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
Vvi2g0522 . . . . Adu05g00967 . Aed11g1665 . Aev05g0917 . Ahy15g0944 . Aip05g00973 . . . . . Apr7g0645 . Arst5g01201 . . . . . . Bva11g02042 Car08g00265 . Cca06g01738 . . . Dod02g1025 . . . . . Gma01g02144 Gma11g00262 . . Gso1g1813 Gso1g1813 . . Lal15g0282 . . . . . Lan18g0885 . . . . . Lapu2g00314 . Lasa2g02841 . . . . . . . . . Lja2g0054 . Mal6g1640 . Mepo5g00424 . Mesa17g00426 . . . Mtr5g0358 . . . Phco4g00382 . . . Psa2g4111 . Pste1g00677 . Pte14g01224 . . . Pumo8g02250 . Pvu2g1564 . Rops1g02115 . Seca10g00409 . Spst2g00369 . Ssu2g2793 . . . Tpr2g3816 . Trre9g00452 . Tsu05g00335 . Vian10g00327 . Vifa1g07797 . Vimu7g02511 . Viun2g02494 . Vivi2g03775 . Vra11g0334 .
Vvi2g0523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0526 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g00252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0527 . . . . . . . . . . . . . . . . . . . Apr10g1449 . . . . . . . . . . . . . . . . . . . . . Gma11g00263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0528 . . . . . . Aed11g1664 Aed6g0496 Aev05g0916 . Ahy15g0945 . Aip05g00974 . . . . . Apr7g0646 . . . . . . . Bva08g00253 . Car08g00266 . Cca06g01737 Cca11g01660 . . Dod02g1024 . . . . . Gma01g01485 . Gma05g00516 Gma17g01271 Gso1g1228 . Gso1g1228 Gso1g1228 Lal15g0281 Lal16g0344 . . . . Lan18g0886 Lan18g0886 . . . . . . . . . . . . . . . . . . Mal6g1638 . . . . . . . Mtr5g0360 . . . . Phco8g00725 . . . . . . . . . . . Pumo4g01620 . Pvu3g2229 . . . . . Spst3g04352 Ssu2g2792 Ssu6g1571 . . Tpr2g3814 . . . Tsu05g00337 . . . . . . Vimu11g00086 . . . . Vra11g0335 Vra7g1418
Vvi2g0529 . . . . . . . Aed6g0497 . . . Ahy11g1401 . Aip01g01514 . . . . . . . . . . . . . Bva11g02040 . . . Cca11g01658 . . . . . . . . . . Gma05g00517 Gma17g01272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00726 . . . . . . . . . . . Pumo4g01621 . Pvu3g2230 . Rops2g04224 . Seca12g01887 . . . Ssu6g1572 . . . . . . . . . Vian1g01369 . . . Vimu11g00087 . Viun3g04215 . . . Vra7g1417
Vvi2g0530 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g02039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g4108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0531 . . . . Adu05g00969 Adu02g02274 Aed11g1663 . Aev05g0915 . Ahy15g0946 . Aip05g00975 . . . . . Apr7g0647 Apr10g1450 Arst5g01203 Arst2g02949 Bach4g00217 Bach6g00795 . . Bva08g00254 Bva11g02038 Car08g00267 . Cca06g01736 . . . Dod02g1023 . . . . . Gma01g01484 Gma11g00264 . . Gso1g1227 Gso1g1227 . . Lal15g0280 Lal16g0343 . . . . Lan18g0887 Lan18g0887 . . . . Lapu2g00316 