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
Vvi2g0752 . . . . Adu05g00527 . Aed11g1526 . Aev05g0773 . Ahy15g0496 . Aip05g00502 . . . . . Apr7g0790 . Arst5g00661 . Bach4g00391 . . . Bva08g00455 Bva11g01863 Car08g00384 . Cca06g01584 . . . Dod02g0858 . . . . . Gma01g02014 Gma11g00396 . . Gso1g1703 Gso1g1703 . . . Lal16g0280 . . . . . . . . . . Lapu2g00457 . Lasa2g02996 . . . . . . . . . Lja2g0202 . Mal6g1455 . Mepo5g00586 . Mesa17g00611 . . . Mtr5g0520 . Phac2g00768 . Phco4g01242 . . . Psa2g3939 . . . . Pte12g00264 . . Pumo8g02080 . Pvu2g0074 . Rops1g01936 . Seca10g00588 . Spst2g00540 . Ssu2g2626 . . Sto11g1808 Tpr2g5616 . Trre9g00670 . Tsu05g00485 . Vian10g00471 . . . Vimu7g02688 . Viun2g02251 . Vivi2g03570 . Vra11g0475 .
Vvi2g0753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3538 . . . . . . . . . . . . . . . . . . .
Vvi2g0755 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g00456 Bva11g01862 Car08g00387 . . . . . . . . . . . Gma01g02013 Gma11g00397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0204 . . . . . . . . . . . . . . . . . Psa2g3936 . . . . . . . . . . . . . . . . . . . . Sto11g1807 . . . . . . . . . . . . . . . . . .
Vvi2g0756 Acco11g1246 . Accr9g01054 . Adu05g00081 Adu01g00669 Aed6g0195 Aed7g1483 Aev05g0121 . Ahy15g0076 . Aip05g00075 . Alju09g1257 . . . Apr7g1741 Apr3g0662 Arst5g00111 . Bach4g01008 Bach10g00821 Bisa11g2128 . Bva08g01169 Bva11g01268 . Car07g01902 Cca06g00945 Cca11g00789 Dere09g1409 . Dod02g0126 . Enph13g0012 . Glsi05g1009 . Gma01g00957 Gma09g01892 . . Gso1g0814 Gso1g0814 . . . Lal16g0475 . . . Lal23g1107 . . . . . . . . Lasa2g03796 Lasa4g01852 . Lele50g0985 . Lele52g0964 . . . . Lja2g0855 . Mal6g0723 Mal5g2729 Mepo5g01403 . Mesa17g01524 . Mibi12g1042 . Mtr5g1258 Mtr8g2068 Phac2g02242 Phac3g04447 Phco4g00489 Phco8g00148 Prci10g1508 . Psa2g3079 Psa4g2816 Pste1g01079 Pste7g00140 Pte14g00680 Pte12g00675 Pte14g00680 . Pumo8g01360 . Pvu2g1464 Pvu3g2939 Rops1g01232 Rops2g02862 Seca10g01335 Seca12g03579 Spst3g02679 . Ssu2g1922 Ssu5g0991 Sto6g4206 Sto11g1324 Tpr2g1503 . Trre9g01911 . Tsu05g01277 Tsu04g02970 . Vian1g02084 Vifa1g05784 Vifa4g01905 Vimu7g03526 Vimu7g03526 Viun2g01395 Viun3g03115 Vivi2g02361 . Vra11g1086 Vra7g0856
Vvi2g0757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0854 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g1323 . . . . . . . . . . . . . . . . . .
