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
Vvi4g0294 . . . . . . . . . . . . . . . . . . . Apr9g0119 . . . . . . . . . Car04g03133 . . . . . . . . . . . . . . . . . . . . . . Lal8g1537 . . . . . . . . . . . . . . . . . . . . . . Mal1g5442 . . . . . . . Mtr1g0163 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0769 . . Tpr1g3327 . . . Tsu01g00753 . . . . . . . . . . . .
Vvi4g0295 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02463 . . . . . . . . . . . . . . . . . . . . . . . . Lal8g1541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0722 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0297 Acco10g2068 . Accr4g00726 . Adu08g02432 . . . . . . . . . Alju08g0740 . . . . Apr9g0121 Arst8g03343 . Bach12g00549 . Bisa09g1271 . . Bva06g02464 . Car04g03131 . . Dere04g0641 . . . Enph1g1431 . Glsi08g1520 . . . . . . . . . . . . . . . . . . . . . Lapu9g01822 . . . Lele01g0590 Lele02g0582 Lele03g0593 Lele04g0600 . . . . . . . . Mepo3g07512 . Mesa9g05188 . Mibi05g0661 . . . . . Phco7g00827 . Prci15g0921 . . . Pste2g01955 . . . . . Pumo10g00006 . Pvu9g1024 . Rops10g01476 . Seca4g00845 . Spst9g00857 . . . . . . . Trre5g05325 . . . Vian4g01907 . . . Vimu10g02852 . Viun9g02965 . . . . .
Vvi4g0298 . . . . . . . . . . . . . . . . . . . Apr9g0122 . . . . . . . Bva06g02465 . Car04g03128 . . . . . . . . . . . . . . . . . . Lal21g0360 . . . . . Lan3g1045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0299 . . . . . . . . . . . . . . . . . . . Apr9g0123 . . . . . . . Bva06g02466 . Car04g03127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g5439 . . . . . . . Mtr1g0161 . . . . . . . Psa6g0725 . . . . . . . . . . . . . . . . . . Sto5g0767 . . Tpr1g3321 . . . Tsu01g00758 . . . . . . . . . . . .
Vvi4g0300 . . . . . . . . . . . . . . . . . . . Apr9g0124 . . . . . . . . . Car04g03126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g5438 . . . . . . . Mtr1g0160 . . . . . . . Psa6g0726 . . . . . . . . . . . . . . . . . . Sto5g0766 . . Tpr1g3320 . . . Tsu01g00759 . . . . . . . . . . . .
Vvi4g0301 . . . . . . . . . . . . . . . . . . . Apr9g0125 . . . . . . . Bva06g02467 . Car04g03125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0765 . . . . . . . . . . . . . . . . . . .
Vvi4g0302 . . . . . . . . . . . . . . . . . . . Apr9g0126 . . . . . . . . . Car04g03124 . . . . . . . . . . . . Gma04g00677 Gma06g00671 . . . . . . Lal17g0264 . . . . . . . . . . . . . . . . . . . . . . . . Mal1g5433 Mepo3g05961 . . . . . . Mtr1g0158 Phac9g00492 . Phco7g00828 . . . . Psa6g0727 Pste2g01956 . . . . . Pumo10g00005 . Pvu9g1025 . Rops10g01477 . Seca4g00844 . Spst9g00864 . . . Sto5g0764 . . . . . . . Vian4g01906 . Vifa2g04092 . Vimu10g02851 . Viun9g02964 . Vivi3g01170 . . .
Vvi4g0303 . . . . . . . . . . . . . . . . . . . . Arst10g02703 . . . . . . Bva06g02503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu9g01798 . Lasa5g04199 . . . . . . . . . . . . . Mepo3g07542 . Mesa9g05228 . . . . . Phac9g00545 . Phco7g00862 . . . Psa5g0559 . Pste2g02038 . . . . . Pumo10g00883 . Pvu9g1054 . . . Seca4g00804 . Spst9g00896 . . . Sto5g0734 . . . Trre5g05366 . . . Vian4g01878 . Vifa2g04146 . Vimu10g02819 . Viun9g02922 . Vivi3g00023 . . .