Lapu10g01529 Lasa2g02843 . . . . . . . . . Lja2g0056 . Mal6g1637 . Mepo5g00427 Mepo1g03566 . Mesa29g04091 . . Mtr5g0362 . Phac2g00550 . Phco4g00385 Phco1g00938 . . Psa2g4106 . Pste1g00686 Pste6g02380 Pte14g01219 . . . Pumo8g02248 Pumo7g01011 Pvu2g1562 Pvu10g0888 Rops1g02112 Rops4g01294 Seca10g00413 Seca4g11111 Spst2g00373 Spst4g01686 Ssu2g2791 . Sto6g3326 . Tpr2g3813 . Trre9g00454 Trre15g01360 Tsu05g00338 . . Vian9g00821 Vifa1g07792 Vifa4g00734 . Vimu9g00546 Viun2g02491 Viun10g01666 Vivi2g03773 Vivi7g04651 Vra11g0336 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0522 Chr2 4494764 4500109 +
Adu Adu05g00967 Chr05 12423606 12424934 +
Aed Aed11g1665 Chr11 20462510 20465877 -
Aev Aev05g0917 Chr05 6480758 6481994 -
Ahy Ahy15g0944 Chr15 14139709 14141740 +
Aip Aip05g00973 Chr05 13650020 13651383 +
Apr Apr7g0645 Chr7 13169469 13171964 +
Arst Arst5g01201 Chr5 12462067 12468607 +
Bva Bva11g02042 Chr11 17194379 17196356 -
Car Car08g00265 Chr08 2111397 2113466 +
Cca Cca06g01738 Chr06 32696408 32699421 -
Dod Dod02g1025 Chr02 12926808 12928666 -
Gma Gma01g02144 Chr01 56775510 56777706 -
Gma Gma11g00262 Chr11 2069852 2072188 +
Gso Gso1g1813 Chr1 54952265 54954543 -
Gso Gso1g1813 Chr1 54952265 54954543 -
Lal Lal15g0282 Chr15 1912946 1916171 -
Lan Lan18g0885 Chr18 14148358 14150877 +
Lapu Lapu2g00314 Chr2 2572335 2575277 +
Lasa Lasa2g02841 Chr2 512281654 512282511 +
Lja Lja2g0054 Chr2 419691 422545 +
Mal Mal6g1640 Chr6 30363503 30365921 -
Mepo Mepo5g00424 Chr5 3719234 3722490 +
Mesa Mesa17g00426 Chr17 4883826 4886498 +
Mtr Mtr5g0358 Chr5 3301484 3305300 +
Phco Phco4g00382 Chr4 2481125 2482928 +
Psa Psa2g4111 Chr2 419457808 419460047 -
Pste Pste1g00677 Chr1 2135000 2137165 +
Pte Pte14g01224 Chr14 33546243 33548909 -
Pumo Pumo8g02250 Chr8 59650932 59653143 -
Pvu Pvu2g1564 Chr2 29285616 29288487 -
Rops Rops1g02115 Chr1 42389110 42392513 -
Seca Seca10g00409 Chr10 3568579 3571934 +
Spst Spst2g00369 Chr2 2877971 2885496 +
Ssu Ssu2g2793 Chr2 88810453 88812851 -
Tpr Tpr2g3816 Chr2 41010509 41014191 -
Trre Trre9g00452 Chr9 3219835 3223250 +
Tsu Tsu05g00335 Chr05 2462070 2463745 +
Vian Vian10g00327 Chr10 2959264 2961381 +
Vifa Vifa1g07797 Chr1 1218494838 1218496035 -
Vimu Vimu7g02511 Chr7 21393192 21393886 +
Viun Viun2g02494 Chr2 31363585 31365729 -
Vivi Vivi2g03775 Chr2 149010759 149012531 -
Vra Vra11g0334 Chr11 2394064 2396752 +
Vvi Vvi2g0523 Chr2 4501278 4502162 +
Vvi Vvi2g0524 Chr2 4502567 4502952 -
Vvi Vvi2g0525 Chr2 4503160 4503855 +
Vvi Vvi2g0526 Chr2 4510366 4510884 +
Bva Bva08g00252 Chr08 1213480 1215083 +
Vvi Vvi2g0527 Chr2 4511891 4531803 +
