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
Vvi2g0182 Acco11g1483 . Accr9g00959 . Adu03g02616 . . . . Aev03g3163 . Ahy13g2674 . Aip03g03017 Alju09g1484 . . . . Apr2g1290 Arst3g03473 . . . Bisa11g0818 . . Bva11g02235 . Car06g00425 . . . . . Dod04g2847 Enph13g1507 . Glsi05g2212 . . . . Gma08g00230 . . . . . . Lal23g0495 . . . . . . . . . Lapu3g03676 . . . Lele49g0758 Lele50g0801 Lele51g0782 Lele52g0787 . . . . Lja4g0321 Lja4g0321 . Mal7g5063 Mepo2g04747 . Mesa13g00372 . Mibi12g1259 . . Mtr8g3572 . . Phco4g03404 . Prci10g1232 . . . Pste3g00774 . . . . . Pumo6g00394 . Pvu2g3087 . Rops2g00439 . Seca12g06608 . . . . . Sto6g3090 . . Tpr3g0540 Trre7g05584 . . Tsu02g00351 Vian1g03921 . Vifa6g03717 . Vimu11g04542 . Viun3g00440 . Vivi5g06084 . . .
Vvi2g0183 Acco11g1480 . Accr9g00961 . Adu03g02614 . . . . Aev03g3165 . Ahy13g2672 . Aip03g03015 Alju09g1482 . . . . Apr2g1292 Arst3g03471 . Bach4g00032 . Bisa11g0815 . Bva08g00033 . . Car06g00423 . . Dere09g0065 . . Dod04g2849 Enph13g1509 . Glsi05g2214 . . . Gma05g02126 . . . . . . . . . Lal16g1141 . . . . . . . Lapu3g03678 . . . Lele49g0760 Lele50g0802 Lele51g0784 Lele52g0788 . . . . Lja4g0319 Lja4g0319 . Mal7g5065 Mepo2g04749 . Mesa13g00369 . Mibi12g1257 . . Mtr8g3574 . . Phco4g03406 . Prci10g1234 . . . Pste3g00770 . . . . . Pumo6g00392 . Pvu2g3089 . Rops2g00437 . Seca12g06610 . Spst3g00987 . . . Sto6g3089 . . Tpr3g0538 Trre7g05587 . . Tsu02g00349 Vian1g03923 . . . Vimu11g04544 . Viun3g00438 . Vivi5g06086 . . .
Vvi2g0184 Acco11g1478 . Accr9g00962 . . . . . . Aev03g3166 . Ahy13g2670 . Aip03g03012 Alju09g1480 . . Amo13g3243 . Apr2g1293 . . Bach4g00031 . Bisa11g0813 . Bva08g00032 Bva11g02237 . Car06g00422 . . Dere09g0062 . . Dod04g2850 Enph13g1510 . Glsi05g2216 . . . Gma05g02127 Gma08g00234 . . . . . . . Lal15g1457 Lal16g1140 . . . . . . . Lapu3g03679 . . . Lele49g0762 Lele50g0803 Lele51g0785 Lele52g0789 . . . . Lja4g0318 Lja4g0318 . Mal7g5067 Mepo2g04750 . Mesa13g00367 . Mibi12g1255 . . Mtr8g3575 . . Phco4g03407 . Prci10g1235 . . . Pste3g00765 . Pte14g01322 Pte12g00016 . . . . Pvu2g3090 . . . . . Spst3g00986 . . . Sto6g3088 . . Tpr3g0537 Trre7g05589 . . Tsu02g00347 . . . . Vimu11g04547 . . . Vivi5g06087 . . .
Vvi2g0185 . . . . . . . . . . . . . . . . . . . Apr2g1294 . . . . . . . . . Car06g00421 . . . . . . . . . . . . Gma05g02128 Gma08g00235 . . . . . . . Lal15g1458 . . . . . . . . . . . . . . . . . . . . Lja4g0317 Lja4g0317 . Mal7g5068 Mepo2g04754 . Mesa13g00363 . . . . Mtr8g3576 . . Phco4g03408 . . . . Psa7g0546 Pste3g00764 . . . . . . . Pvu2g3091 . . . . . Spst3g00985 . . . . . . Tpr3g0536 Trre7g05590 . . Tsu02g00346 . . . . Vimu11g04548 . . . . . . .