   
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Select Species Gene Chromosome Start End Strand
Bva Bva06g02503 Chr06 15877171 15883595 -
Vvi Vvi4g0294 Chr4 2562906 2563700 +
Apr Apr9g0119 Chr9 1443135 1445374 +
Car Car04g03133 Chr04 59490601 59497889 -
Lal Lal8g1537 Chr8 19695520 19697085 +
Mal Mal1g5442 Chr1 128836713 128838489 -
Mtr Mtr1g0163 Chr1 1794434 1795893 -
Sto Sto5g0769 Chr5 5220407 5221153 -
Tpr Tpr1g3327 Chr1 37635333 37636497 -
Tsu Tsu01g00753 Chr01 6722398 6727238 +
Vvi Vvi4g0295 Chr4 2564468 2571005 +
Bva Bva06g02463 Chr06 15702811 15706984 +
Lal Lal8g1541 Chr8 19746978 19751467 -
Psa Psa6g0722 Chr6 25228548 25229724 +
Vvi Vvi4g0296 Chr4 2572213 2580989 -
Vvi Vvi4g0297 Chr4 2582532 2595257 +
Acco Acco10g2068 Chr10 33042846 33053648 +
Accr Accr4g00726 Chr4 6955462 6965421 -
Adu Adu08g02432 Chr08 40002630 40010451 -
Alju Alju08g0740 Chr08 5507665 5516898 -
Apr Apr9g0121 Chr9 1460158 1475275 -
Arst Arst8g03343 Chr8 44367783 44375510 -
Bach Bach12g00549 Chr12 3743209 3752261 +
Bisa Bisa09g1271 Chr09 18370658 18385378 +
Bva Bva06g02464 Chr06 15707533 15716159 +
Car Car04g03131 Chr04 59443111 59457747 -
Dere Dere04g0641 Chr04 6387730 6398455 +
Enph Enph1g1431 Chr1 39749819 39760532 +
Glsi Glsi08g1520 Chr08 11008859 11019179 -
Lapu Lapu9g01822 Chr9 33077597 33087188 -
Lele Lele01g0590 Chr01 3466867 3474474 -
Lele Lele02g0582 Chr02 3479632 3490421 -
Lele Lele03g0593 Chr03 3494618 3502274 -
Lele Lele04g0600 Chr04 3626093 3634127 -
Mepo Mepo3g07512 Chr3 88466616 88478996 +
Mesa Mesa9g05188 Chr9 86625050 86637042 +
Mibi Mibi05g0661 Chr05 6277935 6287129 -
Phco Phco7g00827 Chr7 6505009 6515961 +
Prci Prci15g0921 Chr15 5892575 5903608 -
Pste Pste2g01955 Chr2 19825755 19836181 +
Pumo Pumo10g00006 Chr10 568702 578156 -
Pvu Pvu9g1024 Chr9 15216636 15226686 +
Rops Rops10g01476 Chr10 28073720 28084924 +
Seca Seca4g00845 Chr4 13932644 13944833 -
Spst Spst9g00857 Chr9 7541422 7550560 +
Trre Trre5g05325 Chr5 54081556 54094198 +
Vian Vian4g01907 Chr4 35575800 35584497 -
Vimu Vimu10g02852 Chr10 39801871 39814250 -
Viun Viun9g02965 Chr9 37667293 37681423 -
Vvi Vvi4g0298 Chr4 2597499 2602256 +
Apr Apr9g0122 Chr9 1476774 1480457 +
Bva Bva06g02465 Chr06 15716699 15720166 +
Car Car04g03128 Chr04 59373980 59378090 -
Lal Lal21g0360 Chr21 2451473 2455216 -
Lan Lan3g1045 Chr3 22780011 22783591 +
Vvi Vvi4g0299 Chr4 2604513 2610678 -
Apr Apr9g0123 Chr9 1480851 1485430 -
Bva Bva06g02466 Chr06 15720167 15725674 -
Car Car04g03127 Chr04 59369390 59373771 +
Mal Mal1g5439 Chr1 128792857 128796250 +
Mtr Mtr1g0161 Chr1 1778235 1782223 +
