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
Vvi1g1291 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00316 . . Cca06g00087 . . . . . . . . . . . . . . . . . Lal6g1132 . . . . . Lan11g1150 . . . . . . Lapu2g01790 . . . . . . . . . . . . . . . Mepo4g01289 . . . . . . . . . . . . . . . Pste1g03745 . . Pte14g00578 . . Pumo8g00129 . Pvu3g0084 . Rops1g00320 . . . Spst2g02183 Ssu2g1042 . . Sto6g2533 . . . Trre1g01365 . . . Vian10g01846 . Vifa3g03809 . Vimu7g00418 . Viun2g00048 . Vivi4g03918 Vra11g1308 .
Vvi1g1292 . . . . . Adu10g03004 Aed11g1000 . . . . . . . . . . . . . . . . . . . . Bva11g00334 . . Cca06g00088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g01789 . . . . . . . . . . . . . . . Mepo4g01287 . . . . . . . . . . . . . . . Pste1g03741 . . . . . Pumo8g00844 . Pvu3g0086 . Rops1g00635 . Seca10g01925 . Spst2g02181 Ssu2g1043 . . Sto6g2505 . . . Trre1g01364 . . . . . Vifa1g09058 . Vimu7g00417 . . . Vivi4g03917 Vra11g1309 .
Vvi1g1293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1296 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1297 . . . . . Adu10g03005 Aed11g0992 . . . . . . . . . . . . . . . . . . . . Bva11g00336 . . Cca06g00093 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g01787 . . . . . . . . . . . . . . . Mepo4g01547 . . . . . . . . . . . . . . . Pste1g03732 . . . . . Pumo8g00133 . Pvu3g0088 . Rops1g00312 . Seca10g05285 . Spst2g02179 Ssu2g1045 . Sto11g1208 . . . . . . . . Vian10g01843 . Vifa1g03638 . Vimu7g00414 . Viun2g00042 . . Vra11g1313 .
Vvi1g1298 . . Accr8g00828 . Adu10g00753 . . . . . . Ahy20g1043 . Aip10g01101 Alju06g1853 . . . . . Arst10g00972 . . . . . Bva06g01784 . . . . . Dere03g0129 . . Dod04g0552 Enph6g0139 . Glsi02g0124 . . . . Gma18g00104 . . . . . . . . . . . . . . . . . . Lasa5g02662 . . Lele22g1326 Lele23g0698 Lele24g1284 . . . . . . . . Mepo3g06263 . Mesa9g03737 . Mibi09g0814 . Mtr3g2848 . . . Phco2g02935 . Prci4g2133 . Psa5g2186 . Pste7g02361 . . . . . Pumo1g00411 . Pvu1g2658 . Rops11g03767 . Seca6g01788 . Spst1g01932 . . . Sto3g2941 . Tpr2g4728 . Trre5g03180 . Tsu07g02254 . Vian2g03145 . Vifa2g02499 . Vimu6g01556 . Viun1g03402 . Vivi3g03291 . . .
Vvi1g1299 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01782 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1300 . . . . Adu10g00750 . . . . . . Ahy20g1040 . Aip10g01098 . . . . . . Arst10g00970 . . . . . . Bva05g00018 . . . . . . . Dod04g0555 . . . . . . . Gma18g00102 . . . . . . . . . . . . . . . . Lapu6g00114 . . . . . . . . . . . . . . . Mepo3g06261 . Mesa9g03736 . . . Mtr3g2846 . . . Phco2g02938 . . . Psa5g2188 . Pste7g02362 . . . . . Pumo1g00413 . Pvu1g2660 . Rops11g03765 . Seca6g01785 . Spst1g01930 . . . . . Tpr2g4726 . Trre5g03177 . . . Vian2g03147 . Vifa2g02497 . . . Viun1g03405 . Vivi3g03294 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Gma Gma18g00104 Chr18 822282 837170 +