Vvi2g0758 Acco11g1247 . Accr9g01053 . Adu05g00083 . . . Aev05g0123 . Ahy15g0078 . Aip05g00077 . Alju09g1258 . . . Apr7g1742 . Arst5g00113 . Bach4g01006 . Bisa11g2127 . Bva08g01167 Bva11g01270 . . Cca06g00946 Cca11g00792 Dere09g1408 . Dod02g0128 . Enph13g0013 . Glsi05g1010 . Gma01g00956 Gma09g01894 . . Gso1g0813 Gso1g0813 . . . Lal16g0473 . . . Lal23g1111 . . . . . . Lapu2g00818 . Lasa2g03794 . Lele49g0928 Lele50g0984 Lele51g0945 Lele52g0963 . . . . Lja2g0853 . Mal6g0721 . Mepo5g01400 . . . Mibi12g1044 . Mtr5g1257 . Phac2g02239 . Phco4g00491 . Prci10g1507 . Psa2g3081 . Pste1g01070 . . Pte12g00674 . . Pumo8g01362 . Pvu2g1462 . Rops1g01233 . . . Spst3g02680 . Ssu2g1924 . Sto6g4205 . Tpr2g1501 . Trre9g01897 . Tsu05g01275 . . . Vifa1g05786 . Vimu11g02021 . Viun2g01397 . Vivi2g02363 . . Vra7g0854
Vvi2g0759 . . . . Adu05g00084 . . . . . Ahy15g0079 . Aip05g00078 . . . . . Apr7g1743 . Arst5g00114 . Bach4g01005 . . . Bva08g01166 . . . . . Dere09g1406 . Dod02g0130 . Enph13g0014 . Glsi05g1011 . Gma01g00954 . . . Gso1g0811 . . . Lal15g0414 Lal16g0471 . . . Lal23g1114 Lan18g0754 Lan18g0754 . . . Lan18g0754 Lapu2g00819 . Lasa2g03793 . . . . . . . . . Lja2g0852 . . . . . . . . . . . . . Phco4g00492 . . . Psa2g3091 . . . . . . . . . Pvu2g1461 . . . . . Spst3g02681 . . . Sto6g4202 . . . . . . . . . . . Vimu7g03523 . . . Vivi2g02364 . . .
Vvi2g0760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0761 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0752 Chr2 7304962 7308211 -
Adu Adu05g00527 Chr05 5567623 5570527 -
Aed Aed11g1526 Chr11 19527722 19531036 +
Aev Aev05g0773 Chr05 5409283 5411894 +
Ahy Ahy15g0496 Chr15 5973441 5976592 -
Aip Aip05g00502 Chr05 5780190 5783437 -
Apr Apr7g0790 Chr7 14853223 14856744 -
Arst Arst5g00661 Chr5 5593059 5595884 -
Bach Bach4g00391 Chr4 2600350 2602250 -
Bva Bva08g00455 Chr08 2337334 2340245 -
Bva Bva11g01863 Chr11 16231478 16234322 +
Car Car08g00384 Chr08 3126254 3129455 -
Cca Cca06g01584 Chr06 30987820 30991030 +
Dod Dod02g0858 Chr02 11015906 11019336 +
Gma Gma01g02014 Chr01 55547709 55551339 +
Gma Gma11g00396 Chr11 3239636 3242869 -
Gso Gso1g1703 Chr1 53747542 53750740 +
Gso Gso1g1703 Chr1 53747542 53750740 +
Lal Lal16g0280 Chr16 1673282 1678023 +
Lapu Lapu2g00457 Chr2 3817921 3821602 -
Lasa Lasa2g02996 Chr2 516788740 516790278 -
Lja Lja2g0202 Chr2 1747824 1751543 -
Mal Mal6g1455 Chr6 26632939 26636515 +
Mepo Mepo5g00586 Chr5 5269083 5273002 -
Mesa Mesa17g00611 Chr17 7206580 7209871 -
Mtr Mtr5g0520 Chr5 4858876 4862472 -
Phac Phac2g00768 Chr2 4723175 4726545 +
Phco Phco4g01242 Chr4 10488019 10490771 +
Psa Psa2g3939 Chr2 412260507 412262935 +
Pte Pte12g00264 Chr12 2126571 2129201 -
Pumo Pumo8g02080 Chr8 57731784 57735301 +