Apr Apr10g1449 Chr10 26868752 26878907 +
Gma Gma11g00263 Chr11 2081311 2090520 +
Lja Lja2g0055 Chr2 429782 438956 +
Vvi Vvi2g0528 Chr2 4534247 4534992 +
Aed Aed11g1664 Chr11 20449461 20459069 -
Aed Aed6g0496 Chr6 4287142 4288748 -
Aev Aev05g0916 Chr05 6468807 6475661 -
Ahy Ahy15g0945 Chr15 14165401 14173175 +
Aip Aip05g00974 Chr05 13666660 13674165 +
Apr Apr7g0646 Chr7 13182284 13191461 +
Bva Bva08g00253 Chr08 1217588 1226216 +
Car Car08g00266 Chr08 2118581 2126759 +
Cca Cca06g01737 Chr06 32676147 32685401 -
Cca Cca11g01660 Chr11 40612382 40618052 +
Dod Dod02g1024 Chr02 12905797 12916302 -
Gma Gma01g01485 Chr01 50080269 50095744 -
Gma Gma05g00516 Chr05 4944974 4949459 -
Gma Gma17g01271 Chr17 11246067 11249469 -
Gso Gso1g1228 Chr1 48377092 48393097 -
Gso Gso1g1228 Chr1 48377092 48393097 -
Gso Gso1g1228 Chr1 48377092 48393097 -
Lal Lal15g0281 Chr15 1900710 1908445 -
Lal Lal16g0344 Chr16 2076478 2085347 -
Lan Lan18g0886 Chr18 14156322 14168366 +
Lan Lan18g0886 Chr18 14156322 14168366 +
Mal Mal6g1638 Chr6 30327906 30349354 -
Mtr Mtr5g0360 Chr5 3331715 3340357 +
Phco Phco8g00725 Chr8 7248493 7254117 -
Pumo Pumo4g01620 Chr4 20437577 20444538 -
Pvu Pvu3g2229 Chr3 43242034 43247476 -
Spst Spst3g04352 Chr3 95159362 95163620 +
Ssu Ssu2g2792 Chr2 88790700 88799521 -
Ssu Ssu6g1571 Chr6 25871808 25876207 -
Tpr Tpr2g3814 Chr2 40990517 40998681 -
Tsu Tsu05g00337 Chr05 2474020 2482943 +
Vimu Vimu11g00086 Chr11 790424 797661 -
Vra Vra11g0335 Chr11 2402894 2413037 +
Vra Vra7g1418 Chr7 31421802 31426264 +
Vvi Vvi2g0529 Chr2 4535846 4538675 +
Aed Aed6g0497 Chr6 4290438 4290836 +
Ahy Ahy11g1401 Chr11 53964883 53966071 -
Aip Aip01g01514 Chr01 50903655 50904677 -
Bva Bva11g02040 Chr11 17190000 17191685 -
Cca Cca11g01658 Chr11 40576818 40577416 +
Gma Gma05g00517 Chr05 4965726 4966097 -
Gma Gma17g01272 Chr17 11257728 11258117 -
Phco Phco8g00726 Chr8 7260659 7261102 -
Pumo Pumo4g01621 Chr4 20457887 20458285 -
Pvu Pvu3g2230 Chr3 43251925 43252368 -
Rops Rops2g04224 Chr2 76794874 76795353 -
Seca Seca12g01887 Chr12 21966215 21966682 -
Ssu Ssu6g1572 Chr6 25885412 25885858 -
Vian Vian1g01369 Chr1 14928921 14941946 -
Vimu Vimu11g00087 Chr11 802267 802716 -
Viun Viun3g04215 Chr3 49814972 49815439 +
Vra Vra7g1417 Chr7 31416004 31416453 +
Vvi Vvi2g0530 Chr2 4544176 4558601 +
Bva Bva11g02039 Chr11 17179861 17188089 -
Psa Psa2g4108 Chr2 419402048 419410175 -
Vvi Vvi2g0531 Chr2 4564098 4565006 -
Adu Adu05g00969 Chr05 12457146 12458445 -
Adu Adu02g02274 Chr02 87660349 87662049 +
Aed Aed11g1663 Chr11 20445382 20446263 +
Aev Aev05g0915 Chr05 6462667 6463596 +