Vvi Vvi1g1291 Chr1 19016601 19020259 +
Bva Bva11g00316 Chr11 6981679 6986524 +
Cca Cca06g00087 Chr06 2150236 2155060 +
Lal Lal6g1132 Chr6 8498408 8502395 -
Lan Lan11g1150 Chr11 15981526 15986572 +
Lapu Lapu2g01790 Chr2 31558137 31563413 -
Mepo Mepo4g01289 Chr4 16569708 16574456 -
Pste Pste1g03745 Chr1 18315459 18319807 -
Pte Pte14g00578 Chr14 26502342 26511002 -
Pumo Pumo8g00129 Chr8 2982960 2988242 +
Pvu Pvu3g0084 Chr3 791057 795813 +
Rops Rops1g00320 Chr1 8506500 8511378 -
Spst Spst2g02183 Chr2 20858321 20861800 -
Ssu Ssu2g1042 Chr2 48794852 48798928 +
Sto Sto6g2533 Chr6 32273416 32278467 -
Trre Trre1g01365 Chr1 10298233 10303106 -
Vian Vian10g01846 Chr10 30287305 30291292 -
Vifa Vifa3g03809 Chr3 1117734135 1117737851 +
Vimu Vimu7g00418 Chr7 4570408 4573820 -
Viun Viun2g00048 Chr2 1163475 1168286 -
Vivi Vivi4g03918 Chr4 159526418 159530803 +
Vra Vra11g1308 Chr11 16057933 16062886 +
Vvi Vvi1g1292 Chr1 19044379 19047780 -
Adu Adu10g03004 Chr10 106105716 106109270 +
Aed Aed11g1000 Chr11 15847599 15851307 -
Bva Bva11g00334 Chr11 7073540 7081160 -
Cca Cca06g00088 Chr06 2192433 2201133 -
Lapu Lapu2g01789 Chr2 31543830 31552771 +
Mepo Mepo4g01287 Chr4 16543874 16549349 +
Pste Pste1g03741 Chr1 18294977 18299848 +
Pumo Pumo8g00844 Chr8 32767957 32772662 +
Pvu Pvu3g0086 Chr3 801525 809030 -
Rops Rops1g00635 Chr1 16057537 16062431 +
Seca Seca10g01925 Chr10 21683066 21687562 -
Spst Spst2g02181 Chr2 20845141 20849250 +
Ssu Ssu2g1043 Chr2 48810849 48815202 -
Sto Sto6g2505 Chr6 31995699 31999389 +
Trre Trre1g01364 Chr1 10275017 10279514 +
Vifa Vifa1g09058 Chr1 1435020527 1435023025 +
Vimu Vimu7g00417 Chr7 4555961 4562701 +
Vivi Vivi4g03917 Chr4 159526418 159530803 +
Vra Vra11g1309 Chr11 16070380 16077736 -
Vvi Vvi1g1293 Chr1 19075968 19076365 -
Vvi Vvi1g1294 Chr1 19077121 19077378 -
Vvi Vvi1g1295 Chr1 19095938 19096241 -
Vvi Vvi1g1296 Chr1 19101044 19128698 +
Bva Bva11g00335 Chr11 7092411 7104791 +
Vvi Vvi1g1297 Chr1 19129886 19141980 -
Adu Adu10g03005 Chr10 106115844 106118682 +
Aed Aed11g0992 Chr11 15765071 15767713 -
Bva Bva11g00336 Chr11 7111390 7115204 -
Cca Cca06g00093 Chr06 2276082 2279974 +
Lapu Lapu2g01787 Chr2 31515602 31518951 -
Mepo Mepo4g01547 Chr4 20447893 20449819 -
Pste Pste1g03732 Chr1 18200353 18203600 -
Pumo Pumo8g00133 Chr8 3073536 3077236 +
Pvu Pvu3g0088 Chr3 845613 848824 +
Rops Rops1g00312 Chr1 8279806 8283928 -
Seca Seca10g05285 Chr10 120780892 120785062 +
Spst Spst2g02179 Chr2 20810967 20813835 -
Ssu Ssu2g1045 Chr2 48992379 48995976 +
Sto Sto11g1208 Chr11 11993988 11997773 +
Vian Vian10g01843 Chr10 30222385 30225261 -
Vifa Vifa1g03638 Chr1 560652321 560657780 +
Vimu Vimu7g00414 Chr7 4492073 4494919 -
Viun Viun2g00042 Chr2 1018459 1021727 -
Vra Vra11g1313 Chr11 16124849 16128127 +