Pvu Pvu2g0074 Chr2 829186 832388 -
Rops Rops1g01936 Chr1 39370155 39373601 +
Seca Seca10g00588 Chr10 5353814 5357706 -
Spst Spst2g00540 Chr2 4365240 4367985 -
Ssu Ssu2g2626 Chr2 86025937 86029234 +
Sto Sto11g1808 Chr11 16813108 16815911 +
Tpr Tpr2g5616 Chr2 64978928 64982501 -
Trre Trre9g00670 Chr9 4831566 4834271 -
Tsu Tsu05g00485 Chr05 3789821 3793850 -
Vian Vian10g00471 Chr10 4332894 4335670 -
Vimu Vimu7g02688 Chr7 22627345 22630014 -
Viun Viun2g02251 Chr2 30173420 30176186 +
Vivi Vivi2g03570 Chr2 143821844 143824473 +
Vra Vra11g0475 Chr11 3524041 3527015 -
Vvi Vvi2g0753 Chr2 7320726 7320902 -
Vvi Vvi2g0754 Chr2 7323418 7332336 +
Sto Sto6g3538 Chr6 40880690 40892706 +
Vvi Vvi2g0755 Chr2 7333968 7339268 +
Bva Bva08g00456 Chr08 2342980 2348493 +
Bva Bva11g01862 Chr11 16224493 16229117 -
Car Car08g00387 Chr08 3134106 3140597 +
Gma Gma01g02013 Chr01 55537834 55540038 -
Gma Gma11g00397 Chr11 3250799 3256381 +
Lja Lja2g0204 Chr2 1791609 1799006 +
Psa Psa2g3936 Chr2 412199620 412212440 -
Sto Sto11g1807 Chr11 16796043 16802526 -
Vvi Vvi2g0756 Chr2 7361994 7365302 +
Acco Acco11g1246 Chr11 26290162 26296382 +
Accr Accr9g01054 Chr9 12558733 12560609 -
Adu Adu05g00081 Chr05 886142 889422 +
Adu Adu01g00669 Chr01 9068663 9071742 +
Aed Aed6g0195 Chr6 1670659 1673623 -
Aed Aed7g1483 Chr7 16563500 16565421 -
Aev Aev05g0121 Chr05 946558 947802 +
Ahy Ahy15g0076 Chr15 862926 865761 +
Aip Aip05g00075 Chr05 864608 866779 +
Alju Alju09g1257 Chr09 36112513 36114110 +
Apr Apr7g1741 Chr7 24684534 24688668 +
Apr Apr3g0662 Chr3 16870556 16874679 +
Arst Arst5g00111 Chr5 905907 908675 +
Bach Bach4g01008 Chr4 6769484 6776346 -
Bach Bach10g00821 Chr10 5794942 5797696 -
Bisa Bisa11g2128 Chr11 44588559 44593726 -
Bva Bva08g01169 Chr08 5989049 6000321 -
Bva Bva11g01268 Chr11 13227789 13230874 +
Car Car07g01902 Chr07 21466904 21469699 +
Cca Cca06g00945 Chr06 23134686 23139910 +
Cca Cca11g00789 Chr11 14840256 14851375 +
Dere Dere09g1409 Chr09 18093405 18103590 -
Dod Dod02g0126 Chr02 1931385 1936211 +
Enph Enph13g0012 Chr13 2273294 2276743 +
Glsi Glsi05g1009 Chr05 60097673 60102473 +
Gma Gma01g00957 Chr01 33138237 33141903 -
Gma Gma09g01892 Chr09 44545632 44549909 +
Gso Gso1g0814 Chr1 31683241 31686826 -
Gso Gso1g0814 Chr1 31683241 31686826 -
Lal Lal16g0475 Chr16 2939561 2946826 -
Lal Lal23g1107 Chr23 12685075 12687430 +
Lasa Lasa2g03796 Chr2 555631165 555632139 -
Lasa Lasa4g01852 Chr4 375061700 375062704 -
Lele Lele50g0985 Chr50 6248796 6250855 -
Lele Lele52g0964 Chr52 6295248 6296791 -
Lja Lja2g0855 Chr2 7986989 7988871 -
Mal Mal6g0723 Chr6 10513495 10515940 -
Mal Mal5g2729 Chr5 80605731 80607340 +
Mepo Mepo5g01403 Chr5 14575500 14579212 -
Mesa Mesa17g01524 Chr17 20724982 20726684 -
