2g02484 Chr2 651782497 651788202 -
Vimu Vimu6g01544 Chr6 14460409 14464343 -
Viun Viun1g03425 Chr1 41317286 41321865 +
Vivi Vivi3g03316 Chr3 56005165 56011379 +
Vvi Vvi1g1329 Chr1 19509675 19511554 -
Adu Adu10g00728 Chr10 8985946 8988086 +
Aev Aev03g1414 Chr03 14517117 14529587 +
Ahy Ahy20g1012 Chr20 14972732 14974855 +
Aip Aip10g01072 Chr10 14250880 14253024 +
Amo Amo20g0942 Chr20 15720458 15722288 +
Arst Arst10g00931 Chr10 8633207 8635304 +
Bva Bva06g01769 Chr06 12248150 12249139 +
Bva Bva05g00026 Chr05 126691 128491 -
Dod Dod04g0584 Chr04 8376656 8379132 -
Gma Gma18g00092 Chr18 725420 727285 +
Lapu Lapu6g00104 Chr6 790745 792845 +
Lasa Lasa5g02648 Chr5 495438964 495439935 +
Mepo Mepo3g06248 Chr3 76627111 76628899 +
Mesa Mesa9g03707 Chr9 68698466 68700245 +
Mtr Mtr3g2833 Chr3 42319846 42321704 +
Phco Phco2g02950 Chr2 58410930 58412550 -
Pste Pste7g02371 Chr7 22466272 22468251 -
Pumo Pumo1g00425 Chr1 5931496 5933620 -
Pvu Pvu1g2671 Chr1 51446788 51448998 -
Rops Rops11g03752 Chr11 71220405 71222273 +
Seca Seca6g01749 Chr6 72405109 72406693 +
Tpr Tpr2g4703 Chr2 52417024 52418889 +
Trre Trre5g03158 Chr5 27053290 27054593 +
Vian Vian2g03159 Chr2 52096711 52098130 -
Vifa Vifa2g02483 Chr2 651761815 651763010 +
Vimu Vimu6g01543 Chr6 14455866 14457315 +
Viun Viun1g03426 Chr1 41323778 41325933 -
Vivi Vivi3g03318 Chr3 56020279 56022015 -
Vvi Vvi1g1330 Chr1 19528631 19532161 +
Aev Aev03g2478 Chr03 25813699 25819205 +
Ahy Ahy13g4450 Chr13 144626336 144632270 +
Aip Aip03g04935 Chr03 133961658 133967720 +
Amo Amo13g5549 Chr13 157012883 157018597 -
Dod Dod04g0585 Chr04 8401939 8410601 +
Gma Gma08g00943 Chr08 7955356 7961488 +
Mal Mal7g4155 Chr7 108353340 108359226 +
Mtr Mtr8g2775 Chr8 38419783 38426601 +
Sto Sto3g2916 Chr3 33835390 33841133 -
Tpr Tpr3g1329 Chr3 11770092 11776313 -
Tsu Tsu02g01228 Chr02 10386600 10393280 -
Aev Aev03g2478 Chr03 25813699 25819205 +
Ahy Ahy13g4450 Chr13 144626336 144632270 +
Aip Aip03g04935 Chr03 133961658 133967720 +
Amo Amo13g5549 Chr13 157012883 157018597 -
Dod Dod04g0585 Chr04 8401939 8410601 +
Gma Gma08g00943 Chr08 7955356 7961488 +