Psa Psa6g0725 Chr6 25322239 25324894 -
Sto Sto5g0767 Chr5 5214507 5217345 +
Tpr Tpr1g3321 Chr1 37579430 37582314 +
Tsu Tsu01g00758 Chr01 6780208 6783148 -
Vvi Vvi4g0300 Chr4 2611970 2616442 -
Apr Apr9g0124 Chr9 1487121 1489897 -
Car Car04g03126 Chr04 59366006 59368691 +
Mal Mal1g5438 Chr1 128787527 128791568 +
Mtr Mtr1g0160 Chr1 1773754 1777586 +
Psa Psa6g0726 Chr6 25325060 25327555 -
Sto Sto5g0766 Chr5 5210645 5213101 +
Tpr Tpr1g3320 Chr1 37574935 37578936 +
Tsu Tsu01g00759 Chr01 6783873 6787749 -
Vvi Vvi4g0301 Chr4 2617436 2618111 +
Apr Apr9g0125 Chr9 1490597 1491597 +
Bva Bva06g02467 Chr06 15726528 15727454 +
Car Car04g03125 Chr04 59360551 59362096 -
Sto Sto5g0765 Chr5 5207568 5208313 -
Vvi Vvi4g0302 Chr4 2624577 2635494 -
Apr Apr9g0126 Chr9 1495220 1506178 -
Car Car04g03124 Chr04 59350938 59358927 +
Gma Gma04g00677 Chr04 6276503 6291421 -
Gma Gma06g00671 Chr06 6092899 6103663 -
Lal Lal17g0264 Chr17 1644379 1652679 -
Mal Mal1g5433 Chr1 128752316 128761020 +
Mepo Mepo3g05961 Chr3 73834012 73849647 +
Mtr Mtr1g0158 Chr1 1752129 1762930 +
Phac Phac9g00492 Chr9 3212256 3222320 -
Phco Phco7g00828 Chr7 6518838 6527419 -
Psa Psa6g0727 Chr6 25442116 25454535 -
Pste Pste2g01956 Chr2 19841426 19854587 -
Pumo Pumo10g00005 Chr10 556197 568106 +
Pvu Pvu9g1025 Chr9 15230856 15239408 -
Rops Rops10g01477 Chr10 28090538 28100690 -
Seca Seca4g00844 Chr4 13918304 13928806 +
Spst Spst9g00864 Chr9 7581193 7592982 -
Sto Sto5g0764 Chr5 5199054 5206606 +
Vian Vian4g01906 Chr4 35556065 35565581 +
Vifa Vifa2g04092 Chr2 1196628968 1196637546 -
Vimu Vimu10g02851 Chr10 39785218 39794977 +
Viun Viun9g02964 Chr9 37653590 37664724 +
Vivi Vivi3g01170 Chr3 19580376 19588927 +
Vvi Vvi4g0303 Chr4 2639956 2646313 -
Arst Arst10g02703 Chr10 92495956 92500465 +
Bva Bva06g02503 Chr06 15877171 15883595 -
Lapu Lapu9g01798 Chr9 32808779 32813244 +
Lasa Lasa5g04199 Chr5 639336277 639339694 -
Mepo Mepo3g07542 Chr3 88788967 88793292 -
Mesa Mesa9g05228 Chr9 87011363 87015171 -
Phac Phac9g00545 Chr9 3549953 3557719 -
Phco Phco7g00862 Chr7 6830033 6833908 -
Psa Psa5g0559 Chr5 45607906 45611755 +
Pste Pste2g02038 Chr2 20616687 20620813 -
Pumo Pumo10g00883 Chr10 11569500 11573682 -
Pvu Pvu9g1054 Chr9 15589405 15593387 -
Seca Seca4g00804 Chr4 13382435 13388147 +
Spst Spst9g00896 Chr9 7857171 7861306 -
Sto Sto5g0734 Chr5 4953363 4956383 +
Trre Trre5g05366 Chr5 54411063 54414677 -
Vian Vian4g01878 Chr4 35267743 35272674 +
Vifa Vifa2g04146 Chr2 1210312133 1210315223 -
Vimu Vimu10g02819 Chr10 39521504 39527215 +
Viun Viun9g02922 Chr9 37389338 37393267 +
Vivi Vivi3g00023 Chr3 272421 275570 -