Mibi Mibi12g1042 Chr12 25400106 25401745 +
Mtr Mtr5g1258 Chr5 12926560 12930870 -
Mtr Mtr8g2068 Chr8 30588918 30592976 -
Phac Phac2g02242 Chr2 24171848 24175695 -
Phac Phac3g04447 Chr3 42647624 42650916 +
Phco Phco4g00489 Chr4 3474484 3479563 +
Phco Phco8g00148 Chr8 1306954 1309520 -
Prci Prci10g1508 Chr10 10282651 10286431 -
Psa Psa2g3079 Chr2 353595587 353598764 +
Psa Psa4g2816 Chr4 225177562 225180592 +
Pste Pste1g01079 Chr1 3486788 3491028 -
Pste Pste7g00140 Chr7 1220023 1224756 +
Pte Pte14g00680 Chr14 27840402 27840779 +
Pte Pte12g00675 Chr12 6648681 6651973 -
Pte Pte14g00680 Chr14 27840402 27840779 +
Pumo Pumo8g01360 Chr8 46079055 46080868 +
Pvu Pvu2g1464 Chr2 27671758 27675449 -
Pvu Pvu3g2939 Chr3 51154700 51157621 +
Rops Rops1g01232 Chr1 28292816 28296861 +
Rops Rops2g02862 Chr2 50297682 50302461 -
Seca Seca10g01335 Chr10 13552695 13554271 -
Seca Seca12g03579 Chr12 83917578 83918895 +
Spst Spst3g02679 Chr3 76233776 76234984 +
Ssu Ssu2g1922 Chr2 71623649 71624942 +
Ssu Ssu5g0991 Chr5 31387974 31389301 +
Sto Sto6g4206 Chr6 45223700 45224717 -
Sto Sto11g1324 Chr11 12831540 12832828 -
Tpr Tpr2g1503 Chr2 17764846 17769301 -
Trre Trre9g01911 Chr9 18541247 18543456 -
Tsu Tsu05g01277 Chr05 11572458 11576207 -
Tsu Tsu04g02970 Chr04 36472193 36476397 -
Vian Vian1g02084 Chr1 25275285 25276558 -
Vifa Vifa1g05784 Chr1 901470715 901471721 +
Vifa Vifa4g01905 Chr4 537836877 537838315 -
Vimu Vimu7g03526 Chr7 29990542 29991057 -
Vimu Vimu7g03526 Chr7 29990542 29991057 -
Viun Viun2g01395 Chr2 24509345 24512788 +
Viun Viun3g03115 Chr3 37522461 37524090 -
Vivi Vivi2g02361 Chr2 108853272 108856700 +
Vra Vra11g1086 Chr11 10163997 10167650 -
Vra Vra7g0856 Chr7 18035964 18039656 -
Vvi Vvi2g0757 Chr2 7366653 7368270 +
Lja Lja2g0854 Chr2 7982545 7984865 -
Sto Sto11g1323 Chr11 12829043 12829898 -
Vvi Vvi2g0758 Chr2 7370415 7371905 +
Acco Acco11g1247 Chr11 26310381 26311025 +
Accr Accr9g01053 Chr9 12541819 12542463 -
Adu Adu05g00083 Chr05 904823 905634 +
Aev Aev05g0123 Chr05 956915 957541 +
Ahy Ahy15g0078 Chr15 880626 881859 +
Aip Aip05g00077 Chr05 883024 883653 +
Alju Alju09g1258 Chr09 36141717 36142361 +
Apr Apr7g1742 Chr7 24704436 24705659 +
Arst Arst5g00113 Chr5 924367 925134 +
Bach Bach4g01006 Chr4 6756709 6757759 -
Bisa Bisa11g2127 Chr11 44533704 44534318 -
Bva Bva08g01167 Chr08 5982915 5983950 -
Bva Bva11g01270 Chr11 13235957 13236598 +
Cca Cca06g00946 Chr06 23157879 23159017 -
Cca Cca11g00792 Chr11 14907385 14908537 +
Dere Dere09g1408 Chr09 18086952 18087593 -
Dod Dod02g0128 Chr02 1947420 1948672 +
Enph Enph13g0013 Chr13 2371747 2372388 +
Glsi Glsi05g1010 Chr05 60106466 60107107 +
Gma Gma01g00956 Chr01 32931147 32932105 -
Gma Gma09g01894 Chr09 44561427 44563408 +