Ahy Ahy15g0946 Chr15 14175902 14177879 -
Aip Aip05g00975 Chr05 13677577 13678155 -
Apr Apr7g0647 Chr7 13195292 13196200 -
Apr Apr10g1450 Chr10 26888777 26889694 -
Arst Arst5g01203 Chr5 12500128 12501958 -
Arst Arst2g02949 Chr2 87121883 87123558 +
Bach Bach4g00217 Chr4 1412005 1412904 -
Bach Bach6g00795 Chr6 5914323 5915240 -
Bva Bva08g00254 Chr08 1228533 1229426 -
Bva Bva11g02038 Chr11 17177021 17177926 +
Car Car08g00267 Chr08 2131486 2133216 -
Cca Cca06g01736 Chr06 32670967 32672382 +
Dod Dod02g1023 Chr02 12899695 12900642 +
Gma Gma01g01484 Chr01 50070232 50071676 +
Gma Gma11g00264 Chr11 2096157 2097395 -
Gso Gso1g1227 Chr1 48368741 48370500 +
Gso Gso1g1227 Chr1 48368741 48370500 +
Lal Lal15g0280 Chr15 1896048 1896947 +
Lal Lal16g0343 Chr16 2072003 2073745 +
Lan Lan18g0887 Chr18 14175424 14177042 -
Lan Lan18g0887 Chr18 14175424 14177042 -
Lapu Lapu2g00316 Chr2 2598084 2598983 -
Lapu Lapu10g01529 Chr10 26414160 26415089 +
Lasa Lasa2g02843 Chr2 512398829 512399794 -
Lja Lja2g0056 Chr2 441769 443713 -
Mal Mal6g1637 Chr6 30316955 30317929 +
Mepo Mepo5g00427 Chr5 3761777 3763033 -
Mepo Mepo1g03566 Chr1 41479288 41480879 +
Mesa Mesa29g04091 Chr29 67129833 67130756 +
Mtr Mtr5g0362 Chr5 3348704 3350454 -
Phac Phac2g00550 Chr2 2754154 2756794 -
Phco Phco4g00385 Chr4 2508155 2509712 -
Phco Phco1g00938 Chr1 9439755 9440684 -
Psa Psa2g4106 Chr2 419359361 419362253 +
Pste Pste1g00686 Chr1 2158389 2159189 -
Pste Pste6g02380 Chr6 11609286 11610206 -
Pte Pte14g01219 Chr14 33532647 33533525 +
Pumo Pumo8g02248 Chr8 59602251 59603169 +
Pumo Pumo7g01011 Chr7 18703698 18705482 -
Pvu Pvu2g1562 Chr2 29246342 29248011 +
Pvu Pvu10g0888 Chr10 31769921 31771591 +
Rops Rops1g02112 Chr1 42361846 42362712 +
Rops Rops4g01294 Chr4 34335697 34336617 +
Seca Seca10g00413 Chr10 3602483 3603373 -
Seca Seca4g11111 Chr4 249487093 249488013 +
Spst Spst2g00373 Chr2 2908617 2909516 -
Spst Spst4g01686 Chr4 56593239 56594171 +
Ssu Ssu2g2791 Chr2 88778904 88779785 +
Sto Sto6g3326 Chr6 39400093 39409872 -
Tpr Tpr2g3813 Chr2 40982561 40984284 +
Trre Trre9g00454 Chr9 3243345 3244313 -
Trre Trre15g01360 Chr15 10554507 10555427 -
Tsu Tsu05g00338 Chr05 2488951 2489919 -
Vian Vian9g00821 Chr9 12201978 12202904 +
Vifa Vifa1g07792 Chr1 1217472711 1217473679 +
Vifa Vifa4g00734 Chr4 213343860 213344798 -
Vimu Vimu9g00546 Chr9 6586549 6587481 -
Viun Viun2g02491 Chr2 31340674 31342288 +
Viun Viun10g01666 Chr10 31569241 31570924 +
Vivi Vivi2g03773 Chr2 148966619 148972595 +
Vivi Vivi7g04651 Chr7 118316461 118318068 -
Vra Vra11g0336 Chr11 2416875 2418827 -
Gma Gma05g00516 Chr05 4944974 4949459 -