Vvi Vvi1g1298 Chr1 19146130 19151985 -
Accr Accr8g00828 Chr8 16251038 16256345 -
Adu Adu10g00753 Chr10 9687974 9693638 +
Ahy Ahy20g1043 Chr20 15904805 15910524 +
Aip Aip10g01101 Chr10 15164504 15170009 +
Alju Alju06g1853 Chr06 39673951 39679070 +
Arst Arst10g00972 Chr10 9334848 9340602 +
Bva Bva06g01784 Chr06 12316022 12320634 +
Dere Dere03g0129 Chr03 4764749 4770258 +
Dod Dod04g0552 Chr04 7907757 7914675 -
Enph Enph6g0139 Chr6 4632881 4638675 +
Glsi Glsi02g0124 Chr02 836343 842487 +
Gma Gma18g00104 Chr18 822282 837170 +
Lasa Lasa5g02662 Chr5 496218737 496231204 +
Lele Lele22g1326 Chr22 18985479 18990359 +
Lele Lele23g0698 Chr23 5425914 5430261 -
Lele Lele24g1284 Chr24 18821684 18826743 +
Mepo Mepo3g06263 Chr3 76750847 76755332 +
Mesa Mesa9g03737 Chr9 69055965 69062565 +
Mibi Mibi09g0814 Chr09 11569600 11574848 -
Mtr Mtr3g2848 Chr3 42437464 42442395 +
Phco Phco2g02935 Chr2 58316440 58320921 -
Prci Prci4g2133 Chr4 33572937 33579349 +
Psa Psa5g2186 Chr5 172318463 172333126 -
Pste Pste7g02361 Chr7 22312125 22314748 -
Pumo Pumo1g00411 Chr1 5811609 5816542 -
Pvu Pvu1g2658 Chr1 51352545 51358985 -
Rops Rops11g03767 Chr11 71367561 71372710 +
Seca Seca6g01788 Chr6 73921688 73923226 +
Spst Spst1g01932 Chr1 27566888 27571842 +
Sto Sto3g2941 Chr3 34099461 34104737 +
Tpr Tpr2g4728 Chr2 52661960 52667444 +
Trre Trre5g03180 Chr5 27392795 27397354 +
Tsu Tsu07g02254 Chr07 25422784 25428042 -
Vian Vian2g03145 Chr2 51977797 51982593 -
Vifa Vifa2g02499 Chr2 656292081 656300884 +
Vimu Vimu6g01556 Chr6 14558402 14563139 +
Viun Viun1g03402 Chr1 41212133 41217379 -
Vivi Vivi3g03291 Chr3 55647059 55653470 -
Vvi Vvi1g1299 Chr1 19156487 19162102 -
Bva Bva06g01782 Chr06 12310463 12314808 +
Vvi Vvi1g1300 Chr1 19163776 19171811 -
Adu Adu10g00750 Chr10 9665171 9672460 +
Ahy Ahy20g1040 Chr20 15847103 15854683 +
Aip Aip10g01098 Chr10 15106970 15114685 +
Arst Arst10g00970 Chr10 9311894 9319315 +
Bva Bva05g00018 Chr05 81567 89194 -
Dod Dod04g0555 Chr04 7924429 7928714 -
Gma Gma18g00102 Chr18 805203 817700 +
Lapu Lapu6g00114 Chr6 878652 887206 +
Mepo Mepo3g06261 Chr3 76739015 76746908 +
Mesa Mesa9g03736 Chr9 69047060 69054208 +
Mtr Mtr3g2846 Chr3 42426612 42434585 +
Phco Phco2g02938 Chr2 58327125 58334669 -
Psa Psa5g2188 Chr5 172883578 172891823 -
Pste Pste7g02362 Chr7 22321320 22327567 -
Pumo Pumo1g00413 Chr1 5822518 5830026 -
Pvu Pvu1g2660 Chr1 51363898 51371708 -
Rops Rops11g03765 Chr11 71354007 71362799 +
Seca Seca6g01785 Chr6 73883577 73891548 +
Spst Spst1g01930 Chr1 27551573 27563003 +
Tpr Tpr2g4726 Chr2 52637635 52645525 +
Trre Trre5g03177 Chr5 27381242 27388568 +
Vian Vian2g03147 Chr2 51986476 51994038 -
Vifa Vifa2g02497 Chr2 656252986 656259545 +
Viun Viun1g03405 Chr1 41222005 41231079 -
Vivi Vivi3g03294 Chr3 55772632 55780005 -
Vifa Vifa1g03638 Chr1 560652321 560657780 +