Gso Gso1g0813 Chr1 31481316 31482370 -
Gso Gso1g0813 Chr1 31481316 31482370 -
Lal Lal16g0473 Chr16 2933170 2933793 -
Lal Lal23g1111 Chr23 12698893 12699525 +
Lapu Lapu2g00818 Chr2 7438321 7440045 +
Lasa Lasa2g03794 Chr2 555504034 555504681 -
Lele Lele49g0928 Chr49 5816327 5816968 -
Lele Lele50g0984 Chr50 6241197 6241838 -
Lele Lele51g0945 Chr51 5911959 5912600 -
Lele Lele52g0963 Chr52 6285555 6286196 -
Lja Lja2g0853 Chr2 7969736 7970887 -
Mal Mal6g0721 Chr6 10500175 10500825 -
Mepo Mepo5g01400 Chr5 14560569 14561697 -
Mibi Mibi12g1044 Chr12 25452423 25453130 +
Mtr Mtr5g1257 Chr5 12914164 12915387 -
Phac Phac2g02239 Chr2 24157595 24159876 -
Phco Phco4g00491 Chr4 3492452 3493111 +
Prci Prci10g1507 Chr10 10263279 10264374 -
Psa Psa2g3081 Chr2 353835102 353836664 +
Pste Pste1g01070 Chr1 3455926 3457537 -
Pte Pte12g00674 Chr12 6637890 6639722 -
Pumo Pumo8g01362 Chr8 46109034 46109699 +
Pvu Pvu2g1462 Chr2 27657845 27658201 -
Rops Rops1g01233 Chr1 28316906 28317889 +
Spst Spst3g02680 Chr3 76238840 76239484 +
Ssu Ssu2g1924 Chr2 71643668 71644707 +
Sto Sto6g4205 Chr6 45216039 45218147 -
Tpr Tpr2g1501 Chr2 17748255 17749466 -
Trre Trre9g01897 Chr9 18422779 18423420 -
Tsu Tsu05g01275 Chr05 11553988 11555022 -
Vifa Vifa1g05786 Chr1 901923826 901924479 +
Vimu Vimu11g02021 Chr11 32606408 32607058 -
Viun Viun2g01397 Chr2 24527181 24528537 +
Vivi Vivi2g02363 Chr2 108928177 108929383 +
Vra Vra7g0854 Chr7 17881142 17882217 -
Vvi Vvi2g0759 Chr2 7390611 7391534 -
Adu Adu05g00084 Chr05 918503 920257 -
Ahy Ahy15g0079 Chr15 895215 897504 -
Aip Aip05g00078 Chr05 896495 898868 -
Apr Apr7g1743 Chr7 24714256 24717180 -
Arst Arst5g00114 Chr5 938485 940342 -
Bach Bach4g01005 Chr4 6747571 6749763 +
Bva Bva08g01166 Chr08 5975688 5977859 +
Dere Dere09g1406 Chr09 18072489 18073460 +
Dod Dod02g0130 Chr02 1965122 1965757 -
Enph Enph13g0014 Chr13 2392915 2393883 -
Glsi Glsi05g1011 Chr05 60114713 60115684 -
Gma Gma01g00954 Chr01 32881327 32882196 +
Gso Gso1g0811 Chr1 31425702 31427445 +
Lal Lal15g0414 Chr15 2793449 2795319 +
Lal Lal16g0471 Chr16 2925791 2926729 +
Lal Lal23g1114 Chr23 12709300 12713052 -
Lan Lan18g0754 Chr18 13006697 13008566 -
Lan Lan18g0754 Chr18 13006697 13008566 -
Lan Lan18g0754 Chr18 13006697 13008566 -
Lapu Lapu2g00819 Chr2 7448140 7451939 -
Lasa Lasa2g03793 Chr2 555340985 555341953 +
Lja Lja2g0852 Chr2 7948647 7950856 +
Phco Phco4g00492 Chr4 3505614 3506573 -
Psa Psa2g3091 Chr2 354506938 354510479 +
Pvu Pvu2g1461 Chr2 27640604 27643354 +
Spst Spst3g02681 Chr3 76245904 76246788 -
Sto Sto6g4202 Chr6 45205986 45206951 +
Vimu Vimu7g03523 Chr7 29951600 29960016 +
Vivi Vivi2g02364 Chr2 109075338 109077641 -
Vvi Vvi2g0760 Chr2 7397010 7400572 +
Vvi Vvi2g0761 Chr2 7401268 7401744 +