Vvi2g0186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3087 . . . . . . . . . . . . . . . . . . .
Vvi2g0187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal15g0030 . . . . . Lan18g1154 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0182 Chr2 1624485 1627665 +
Acco Acco11g1483 Chr11 29347437 29351783 -
Accr Accr9g00959 Chr9 11184054 11185874 +
Adu Adu03g02616 Chr03 90663759 90665568 -
Aev Aev03g3163 Chr03 30093114 30094391 +
Ahy Ahy13g2674 Chr13 97737455 97738866 -
Aip Aip03g03017 Chr03 90243498 90244845 -
Alju Alju09g1484 Chr09 38864636 38866487 -
Apr Apr2g1290 Chr2 19132928 19135163 +
Arst Arst3g03473 Chr3 89603693 89605394 -
Bisa Bisa11g0818 Chr11 23370115 23378401 -
Bva Bva11g02235 Chr11 18073056 18075031 +
Car Car06g00425 Chr06 4392152 4395090 -
Dod Dod04g2847 Chr04 52378370 52380711 +
Enph Enph13g1507 Chr13 20540171 20544009 +
Glsi Glsi05g2212 Chr05 68333713 68338797 +
Gma Gma08g00230 Chr08 1967171 1973351 +
Lal Lal23g0495 Chr23 7676389 7679870 +
Lapu Lapu3g03676 Chr3 60232379 60234720 +
Lele Lele49g0758 Chr49 4597900 4599809 +
Lele Lele50g0801 Chr50 4923829 4926037 +
Lele Lele51g0782 Chr51 4721306 4722967 +
Lele Lele52g0787 Chr52 4970108 4971909 +
Lja Lja4g0321 Chr4 2582216 2585003 -
Lja Lja4g0321 Chr4 2582216 2585003 -
Mal Mal7g5063 Chr7 119787432 119792016 +
Mepo Mepo2g04747 Chr2 55734217 55737657 +
Mesa Mesa13g00372 Chr13 4386535 4389900 -
Mibi Mibi12g1259 Chr12 28185423 28187093 -
Mtr Mtr8g3572 Chr8 46283734 46287484 +
Phco Phco4g03404 Chr4 54339292 54341144 +
Prci Prci10g1232 Chr10 8104606 8107182 +
Pste Pste3g00774 Chr3 4813148 4816406 -
Pumo Pumo6g00394 Chr6 5074444 5076362 -
Pvu Pvu2g3087 Chr2 46256666 46258825 +
Rops Rops2g00439 Chr2 6337396 6339484 -
Seca Seca12g06608 Chr12 158178714 158181283 +
Sto Sto6g3090 Chr6 37884622 37886066 -
Tpr Tpr3g0540 Chr3 5418716 5422158 -
Trre Trre7g05584 Chr7 61391614 61393901 +
Tsu Tsu02g00351 Chr02 2956490 2959450 -
Vian Vian1g03921 Chr1 62303246 62305321 +
Vifa Vifa6g03717 Chr6 1220128458 1220130423 +
Vimu Vimu11g04542 Chr11 66242465 66244588 +
Viun Viun3g00440 Chr3 2655601 2657999 -
Vivi Vivi5g06084 Chr5 165921003 165923348 -
Vvi Vvi2g0183 Chr2 1628619 1630021 +
Acco Acco11g1480 Chr11 29342243 29343346 -
Accr Accr9g00961 Chr9 11205094 11206197 +
Adu Adu03g02614 Chr03 90652756 90654307 -
Aev Aev03g3165 Chr03 30098471 30099586 +
Ahy Ahy13g2672 Chr13 97722839 97724325 -
Aip Aip03g03015 Chr03 90231744 90232835 -
Alju Alju09g1482 Chr09 38858707 38859810 -
Apr Apr2g1292 Chr2 19143536 19144819 +
Arst Arst3g03471 Chr3 89592308 89594146 -
Bach Bach4g00032 Chr4 247845 249008 -
Bisa Bisa11g0815 Chr11 23363253 23364296 -
Bva Bva08g00033 Chr08 180659 181906 -
Car Car06g00423 Chr06 4385419 4386738 -
Dere Dere09g0065 Chr09 3568324 3569406 +
Dod Dod04g2849 Chr04 52384358 52385827 +
Enph Enph13g1509 Chr13 20555684 20556775 +
Glsi Glsi05g2214 Chr05 68349881 68350897 +
Gma Gma05g02126 Chr05 42456338 42457733 +
Lal Lal16g1141 Chr16 7782019 7783128 -
Lapu Lapu3g03678 Chr3 60238996 60240160 +
Lele Lele49g0760 Chr49 4602941 4604047 +
Lele Lele50g0802 Chr50 4927467 4928573 +
Lele Lele51g0784 Chr51 4726016 4727122 +
Lele Lele52g0788 Chr52 4981126 4982232 +
Lja Lja4g0319 Chr4 2576054 2577679 -
Lja Lja4g0319 Chr4 2576054 2577679 -
Mal Mal7g5065 Chr7 119800929 119801990 +
Mepo Mepo2g04749 Chr2 55755422 55757485 +
Mesa Mesa13g00369 Chr13 4369296 4370396 -
Mibi Mibi12g1257 Chr12 28179006 28180097 -
Mtr Mtr8g3574 Chr8 46294464 46295977 +
Phco Phco4g03406 Chr4 54349994 54351034 +
Prci Prci10g1234 Chr10 8110748 8112193 +
Pste Pste3g00770 Chr3 4800778 4801710 -
Pumo Pumo6g00392 Chr6 5065590 5067030 -
Pvu Pvu2g3089 Chr2 46265359 46266690 +
Rops Rops2g00437 Chr2 6325574 6326945 -
Seca Seca12g06610 Chr12 158188456 158189505 +
Spst Spst3g00987 Chr3 13328173 13329189 -
Sto Sto6g3089 Chr6 37879561 37880670 -
Tpr Tpr3g0538 Chr3 5408650 5410969 -
Trre Trre7g05587 Chr7 61403431 61404519 +
Tsu Tsu02g00349 Chr02 2950618 2951931 -
Vian Vian1g03923 Chr1 62313025 62314050 +
Vimu Vimu11g04544 Chr11 66250826 66252609 +
Viun Viun3g00438 Chr3 2649763 2651237 -
Vivi Vivi5g06086 Chr5 165951839 165953168 +
Vvi Vvi2g0184 Chr2 1638274 1640084 -
Acco Acco11g1478 Chr11 29336933 29338705 +
Accr Accr9g00962 Chr9 11212390 11214144 -
Aev Aev03g3166 Chr03 30105016 30106716 -
Ahy Ahy13g2670 Chr13 97195998 97198051 +
Aip Aip03g03012 Chr03 89745715 89748422 +
Alju Alju09g1480 Chr09 38851243 38852999 +
Amo Amo13g3243 Chr13 101895488 101898206 -
Apr Apr2g1293 Chr2 19149271 19151611 -
Bach Bach4g00031 Chr4 244450 246778 +
Bisa Bisa11g0813 Chr11 23355314 23357108 +
Bva Bva08g00032 Chr08 177818 180142 +
Bva Bva11g02237 Chr11 18077876 18079959 -
Car Car06g00422 Chr06 4379244 4381969 +
Dere Dere09g0062 Chr09 3562575 3564321 +
Dod Dod04g2850 Chr04 52394714 52397857 -
Enph Enph13g1510 Chr13 20561849 20564643 -
Glsi Glsi05g2216 Chr05 68352504 68354250 -
Gma Gma05g02127 Chr05 42459463 42461258 -
Gma Gma08g00234 Chr08 1983704 1986458 -
Lal Lal15g1457 Chr15 16789061 16791543 -
Lal Lal16g1140 Chr16 7774937 7778088 +
Lapu Lapu3g03679 Chr3 60243732 60246922 -
Lele Lele49g0762 Chr49 4606935 4608848 -
Lele Lele50g0803 Chr50 4932187 4933995 -
Lele Lele51g0785 Chr51 4729733 4731508 -
Lele Lele52g0789 Chr52 4986492 4988306 -
Lja Lja4g0318 Chr4 2571214 2574330 +
Lja Lja4g0318 Chr4 2571214 2574330 +
Mal Mal7g5067 Chr7 119807177 119809433 -
Mepo Mepo2g04750 Chr2 55762399 55765417 -
Mesa Mesa13g00367 Chr13 4349629 4352178 +
Mibi Mibi12g1255 Chr12 28172655 28174429 +
Mtr Mtr8g3575 Chr8 46304052 46307082 -
Phco Phco4g03407 Chr4 54354511 54356338 -
Prci Prci10g1235 Chr10 8116942 8119186 -
Pste Pste3g00765 Chr3 4785904 4788444 +
Pte Pte14g01322 Chr14 34412873 34414898 -
Pte Pte12g00016 Chr12 270571 273167 +
Pvu Pvu2g3090 Chr2 46269760 46272244 -
Spst Spst3g00986 Chr3 13319820 13321628 +
Sto Sto6g3088 Chr6 37874339 37876050 +
Tpr Tpr3g0537 Chr3 5401768 5404654 +
Trre Trre7g05589 Chr7 61414813 61417199 -
Tsu Tsu02g00347 Chr02 2940970 2944484 +
Vimu Vimu11g04547 Chr11 66255915 66257620 -
Vivi Vivi5g06087 Chr5 165967228 165969713 -
Vvi Vvi2g0185 Chr2 1643880 1646636 +
Apr Apr2g1294 Chr2 19156980 19160143 +
Car Car06g00421 Chr06 4369861 4374197 +
Gma Gma05g02128 Chr05 42466076 42470042 +
Gma Gma08g00235 Chr08 1993200 1997032 +
Lal Lal15g1458 Chr15 16803365 16806865 +
Lja Lja4g0317 Chr4 2563470 2567116 -
Lja Lja4g0317 Chr4 2563470 2567116 -
Mal Mal7g5068 Chr7 119819543 119822722 +
Mepo Mepo2g04754 Chr2 55779888 55781175 +
Mesa Mesa13g00363 Chr13 4300756 4303392 -
Mtr Mtr8g3576 Chr8 46317668 46321238 +
Phco Phco4g03408 Chr4 54362635 54365597 +
Psa Psa7g0546 Chr7 37018653 37022519 +
Pste Pste3g00764 Chr3 4773129 4781967 -
Pvu Pvu2g3091 Chr2 46276020 46279427 +
Spst Spst3g00985 Chr3 13311670 13314982 -
Tpr Tpr3g0536 Chr3 5391394 5395124 -
Trre Trre7g05590 Chr7 61428812 61432905 +
Tsu Tsu02g00346 Chr02 2929986 2933416 -
Vimu Vimu11g04548 Chr11 66261557 66265225 +
Vvi Vvi2g0186 Chr2 1653905 1657439 +
Sto Sto6g3087 Chr6 37850281 37855532 -
Vvi Vvi2g0187 Chr2 1662924 1666932 +
Vvi Vvi2g0188 Chr2 1667929 1673179 +
Vvi Vvi2g0189 Chr2 1675840 1677891 +
Vvi Vvi2g0190 Chr2 1682443 1686253 +
Lal Lal15g0030 Chr15 234390 239851 +
Lan Lan18g1154 Chr18 16360794 16366286 -
Vvi Vvi2g0191 Chr2 1686388 1688345 +
Lal Lal15g0030 Chr15 234390 239851 +